From f079876353251550476963ad9d19e18a120380cc Mon Sep 17 00:00:00 2001 From: DLS Jenkins Date: Sun, 17 Dec 2023 02:08:56 +0000 Subject: [PATCH] htdocs update --- cctbx/cctbx.command_line.precession_view.html | 2 +- cctbx/cctbx.maptbx.mem.html | 2 +- iotbx/iotbx.managers.html | 12 ++--- mmtbx/mmtbx.building.html | 10 ++-- mmtbx/mmtbx.cablam.html | 46 +++++++++---------- mmtbx/mmtbx.ions.identify.html | 18 ++++---- mmtbx/mmtbx.ions.svm.html | 6 +-- mmtbx/mmtbx.refinement.html | 6 +-- mmtbx/mmtbx.solvent.html | 2 +- mmtbx/mmtbx.validation.html | 34 +++++++------- searchindex.js | 2 +- 11 files changed, 70 insertions(+), 70 deletions(-) diff --git a/cctbx/cctbx.command_line.precession_view.html b/cctbx/cctbx.command_line.precession_view.html index c929dc52..837e472b 100644 --- a/cctbx/cctbx.command_line.precession_view.html +++ b/cctbx/cctbx.command_line.precession_view.html @@ -121,7 +121,7 @@

Navigation

-cctbx.command_line.precession_view.run(args, out=<colorama.ansitowin32.StreamWrapper object>, silent=True)
+cctbx.command_line.precession_view.run(args, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, silent=True)
diff --git a/cctbx/cctbx.maptbx.mem.html b/cctbx/cctbx.maptbx.mem.html index f514832b..bc1b7a56 100644 --- a/cctbx/cctbx.maptbx.mem.html +++ b/cctbx/cctbx.maptbx.mem.html @@ -115,7 +115,7 @@

Navigation

-cctbx.maptbx.mem.show_map_stat(m, prefix, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+cctbx.maptbx.mem.show_map_stat(m, prefix, out=<colorama.ansitowin32.StreamWrapper object>)
diff --git a/iotbx/iotbx.managers.html b/iotbx/iotbx.managers.html index bf770ed3..1379479c 100644 --- a/iotbx/iotbx.managers.html +++ b/iotbx/iotbx.managers.html @@ -803,7 +803,7 @@

Parameters:
-set_log(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+set_log(log=<colorama.ansitowin32.StreamWrapper object>)

Set output log file

@@ -1266,7 +1266,7 @@

Parameters:
-iotbx.map_model_manager.get_selections_and_boxes_to_split_model(model_id=None, map_model_manager=None, selection_method='by_chain', selection_list=None, skip_waters=False, skip_hetero=False, target_for_boxes=24, box_cushion=3, select_final_boxes_based_on_model=None, skip_empty_boxes=True, mask_around_unselected_atoms=None, mask_all_maps_around_edges=None, mask_radius=3, masked_value=-10, get_unique_set_for_boxes=True, mask_id=None, exclude_points_outside_density=None, minimum_boxes_inside_density=25, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+iotbx.map_model_manager.get_selections_and_boxes_to_split_model(model_id=None, map_model_manager=None, selection_method='by_chain', selection_list=None, skip_waters=False, skip_hetero=False, target_for_boxes=24, box_cushion=3, select_final_boxes_based_on_model=None, skip_empty_boxes=True, mask_around_unselected_atoms=None, mask_all_maps_around_edges=None, mask_radius=3, masked_value=-10, get_unique_set_for_boxes=True, mask_id=None, exclude_points_outside_density=None, minimum_boxes_inside_density=25, log=<colorama.ansitowin32.StreamWrapper object>)

Split up model into pieces using selection_method Choices are [‘by_chain’, ‘by_segment’,’all’, ‘boxes’] by_chain: each chain is a selection @@ -1346,7 +1346,7 @@

Parameters:
-iotbx.map_model_manager.get_tlso_group_info_from_model(model, nproc=1, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+iotbx.map_model_manager.get_tlso_group_info_from_model(model, nproc=1, log=<colorama.ansitowin32.StreamWrapper object>)

Extract tlso_group_info from aniso records in model

@@ -2517,7 +2517,7 @@

Parameters:
-set_log(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+set_log(log=<colorama.ansitowin32.StreamWrapper object>)

Set output log file

@@ -2716,7 +2716,7 @@

Parameters:
-show_summary(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+show_summary(log=<colorama.ansitowin32.StreamWrapper object>)
@@ -2999,7 +2999,7 @@

Parameters:
-set_log(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+set_log(log=<colorama.ansitowin32.StreamWrapper object>)

Set output log file

diff --git a/mmtbx/mmtbx.building.html b/mmtbx/mmtbx.building.html index dd76bb43..7f300416 100644 --- a/mmtbx/mmtbx.building.html +++ b/mmtbx/mmtbx.building.html @@ -79,7 +79,7 @@

Submodules
-mmtbx.building.extend_sidechains.correct_sequence(pdb_hierarchy, sequences, truncate_to_cbeta=False, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.building.extend_sidechains.correct_sequence(pdb_hierarchy, sequences, truncate_to_cbeta=False, out=<colorama.ansitowin32.StreamWrapper object>)

Modify the sequence for the pdb hierarchy to match that of the aligned sequence. This will remove incompatible atoms; the sidechains will still need to be extended separated. For proteins only - mismatches in nucleic @@ -102,7 +102,7 @@

Submodules
-class mmtbx.building.extend_sidechains.extend_and_refine(pdb_hierarchy, xray_structure, fmodel, params, cif_objects=(), out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, output_model=None, output_map_coeffs=None, prefix=None, write_files=True, reset_segid=True, verbose=True)
+class mmtbx.building.extend_sidechains.extend_and_refine(pdb_hierarchy, xray_structure, fmodel, params, cif_objects=(), out=<colorama.ansitowin32.StreamWrapper object>, output_model=None, output_map_coeffs=None, prefix=None, write_files=True, reset_segid=True, verbose=True)

Bases: object

Run the combined sidechain extension and real-space fitting, and optionally write final model and map coefficients.

@@ -149,7 +149,7 @@

Submodules
-mmtbx.building.extend_sidechains.refit_residues(pdb_hierarchy, cif_objects, fmodel, use_rotamers=True, anneal=False, verbose=True, allow_modified_residues=False, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.building.extend_sidechains.refit_residues(pdb_hierarchy, cif_objects, fmodel, use_rotamers=True, anneal=False, verbose=True, allow_modified_residues=False, out=<colorama.ansitowin32.StreamWrapper object>)

Use real-space refinement tools to fit newly extended residues.

@@ -184,7 +184,7 @@

Submodules
-mmtbx.building.make_library.extract_and_superpose(reference_hierarchy, search_directory, sequence, params, nproc=<libtbx.AutoType object>, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.building.make_library.extract_and_superpose(reference_hierarchy, search_directory, sequence, params, nproc=<libtbx.AutoType object>, out=<colorama.ansitowin32.StreamWrapper object>)
@@ -530,7 +530,7 @@

Submodules
-mmtbx.building.show_chain_resseq_ranges(residues, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
+mmtbx.building.show_chain_resseq_ranges(residues, out=<colorama.ansitowin32.StreamWrapper object>, prefix='')

Given a list of residues (either residue_group or atom_group objects), print a summary of the chains and residue ranges present.

diff --git a/mmtbx/mmtbx.cablam.html b/mmtbx/mmtbx.cablam.html index 0acefd03..a2beb21e 100644 --- a/mmtbx/mmtbx.cablam.html +++ b/mmtbx/mmtbx.cablam.html @@ -391,12 +391,12 @@

Submodules
-printtocsv(kinorder, doconnections=False, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+printtocsv(kinorder, doconnections=False, writeto=<colorama.ansitowin32.StreamWrapper object>)
-printtokin(kinorder, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+printtokin(kinorder, writeto=<colorama.ansitowin32.StreamWrapper object>)
@@ -426,12 +426,12 @@

Submodules
-mmtbx.cablam.cablam_training.csv_header(kinorder, doconnections=False, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.csv_header(kinorder, doconnections=False, writeto=<colorama.ansitowin32.StreamWrapper object>)

-mmtbx.cablam.cablam_training.csv_print(protein, kinorder, skiplist=[], inclist=[], doconnections=False, cis_or_trans='both', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.csv_print(protein, kinorder, skiplist=[], inclist=[], doconnections=False, cis_or_trans='both', writeto=<colorama.ansitowin32.StreamWrapper object>)
@@ -441,17 +441,17 @@

Submodules
-mmtbx.cablam.cablam_training.kin_frame(writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.kin_frame(writeto=<colorama.ansitowin32.StreamWrapper object>)

-mmtbx.cablam.cablam_training.kin_header(kinorder, kinranges, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.kin_header(kinorder, kinranges, writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_training.kin_print(protein, kinorder, skiplist=[], inclist=[], cis_or_trans='both', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.kin_print(protein, kinorder, skiplist=[], inclist=[], cis_or_trans='both', writeto=<colorama.ansitowin32.StreamWrapper object>)
@@ -471,7 +471,7 @@

Submodules
-mmtbx.cablam.cablam_training.kin_print_probe_annote(motif_instances, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.kin_print_probe_annote(motif_instances, writeto=<colorama.ansitowin32.StreamWrapper object>)

@@ -486,7 +486,7 @@

Submodules
-mmtbx.cablam.cablam_training.old_kin_print_probe_annote(resdata, motif_list, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_training.old_kin_print_probe_annote(resdata, motif_list, writeto=<colorama.ansitowin32.StreamWrapper object>)

@@ -549,7 +549,7 @@

Submodules
-mmtbx.cablam.cablam_validate.cablam_multicrit_kin(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.cablam_multicrit_kin(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<colorama.ansitowin32.StreamWrapper object>)

@@ -610,22 +610,22 @@

Submodules
-mmtbx.cablam.cablam_validate.give_ca_kin(outliers, outlier_cutoff, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.give_ca_kin(outliers, outlier_cutoff, writeto=<colorama.ansitowin32.StreamWrapper object>)

-mmtbx.cablam.cablam_validate.give_kin(outliers, outlier_cutoff, color='purple', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.give_kin(outliers, outlier_cutoff, color='purple', writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.give_points(outliers, outlier_cutoff=0.05, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.give_points(outliers, outlier_cutoff=0.05, writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.give_text(outliers, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.give_text(outliers, writeto=<colorama.ansitowin32.StreamWrapper object>)
@@ -649,22 +649,22 @@

Submodulesobject

-print_helix_record(helix_num=1, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+print_helix_record(helix_num=1, writeto=<colorama.ansitowin32.StreamWrapper object>)
-print_record(writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+print_record(writeto=<colorama.ansitowin32.StreamWrapper object>)
-print_sheet_record(sheet_id='U', strand_num=1, strand_count=1, strand_sense=0, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+print_sheet_record(sheet_id='U', strand_num=1, strand_count=1, strand_sense=0, writeto=<colorama.ansitowin32.StreamWrapper object>)
-print_threeten_record(helix_num=1, writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+print_threeten_record(helix_num=1, writeto=<colorama.ansitowin32.StreamWrapper object>)

@@ -683,27 +683,27 @@

Submodules
-mmtbx.cablam.cablam_validate.oneline(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.oneline(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.oneline_header(writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.oneline_header(writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.print_cablam_markup_kin(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.print_cablam_markup_kin(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid='pdbid', writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.print_helix_sheet_records(hierarchy, ca_cutoff=0.005, pdbid='pdbid', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.print_helix_sheet_records(hierarchy, ca_cutoff=0.005, pdbid='pdbid', writeto=<colorama.ansitowin32.StreamWrapper object>)
-mmtbx.cablam.cablam_validate.print_pdb_with_new_helix_sheet_records(hierarchy, ca_cutoff=0.005, pdbid='pdbid', writeto=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+mmtbx.cablam.cablam_validate.print_pdb_with_new_helix_sheet_records(hierarchy, ca_cutoff=0.005, pdbid='pdbid', writeto=<colorama.ansitowin32.StreamWrapper object>)
diff --git a/mmtbx/mmtbx.ions.identify.html b/mmtbx/mmtbx.ions.identify.html index f75929d1..5f25f141 100644 --- a/mmtbx/mmtbx.ions.identify.html +++ b/mmtbx/mmtbx.ions.identify.html @@ -405,7 +405,7 @@

Navigation

-show_ion_results(identity=None, out=<colorama.ansitowin32.StreamWrapper object>, confirmed=False, valence_used=True)
+show_ion_results(identity=None, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, confirmed=False, valence_used=True)

Show statistics for a proposed element identity.

Parameters:
@@ -421,7 +421,7 @@

Navigation

-show_properties(identity, out=<colorama.ansitowin32.StreamWrapper object>)
+show_properties(identity, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Show atomic properties that are independent of the suspected identity.

Parameters:
@@ -562,12 +562,12 @@

Navigation

-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
-show_brief(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_brief(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
@@ -605,7 +605,7 @@

Navigation

-analyze_water(i_seq, debug=True, candidates=<libtbx.AutoType object>, no_final=False, out=<colorama.ansitowin32.StreamWrapper object>)
+analyze_water(i_seq, debug=True, candidates=<libtbx.AutoType object>, no_final=False, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Examines the environment around a single atom to determine if it is actually a misidentified metal ion.

no_final is used internally, when candidates is not Auto, to try all of the @@ -629,7 +629,7 @@

Navigation

-analyze_waters(out=<colorama.ansitowin32.StreamWrapper object>, debug=True, candidates=<libtbx.AutoType object>)
+analyze_waters(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, debug=True, candidates=<libtbx.AutoType object>)

Iterates through all of the waters in a model, examining the maps and local environment to check their identity and suggest likely ions where appropriate.

@@ -895,7 +895,7 @@

Navigation

-show_current_scattering_statistics(out=<colorama.ansitowin32.StreamWrapper object>)
+show_current_scattering_statistics(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Prints out information about an entire model’s scattering statistics, such as mean map heights and b-factors for carbons and waters.

@@ -936,7 +936,7 @@

Navigation

-validate_ion(i_seq, out=<colorama.ansitowin32.StreamWrapper object>, debug=True)
+validate_ion(i_seq, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, debug=True)

Examines one site in the model and determines if it was correctly modelled, returning a boolean indicating correctness.

@@ -952,7 +952,7 @@

Navigation

-validate_ions(out=<colorama.ansitowin32.StreamWrapper object>, debug=True, segid=None)
+validate_ions(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, debug=True, segid=None)

Iterate over all the ions built into the model by this module and double check their correctness. Looks for tell-tale signs such as negative peaks in the mFo-DFc and anomalous difference maps, abnormal b-factor, and diff --git a/mmtbx/mmtbx.ions.svm.html b/mmtbx/mmtbx.ions.svm.html index 3a52ae0b..df6d6707 100644 --- a/mmtbx/mmtbx.ions.svm.html +++ b/mmtbx/mmtbx.ions.svm.html @@ -314,7 +314,7 @@

Submodules
-analyze_waters(out=<colorama.ansitowin32.StreamWrapper object>, debug=True, candidates=<libtbx.AutoType object>)
+analyze_waters(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, debug=True, candidates=<libtbx.AutoType object>)

Uses a SVM to analyze all of a model’s water sites and decide whether to re-assign them as ions.

@@ -474,7 +474,7 @@

Submodules
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

Shows information about a SVM’s prediction of a site’s identity.

Parameters:
@@ -488,7 +488,7 @@

Submodules
-show_brief(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_brief(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

Shows a brief description of a SVM’s prediction of a site’s identity, for use in output as a table.

diff --git a/mmtbx/mmtbx.refinement.html b/mmtbx/mmtbx.refinement.html index fb713599..b970414e 100644 --- a/mmtbx/mmtbx.refinement.html +++ b/mmtbx/mmtbx.refinement.html @@ -1268,7 +1268,7 @@

mmtbx.refinement.flip_peptides module
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

@@ -1280,7 +1280,7 @@

mmtbx.refinement.flip_peptides module
-class mmtbx.refinement.select_best_starting_model.select_model(model_names, model_data, f_obs, r_free_flags, params=None, skip_twin_detection=False, nproc=1, log=<colorama.ansitowin32.StreamWrapper object>)
+class mmtbx.refinement.select_best_starting_model.select_model(model_names, model_data, f_obs, r_free_flags, params=None, skip_twin_detection=False, nproc=1, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Bases: object

@@ -1314,7 +1314,7 @@

mmtbx.refinement.flip_peptides module
-show(out=<colorama.ansitowin32.StreamWrapper object>, verbose=False)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, verbose=False)

diff --git a/mmtbx/mmtbx.solvent.html b/mmtbx/mmtbx.solvent.html index ea08ed56..8397a9ce 100644 --- a/mmtbx/mmtbx.solvent.html +++ b/mmtbx/mmtbx.solvent.html @@ -117,7 +117,7 @@

Submodules

mmtbx.solvent.ordered_solvent module

-class mmtbx.solvent.ordered_solvent.manager(fmodel, fmodels, model, is_neutron_scat_table, params=<libtbx.phil.scope_extract object>, find_peaks_params=None, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
+class mmtbx.solvent.ordered_solvent.manager(fmodel, fmodels, model, is_neutron_scat_table, params=<libtbx.phil.scope_extract object>, find_peaks_params=None, log=<colorama.ansitowin32.StreamWrapper object>)

Bases: object

diff --git a/mmtbx/mmtbx.validation.html b/mmtbx/mmtbx.validation.html index df247d57..36622e44 100644 --- a/mmtbx/mmtbx.validation.html +++ b/mmtbx/mmtbx.validation.html @@ -3595,7 +3595,7 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='', verbose=True)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='', verbose=True)

@@ -4138,7 +4138,7 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='  ', verbose=True)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='  ', verbose=True)

@@ -4150,7 +4150,7 @@

C-beta deviations
-show_summary(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_summary(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

@@ -4903,12 +4903,12 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

-show_summary(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_summary(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
@@ -5024,12 +5024,12 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='  ', verbose=True)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='  ', verbose=True)

-show_summary(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_summary(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
@@ -5260,12 +5260,12 @@

C-beta deviations

mmtbx.validation.ligands module

-mmtbx.validation.ligands.compare_ligands(ligand_code, hierarchy_1=None, hierarchy_2=None, pdb_file_1=None, pdb_file_2=None, max_distance_between_centers_of_mass=8.0, exclude_hydrogens=True, verbose=False, implicit_matching=False, out=<colorama.ansitowin32.StreamWrapper object>)
+mmtbx.validation.ligands.compare_ligands(ligand_code, hierarchy_1=None, hierarchy_2=None, pdb_file_1=None, pdb_file_2=None, max_distance_between_centers_of_mass=8.0, exclude_hydrogens=True, verbose=False, implicit_matching=False, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
-mmtbx.validation.ligands.compare_ligands_impl(ligand, reference_ligands, max_distance_between_centers_of_mass=8.0, exclude_hydrogens=True, implicit_matching=False, verbose=False, quiet=False, raise_sorry_if_no_matching_atoms=True, out=<colorama.ansitowin32.StreamWrapper object>)
+mmtbx.validation.ligands.compare_ligands_impl(ligand, reference_ligands, max_distance_between_centers_of_mass=8.0, exclude_hydrogens=True, implicit_matching=False, verbose=False, quiet=False, raise_sorry_if_no_matching_atoms=True, out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Given a target ligand and a list of reference ligands, return the RMSD(s) for any ligand determined to be approximately equivalent. (Usually there will be just one of these, but this allows for alternate conformations.)

@@ -5347,12 +5347,12 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

-show_simple(out=<colorama.ansitowin32.StreamWrapper object>, warnings=True)
+show_simple(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, warnings=True)
@@ -5647,7 +5647,7 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

@@ -5963,17 +5963,17 @@

C-beta deviations
-show_bad_occupancy(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_bad_occupancy(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')

-show_bfactors(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_bfactors(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
-show_summary(out=<colorama.ansitowin32.StreamWrapper object>, prefix='')
+show_summary(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='')
@@ -6441,12 +6441,12 @@

C-beta deviations
-show(out=<colorama.ansitowin32.StreamWrapper object>, prefix='  ', verbose=True)
+show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='  ', verbose=True)

-show_summary(out=<colorama.ansitowin32.StreamWrapper object>, prefix='  ')
+show_summary(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='  ')

diff --git a/searchindex.js b/searchindex.js index 6dcff673..6b35905a 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["boost_adaptbx/index", "cctbx/cctbx", "cctbx/cctbx.adp_restraints", "cctbx/cctbx.adp_restraints.energies", "cctbx/cctbx.adp_restraints.flags", "cctbx/cctbx.adptbx", "cctbx/cctbx.array_family", "cctbx/cctbx.array_family.flex", "cctbx/cctbx.command_line", "cctbx/cctbx.command_line.brehm_diederichs", "cctbx/cctbx.command_line.cod_select_and_pickle", "cctbx/cctbx.command_line.eltbx.show_fp_fdp", "cctbx/cctbx.command_line.euclidean_model_matching", "cctbx/cctbx.command_line.find_reticular_twin_laws", "cctbx/cctbx.command_line.form_factor_query", "cctbx/cctbx.command_line.precession_view", "cctbx/cctbx.command_line.space_group_info", "cctbx/cctbx.command_line.structure_factor_timings", "cctbx/cctbx.command_line.subgroups", "cctbx/cctbx.command_line.version", "cctbx/cctbx.command_line.wavelength_units", "cctbx/cctbx.command_line.xray_structure.show", "cctbx/cctbx.covariance", "cctbx/cctbx.crystal", "cctbx/cctbx.crystal.burzlaff_zimmermann_dewolff", "cctbx/cctbx.crystal.close_packing", "cctbx/cctbx.crystal.coordination_sequences", "cctbx/cctbx.crystal.direct_space_asu", "cctbx/cctbx.crystal.distance_based_connectivity", "cctbx/cctbx.crystal.find_best_cell", "cctbx/cctbx.crystal.reindex", "cctbx/cctbx.crystal_orientation", "cctbx/cctbx.development", "cctbx/cctbx.development.cns_density_modification", "cctbx/cctbx.development.debug_utils", "cctbx/cctbx.development.direct_or_fft", "cctbx/cctbx.development.electron_density_sampling", "cctbx/cctbx.development.fmt_utils", "cctbx/cctbx.development.make_cns_input", "cctbx/cctbx.development.make_settings", "cctbx/cctbx.development.random_structure", "cctbx/cctbx.development.run_shelx", "cctbx/cctbx.development.run_shelx76", "cctbx/cctbx.development.space_group_option_parser", "cctbx/cctbx.development.structure_factor_utils", "cctbx/cctbx.dmtbx", "cctbx/cctbx.eltbx", "cctbx/cctbx.eltbx.attenuation_coefficient", "cctbx/cctbx.eltbx.chemical_elements", "cctbx/cctbx.eltbx.covalent_radii", "cctbx/cctbx.eltbx.development", "cctbx/cctbx.eltbx.development.combine_fits", "cctbx/cctbx.eltbx.development.create_n_gaussian_raw_cpp", "cctbx/cctbx.eltbx.development.e_scattering_plots", "cctbx/cctbx.eltbx.development.format_gaussian_fits", "cctbx/cctbx.eltbx.development.hydrogen_plots", "cctbx/cctbx.eltbx.development.itvc_approx", "cctbx/cctbx.eltbx.development.itvc_cross_validation", "cctbx/cctbx.eltbx.development.itvc_fits", "cctbx/cctbx.eltbx.development.itvc_kissel", "cctbx/cctbx.eltbx.development.itvc_section61_io", "cctbx/cctbx.eltbx.development.kissel_fits", "cctbx/cctbx.eltbx.development.kissel_io", "cctbx/cctbx.eltbx.development.rez_rez_grant", "cctbx/cctbx.eltbx.distance_based_connectivity", "cctbx/cctbx.eltbx.e_scattering", "cctbx/cctbx.eltbx.formula", "cctbx/cctbx.eltbx.fp_fdp", "cctbx/cctbx.eltbx.gaussian_fit", "cctbx/cctbx.eltbx.henke", "cctbx/cctbx.eltbx.icsd_radii", "cctbx/cctbx.eltbx.neutron", "cctbx/cctbx.eltbx.sasaki", "cctbx/cctbx.eltbx.tiny_pse", "cctbx/cctbx.eltbx.van_der_waals_radii", "cctbx/cctbx.eltbx.wavelengths", "cctbx/cctbx.eltbx.xray_scattering", "cctbx/cctbx.euclidean_model_matching", "cctbx/cctbx.examples", "cctbx/cctbx.examples.adp_symmetry_constraints", "cctbx/cctbx.examples.all_axes", "cctbx/cctbx.examples.analyze_adp", "cctbx/cctbx.examples.change_hand_p31", "cctbx/cctbx.examples.convert_ccp4_symop_lib", "cctbx/cctbx.examples.cr2o3_consistency_checks", "cctbx/cctbx.examples.cr2o3_primitive_cell", "cctbx/cctbx.examples.exp_i_alpha_derivatives", "cctbx/cctbx.examples.f_model_example", "cctbx/cctbx.examples.fft_map_electron_density_around_atom", "cctbx/cctbx.examples.find_distances_using_cpp_objects", "cctbx/cctbx.examples.find_sys_abs_equiv_space_groups", "cctbx/cctbx.examples.g_exp_i_alpha_derivatives", "cctbx/cctbx.examples.g_exp_i_partial_derivatives", "cctbx/cctbx.examples.getting_started", "cctbx/cctbx.examples.hirshfeld_test", "cctbx/cctbx.examples.le_page_1982_vs_lebedev_2005", "cctbx/cctbx.examples.lebedev_2005_perturbation", "cctbx/cctbx.examples.list_non_principal_continuous_shifts", "cctbx/cctbx.examples.location_part", "cctbx/cctbx.examples.map_skewness", "cctbx/cctbx.examples.maximum_subgroups", "cctbx/cctbx.examples.miller_common_sets", "cctbx/cctbx.examples.miller_transform", "cctbx/cctbx.examples.neutron_structure_factors", "cctbx/cctbx.examples.phase_o_phrenia", "cctbx/cctbx.examples.quartz_structure", "cctbx/cctbx.examples.random_f_calc", "cctbx/cctbx.examples.random_puckers", "cctbx/cctbx.examples.reduced_cell_two_folds", "cctbx/cctbx.examples.site_symmetry_constraints", "cctbx/cctbx.examples.site_symmetry_table", "cctbx/cctbx.examples.space_group_matrices", "cctbx/cctbx.examples.space_subgroups", "cctbx/cctbx.examples.steve_collins", "cctbx/cctbx.examples.structure_factor_calculus", "cctbx/cctbx.examples.structure_factor_calculus.site_derivatives", "cctbx/cctbx.examples.structure_factor_calculus.sites_derivatives", "cctbx/cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives", "cctbx/cctbx.examples.structure_factor_calculus.u_star_derivatives", "cctbx/cctbx.examples.structure_factor_derivatives", "cctbx/cctbx.examples.structure_factor_derivatives_2", "cctbx/cctbx.examples.structure_factor_derivatives_3", "cctbx/cctbx.examples.structure_factor_derivatives_4", "cctbx/cctbx.examples.sub_group_graph", "cctbx/cctbx.examples.symops_530", "cctbx/cctbx.examples.trigonal_r_vs_tetragonal_i", "cctbx/cctbx.examples.unit_cell_minimizers", "cctbx/cctbx.examples.unit_cell_refinement", "cctbx/cctbx.examples.view_fft_map", "cctbx/cctbx.french_wilson", "cctbx/cctbx.geometry", "cctbx/cctbx.geometry_restraints", "cctbx/cctbx.geometry_restraints.energies", "cctbx/cctbx.geometry_restraints.flags", "cctbx/cctbx.geometry_restraints.lbfgs", "cctbx/cctbx.geometry_restraints.manager", "cctbx/cctbx.libtbx_refresh", "cctbx/cctbx.macro_mol", "cctbx/cctbx.macro_mol.rotation_parameters", "cctbx/cctbx.maptbx", "cctbx/cctbx.maptbx.mem", "cctbx/cctbx.maptbx.real_space_refinement", "cctbx/cctbx.maptbx.real_space_refinement_simple", "cctbx/cctbx.maptbx.real_space_target_and_gradients", "cctbx/cctbx.masks", "cctbx/cctbx.math_module", "cctbx/cctbx.merging", "cctbx/cctbx.merging.brehm_diederichs", "cctbx/cctbx.miller", "cctbx/cctbx.miller.display", "cctbx/cctbx.miller.reindexing", "cctbx/cctbx.multipolar", "cctbx/cctbx.neutron", "cctbx/cctbx.omz", "cctbx/cctbx.omz.bfgs", "cctbx/cctbx.omz.cif_refine", "cctbx/cctbx.omz.cod_refine", "cctbx/cctbx.omz.cod_select_and_pickle", "cctbx/cctbx.omz.dev", "cctbx/cctbx.omz.eval_iso_vs_refined", "cctbx/cctbx.omz.pdb_dev", "cctbx/cctbx.omz.tardy_adaptor", "cctbx/cctbx.r_free_utils", "cctbx/cctbx.run_examples", "cctbx/cctbx.run_tests", "cctbx/cctbx.sgtbx", "cctbx/cctbx.sgtbx.bravais_types", "cctbx/cctbx.sgtbx.cosets", "cctbx/cctbx.sgtbx.direct_space_asu", "cctbx/cctbx.sgtbx.direct_space_asu.check_redundancies", "cctbx/cctbx.sgtbx.direct_space_asu.cut_plane", "cctbx/cctbx.sgtbx.direct_space_asu.facet_analysis", "cctbx/cctbx.sgtbx.direct_space_asu.plane_group_reference_table", "cctbx/cctbx.sgtbx.direct_space_asu.proto", "cctbx/cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table", "cctbx/cctbx.sgtbx.direct_space_asu.reference_table", "cctbx/cctbx.sgtbx.direct_space_asu.short_cuts", "cctbx/cctbx.sgtbx.harker", "cctbx/cctbx.sgtbx.lattice_symmetry", "cctbx/cctbx.sgtbx.literal_description", "cctbx/cctbx.sgtbx.plane_groups", "cctbx/cctbx.sgtbx.pointgroup_tools", "cctbx/cctbx.sgtbx.rational_matrices_point_groups", "cctbx/cctbx.sgtbx.reticular_pg_tools", "cctbx/cctbx.sgtbx.reticular_twin_laws", "cctbx/cctbx.sgtbx.show_cosets", "cctbx/cctbx.sgtbx.sub_lattice_tools", "cctbx/cctbx.sgtbx.subgroups", "cctbx/cctbx.sgtbx.symbol_confidence", "cctbx/cctbx.sgtbx.sys_abs_equiv", "cctbx/cctbx.source_generators", "cctbx/cctbx.source_generators.eltbx", "cctbx/cctbx.source_generators.eltbx.generate_henke_cpp", "cctbx/cctbx.source_generators.eltbx.generate_sasaki_cpp", "cctbx/cctbx.source_generators.flex_fwd_h", "cctbx/cctbx.statistics", "cctbx/cctbx.symmetry_search", "cctbx/cctbx.translation_search", "cctbx/cctbx.uctbx", "cctbx/cctbx.uctbx.determine_unit_cell", "cctbx/cctbx.uctbx.gruber_1973", "cctbx/cctbx.uctbx.gruber_1973_table_1", "cctbx/cctbx.uctbx.krivy_gruber_1976", "cctbx/cctbx.uctbx.reduction_base", "cctbx/cctbx.web", "cctbx/cctbx.web.all_axes", "cctbx/cctbx.web.asu_gallery", "cctbx/cctbx.web.asu_gallery.guide_to_notation", "cctbx/cctbx.web.asu_gallery.jv_asu", "cctbx/cctbx.web.asu_gallery.jv_index", "cctbx/cctbx.web.asu_gallery.jvx", "cctbx/cctbx.web.asu_gallery.web_links", "cctbx/cctbx.web.browse_settings", "cctbx/cctbx.web.cgi_utils", "cctbx/cctbx.web.change_basis", "cctbx/cctbx.web.change_hand", "cctbx/cctbx.web.change_setting", "cctbx/cctbx.web.dispatcher", "cctbx/cctbx.web.emma", "cctbx/cctbx.web.explore_symmetry", "cctbx/cctbx.web.frac_cart", "cctbx/cctbx.web.io_utils", "cctbx/cctbx.web.iotbx_cif_validate", "cctbx/cctbx.web.lattice_symmetry", "cctbx/cctbx.web.libtbx_help", "cctbx/cctbx.web.multiple_cell", "cctbx/cctbx.web.phase_o_phrenia", "cctbx/cctbx.web.replay", "cctbx/cctbx.web.shelx", "cctbx/cctbx.web.structure_factors", "cctbx/cctbx.web.structure_factors_pdb", "cctbx/cctbx.web.wyckoff", "cctbx/cctbx.xray", "cctbx/cctbx.xray.ext", "cctbx/cctbx.xray.minimization", "cctbx/cctbx.xray.observation_types", "cctbx/cctbx.xray.observations", "cctbx/cctbx.xray.scatterer", "cctbx/cctbx.xray.structure", "cctbx/cctbx.xray.structure_factors", "cctbx/cctbx.xray.structure_factors.from_scatterers", "cctbx/cctbx.xray.structure_factors.from_scatterers_direct", "cctbx/cctbx.xray.structure_factors.from_scatterers_direct_parallel", "cctbx/cctbx.xray.structure_factors.from_scatterers_fft", "cctbx/cctbx.xray.structure_factors.global_counters", "cctbx/cctbx.xray.structure_factors.gradient_flags", "cctbx/cctbx.xray.structure_factors.gradients", "cctbx/cctbx.xray.structure_factors.gradients_base", "cctbx/cctbx.xray.structure_factors.gradients_direct", "cctbx/cctbx.xray.structure_factors.gradients_fft", "cctbx/cctbx.xray.structure_factors.manager", "cctbx/cctbx.xray.structure_factors.misc", "cctbx/cctbx.xray.target_functors", "cctbx/cctbx.xray.targets", "cctbx/cctbx.xray.targets.r1", "cctbx/cctbx.xray.weighting_schemes", "cctbx/modules", "dxtbx/dxtbx.model", "dxtbx/dxtbx.serialize", "dxtbx/index", "history", "index", "installation", "iotbx/index", "iotbx/iotbx.cif", "iotbx/iotbx.file_reader", "iotbx/iotbx.managers", "iotbx/iotbx.ncs", "iotbx/iotbx.pdb", "iotbx/iotbx.pdb_tutorial", "iotbx/iotbx.reflection_file_reader", "iotbx/iotbx.shelx", "iotbx/iotbx.xds", "libtbx/index", "libtbx/libtbx.easy_mp", "libtbx/libtbx.program_template", "mmtbx/mmtbx", "mmtbx/mmtbx.building", "mmtbx/mmtbx.bulk_solvent", "mmtbx/mmtbx.cablam", "mmtbx/mmtbx.cablam.fingerprints", "mmtbx/mmtbx.chemical_components", "mmtbx/mmtbx.command_line", "mmtbx/mmtbx.conformation_dependent_library", "mmtbx/mmtbx.den", "mmtbx/mmtbx.density_modification", "mmtbx/mmtbx.disorder", "mmtbx/mmtbx.dynamics", "mmtbx/mmtbx.f_model", "mmtbx/mmtbx.geometry", "mmtbx/mmtbx.geometry_restraints", "mmtbx/mmtbx.hydrogens", "mmtbx/mmtbx.ias", "mmtbx/mmtbx.ions", "mmtbx/mmtbx.ions.build", "mmtbx/mmtbx.ions.environment", "mmtbx/mmtbx.ions.geometry", "mmtbx/mmtbx.ions.halides", "mmtbx/mmtbx.ions.identify", "mmtbx/mmtbx.ions.svm", "mmtbx/mmtbx.ions.svm.dump_sites", "mmtbx/mmtbx.ions.svm.utils", "mmtbx/mmtbx.ions.utils", "mmtbx/mmtbx.kinemage", "mmtbx/mmtbx.ligands", "mmtbx/mmtbx.maps", "mmtbx/mmtbx.masks", "mmtbx/mmtbx.max_lik", "mmtbx/mmtbx.monomer_library", "mmtbx/mmtbx.ncs", "mmtbx/mmtbx.pdbtools", "mmtbx/mmtbx.polygon", "mmtbx/mmtbx.real_space", "mmtbx/mmtbx.refinement", "mmtbx/mmtbx.refinement.ensemble_refinement", "mmtbx/mmtbx.refinement.real_space", "mmtbx/mmtbx.rotamer", "mmtbx/mmtbx.rsr", "mmtbx/mmtbx.scaling", "mmtbx/mmtbx.secondary_structure", "mmtbx/mmtbx.secondary_structure.build", "mmtbx/mmtbx.solvent", "mmtbx/mmtbx.tls", "mmtbx/mmtbx.torsion_restraints", "mmtbx/mmtbx.twinning", "mmtbx/mmtbx.utils", "mmtbx/mmtbx.validation", "mmtbx/mmtbx.validation.molprobity", "mmtbx/mmtbx.wwpdb", "mmtbx/modules", "scitbx/index", "scitbx/scitbx.array_family", "scitbx/scitbx.lbfgs", "scitbx/scitbx.lstbx", "scitbx/scitbx.matrix", "tour", "xfel/modules", "xfel/xfel", "xfel/xfel.cftbx", "xfel/xfel.cftbx.detector", "xfel/xfel.clustering", "xfel/xfel.command_line", "xfel/xfel.cxi", "xfel/xfel.cxi.cspad_ana", "xfel/xfel.cxi.gfx", "xfel/xfel.cxi.merging", "xfel/xfel.cxi.postrefine", "xfel/xfel.metrology", "xfel/xfel.metrology.legacy_scale", "xfel/xfel.mono_simulation"], "filenames": ["boost_adaptbx/index.rst", "cctbx/cctbx.rst", "cctbx/cctbx.adp_restraints.rst", 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module", "cctbx.geometry_restraints.flags module", "cctbx.geometry_restraints.lbfgs module", "cctbx.geometry_restraints.manager module", "cctbx.libtbx_refresh module", "cctbx.macro_mol package", "cctbx.macro_mol.rotation_parameters module", "cctbx.maptbx package", "cctbx.maptbx.mem module", "cctbx.maptbx.real_space_refinement module", "cctbx.maptbx.real_space_refinement_simple module", "cctbx.maptbx.real_space_target_and_gradients module", "cctbx.masks package", "cctbx.math_module module", "cctbx.merging package", "cctbx.merging.brehm_diederichs module", "cctbx.miller package", "cctbx.miller.display module", "cctbx.miller.reindexing module", "cctbx.multipolar module", "cctbx.neutron package", "cctbx.omz package", "cctbx.omz.bfgs module", "cctbx.omz.cif_refine module", "cctbx.omz.cod_refine module", "cctbx.omz.cod_select_and_pickle module", "cctbx.omz.dev module", "cctbx.omz.eval_iso_vs_refined module", "cctbx.omz.pdb_dev module", "cctbx.omz.tardy_adaptor module", "cctbx.r_free_utils module", "cctbx.run_examples module", "cctbx.run_tests module", "cctbx.sgtbx package", "cctbx.sgtbx.bravais_types module", "cctbx.sgtbx.cosets module", "cctbx.sgtbx.direct_space_asu package", "cctbx.sgtbx.direct_space_asu.check_redundancies module", "cctbx.sgtbx.direct_space_asu.cut_plane module", "cctbx.sgtbx.direct_space_asu.facet_analysis module", "cctbx.sgtbx.direct_space_asu.plane_group_reference_table module", "cctbx.sgtbx.direct_space_asu.proto package", "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module", "cctbx.sgtbx.direct_space_asu.reference_table module", "cctbx.sgtbx.direct_space_asu.short_cuts module", "cctbx.sgtbx.harker module", "cctbx.sgtbx.lattice_symmetry module", "cctbx.sgtbx.literal_description module", "cctbx.sgtbx.plane_groups module", "cctbx.sgtbx.pointgroup_tools module", "cctbx.sgtbx.rational_matrices_point_groups module", "cctbx.sgtbx.reticular_pg_tools module", "cctbx.sgtbx.reticular_twin_laws module", "cctbx.sgtbx.show_cosets module", 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"module-cctbx.eltbx.formula"]], "cctbx.eltbx.fp_fdp module": [[67, "module-cctbx.eltbx.fp_fdp"]], "cctbx.eltbx.gaussian_fit module": [[68, "module-cctbx.eltbx.gaussian_fit"]], "cctbx.eltbx.henke module": [[69, "module-cctbx.eltbx.henke"]], "cctbx.eltbx.icsd_radii module": [[70, "module-cctbx.eltbx.icsd_radii"]], "cctbx.eltbx.neutron module": [[71, "module-cctbx.eltbx.neutron"]], "cctbx.eltbx.sasaki module": [[72, "module-cctbx.eltbx.sasaki"]], "cctbx.eltbx.tiny_pse module": [[73, "module-cctbx.eltbx.tiny_pse"]], "cctbx.eltbx.van_der_waals_radii module": [[74, "module-cctbx.eltbx.van_der_waals_radii"]], "cctbx.eltbx.wavelengths module": [[75, "module-cctbx.eltbx.wavelengths"]], "cctbx.eltbx.xray_scattering package": [[76, "cctbx-eltbx-xray-scattering-package"]], "cctbx.euclidean_model_matching module": [[77, "module-cctbx.euclidean_model_matching"]], "cctbx.examples package": [[78, "cctbx-examples-package"]], "cctbx.examples.adp_symmetry_constraints module": [[79, "module-cctbx.examples.adp_symmetry_constraints"]], "cctbx.examples.all_axes module": [[80, "module-cctbx.examples.all_axes"]], "cctbx.examples.analyze_adp module": [[81, "module-cctbx.examples.analyze_adp"]], "cctbx.examples.change_hand_p31 module": [[82, "module-cctbx.examples.change_hand_p31"]], "cctbx.examples.convert_ccp4_symop_lib module": [[83, "module-cctbx.examples.convert_ccp4_symop_lib"]], "cctbx.examples.cr2o3_consistency_checks module": [[84, "module-cctbx.examples.cr2o3_consistency_checks"]], "cctbx.examples.cr2o3_primitive_cell module": [[85, "module-cctbx.examples.cr2o3_primitive_cell"]], "cctbx.examples.exp_i_alpha_derivatives module": [[86, "module-cctbx.examples.exp_i_alpha_derivatives"]], "cctbx.examples.f_model_example module": [[87, "module-cctbx.examples.f_model_example"]], "cctbx.examples.fft_map_electron_density_around_atom module": [[88, "module-cctbx.examples.fft_map_electron_density_around_atom"]], "cctbx.examples.find_distances_using_cpp_objects module": [[89, "module-cctbx.examples.find_distances_using_cpp_objects"]], "cctbx.examples.find_sys_abs_equiv_space_groups module": [[90, "module-cctbx.examples.find_sys_abs_equiv_space_groups"]], "cctbx.examples.g_exp_i_alpha_derivatives module": [[91, "module-cctbx.examples.g_exp_i_alpha_derivatives"]], "cctbx.examples.g_exp_i_partial_derivatives module": [[92, "module-cctbx.examples.g_exp_i_partial_derivatives"]], "cctbx.examples.getting_started module": [[93, "module-cctbx.examples.getting_started"]], "cctbx.examples.hirshfeld_test module": [[94, "module-cctbx.examples.hirshfeld_test"]], "cctbx.examples.le_page_1982_vs_lebedev_2005 module": [[95, "module-cctbx.examples.le_page_1982_vs_lebedev_2005"]], "cctbx.examples.lebedev_2005_perturbation module": [[96, "module-cctbx.examples.lebedev_2005_perturbation"]], "cctbx.examples.list_non_principal_continuous_shifts module": [[97, "module-cctbx.examples.list_non_principal_continuous_shifts"]], "cctbx.examples.location_part module": [[98, "module-cctbx.examples.location_part"]], "cctbx.examples.map_skewness module": [[99, "module-cctbx.examples.map_skewness"]], "cctbx.examples.maximum_subgroups module": [[100, "module-cctbx.examples.maximum_subgroups"]], "cctbx.examples.miller_common_sets module": [[101, "module-cctbx.examples.miller_common_sets"]], "cctbx.examples.miller_transform module": [[102, "module-cctbx.examples.miller_transform"]], "cctbx.examples.neutron_structure_factors module": [[103, "module-cctbx.examples.neutron_structure_factors"]], "cctbx.examples.phase_o_phrenia module": [[104, "module-cctbx.examples.phase_o_phrenia"]], "cctbx.examples.quartz_structure module": [[105, "module-cctbx.examples.quartz_structure"]], "cctbx.examples.random_f_calc module": [[106, "module-cctbx.examples.random_f_calc"]], "cctbx.examples.random_puckers module": [[107, "module-cctbx.examples.random_puckers"]], "cctbx.examples.reduced_cell_two_folds module": [[108, "module-cctbx.examples.reduced_cell_two_folds"]], "cctbx.examples.site_symmetry_constraints module": [[109, "module-cctbx.examples.site_symmetry_constraints"]], "cctbx.examples.site_symmetry_table module": [[110, "module-cctbx.examples.site_symmetry_table"]], "cctbx.examples.space_group_matrices module": [[111, "module-cctbx.examples.space_group_matrices"]], "cctbx.examples.space_subgroups module": [[112, "module-cctbx.examples.space_subgroups"]], "cctbx.examples.steve_collins module": [[113, "module-cctbx.examples.steve_collins"]], "cctbx.examples.structure_factor_calculus package": [[114, "cctbx-examples-structure-factor-calculus-package"]], "cctbx.examples.structure_factor_calculus.site_derivatives module": [[115, "module-cctbx.examples.structure_factor_calculus.site_derivatives"]], "cctbx.examples.structure_factor_calculus.sites_derivatives module": [[116, "module-cctbx.examples.structure_factor_calculus.sites_derivatives"]], "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives module": [[117, 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"cctbx.examples.unit_cell_minimizers module": [[126, "module-cctbx.examples.unit_cell_minimizers"]], "cctbx.examples.unit_cell_refinement module": [[127, "module-cctbx.examples.unit_cell_refinement"]], "cctbx.examples.view_fft_map module": [[128, "cctbx-examples-view-fft-map-module"]], "cctbx.french_wilson module": [[129, "module-cctbx.french_wilson"]], "cctbx.geometry package": [[130, "cctbx-geometry-package"]], "cctbx.geometry_restraints package": [[131, "cctbx-geometry-restraints-package"]], "cctbx.geometry_restraints.energies module": [[132, "module-cctbx.geometry_restraints.energies"]], "cctbx.geometry_restraints.flags module": [[133, "module-cctbx.geometry_restraints.flags"]], "cctbx.geometry_restraints.lbfgs module": [[134, "module-cctbx.geometry_restraints.lbfgs"]], "cctbx.geometry_restraints.manager module": [[135, "module-cctbx.geometry_restraints.manager"]], "cctbx.libtbx_refresh module": [[136, "cctbx-libtbx-refresh-module"]], "cctbx.macro_mol package": [[137, 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input data - practical aspects": [[148, "processing-input-data-practical-aspects"]], "Comparing arrays": [[148, "comparing-arrays"]], "Working with experimental data": [[148, "working-with-experimental-data"]], "From arrays to maps": [[148, "from-arrays-to-maps"]], "The Miller set": [[148, "the-miller-set"]], "The Miller array": [[148, "the-miller-array"]], "Utility classes": [[148, "utility-classes"]], "cctbx.miller.display module": [[149, "module-cctbx.miller.display"]], "cctbx.miller.reindexing module": [[150, "module-cctbx.miller.reindexing"]], "cctbx.multipolar module": [[151, "module-cctbx.multipolar"]], "cctbx.neutron package": [[152, "cctbx-neutron-package"]], "cctbx.omz package": [[153, "cctbx-omz-package"]], "cctbx.omz.bfgs module": [[154, "module-cctbx.omz.bfgs"]], "cctbx.omz.cif_refine module": [[155, "module-cctbx.omz.cif_refine"]], "cctbx.omz.cod_refine module": [[156, "module-cctbx.omz.cod_refine"]], "cctbx.omz.cod_select_and_pickle module": [[157, "module-cctbx.omz.cod_select_and_pickle"]], "cctbx.omz.dev module": [[158, "module-cctbx.omz.dev"]], "cctbx.omz.eval_iso_vs_refined module": [[159, "module-cctbx.omz.eval_iso_vs_refined"]], "cctbx.omz.pdb_dev module": [[160, "module-cctbx.omz.pdb_dev"]], "cctbx.omz.tardy_adaptor module": [[161, "module-cctbx.omz.tardy_adaptor"]], "cctbx.r_free_utils module": [[162, "module-cctbx.r_free_utils"]], "cctbx.run_examples module": [[163, "module-cctbx.run_examples"]], "cctbx.run_tests module": [[164, "module-cctbx.run_tests"]], "cctbx.sgtbx package": [[165, "cctbx-sgtbx-package"]], "cctbx.sgtbx.bravais_types module": [[166, "module-cctbx.sgtbx.bravais_types"]], "cctbx.sgtbx.cosets module": [[167, "module-cctbx.sgtbx.cosets"]], "cctbx.sgtbx.direct_space_asu package": [[168, "cctbx-sgtbx-direct-space-asu-package"]], "cctbx.sgtbx.direct_space_asu.check_redundancies module": [[169, "module-cctbx.sgtbx.direct_space_asu.check_redundancies"]], "cctbx.sgtbx.direct_space_asu.cut_plane module": [[170, "module-cctbx.sgtbx.direct_space_asu.cut_plane"]], "cctbx.sgtbx.direct_space_asu.facet_analysis module": [[171, "module-cctbx.sgtbx.direct_space_asu.facet_analysis"]], "cctbx.sgtbx.direct_space_asu.plane_group_reference_table module": [[172, "module-cctbx.sgtbx.direct_space_asu.plane_group_reference_table"]], "cctbx.sgtbx.direct_space_asu.proto package": [[173, "cctbx-sgtbx-direct-space-asu-proto-package"]], "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module": [[174, "module-cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table"]], "cctbx.sgtbx.direct_space_asu.reference_table module": [[175, "module-cctbx.sgtbx.direct_space_asu.reference_table"]], "cctbx.sgtbx.direct_space_asu.short_cuts module": [[176, "module-cctbx.sgtbx.direct_space_asu.short_cuts"]], "cctbx.sgtbx.harker module": [[177, "module-cctbx.sgtbx.harker"]], "cctbx.sgtbx.lattice_symmetry module": [[178, "module-cctbx.sgtbx.lattice_symmetry"]], "cctbx.sgtbx.literal_description module": [[179, "module-cctbx.sgtbx.literal_description"]], "cctbx.sgtbx.plane_groups module": [[180, "module-cctbx.sgtbx.plane_groups"]], "cctbx.sgtbx.pointgroup_tools module": [[181, "module-cctbx.sgtbx.pointgroup_tools"]], "cctbx.sgtbx.rational_matrices_point_groups module": [[182, "module-cctbx.sgtbx.rational_matrices_point_groups"]], "cctbx.sgtbx.reticular_pg_tools module": [[183, "module-cctbx.sgtbx.reticular_pg_tools"]], "cctbx.sgtbx.reticular_twin_laws module": [[184, "module-cctbx.sgtbx.reticular_twin_laws"]], "cctbx.sgtbx.show_cosets module": [[185, "module-cctbx.sgtbx.show_cosets"]], "cctbx.sgtbx.sub_lattice_tools module": [[186, "module-cctbx.sgtbx.sub_lattice_tools"]], "cctbx.sgtbx.subgroups module": [[187, "module-cctbx.sgtbx.subgroups"]], "cctbx.sgtbx.symbol_confidence module": [[188, "module-cctbx.sgtbx.symbol_confidence"]], "cctbx.sgtbx.sys_abs_equiv module": [[189, "module-cctbx.sgtbx.sys_abs_equiv"]], "cctbx.source_generators package": [[190, "cctbx-source-generators-package"]], "cctbx.source_generators.eltbx package": [[191, "cctbx-source-generators-eltbx-package"]], "cctbx.source_generators.eltbx.generate_henke_cpp module": [[192, "module-cctbx.source_generators.eltbx.generate_henke_cpp"]], "cctbx.source_generators.eltbx.generate_sasaki_cpp module": [[193, "module-cctbx.source_generators.eltbx.generate_sasaki_cpp"]], "cctbx.source_generators.flex_fwd_h module": [[194, "module-cctbx.source_generators.flex_fwd_h"]], "cctbx.statistics module": [[195, "module-cctbx.statistics"]], "cctbx.symmetry_search module": [[196, "module-cctbx.symmetry_search"]], "cctbx.translation_search module": [[197, "module-cctbx.translation_search"]], "cctbx.uctbx package": [[198, "cctbx-uctbx-package"]], "The unit cell": [[198, "the-unit-cell"]], "cctbx.uctbx.determine_unit_cell package": [[199, "cctbx-uctbx-determine-unit-cell-package"]], "cctbx.uctbx.gruber_1973 module": [[200, "module-cctbx.uctbx.gruber_1973"]], "cctbx.uctbx.gruber_1973_table_1 module": [[201, "module-cctbx.uctbx.gruber_1973_table_1"]], "cctbx.uctbx.krivy_gruber_1976 module": [[202, "module-cctbx.uctbx.krivy_gruber_1976"]], "cctbx.uctbx.reduction_base module": [[203, "module-cctbx.uctbx.reduction_base"]], "cctbx.web package": [[204, "cctbx-web-package"]], "cctbx.web.all_axes module": [[205, "module-cctbx.web.all_axes"]], "cctbx.web.asu_gallery package": [[206, "cctbx-web-asu-gallery-package"]], "cctbx.web.asu_gallery.guide_to_notation module": [[207, "module-cctbx.web.asu_gallery.guide_to_notation"]], "cctbx.web.asu_gallery.jv_asu module": [[208, "module-cctbx.web.asu_gallery.jv_asu"]], "cctbx.web.asu_gallery.jv_index module": [[209, "module-cctbx.web.asu_gallery.jv_index"]], "cctbx.web.asu_gallery.jvx module": [[210, "module-cctbx.web.asu_gallery.jvx"]], "cctbx.web.asu_gallery.web_links module": [[211, "module-cctbx.web.asu_gallery.web_links"]], "cctbx.web.browse_settings module": [[212, "module-cctbx.web.browse_settings"]], "cctbx.web.cgi_utils module": [[213, "module-cctbx.web.cgi_utils"]], "cctbx.web.change_basis module": [[214, "module-cctbx.web.change_basis"]], "cctbx.web.change_hand module": [[215, "module-cctbx.web.change_hand"]], "cctbx.web.change_setting module": [[216, "module-cctbx.web.change_setting"]], "cctbx.web.dispatcher module": [[217, "module-cctbx.web.dispatcher"]], "cctbx.web.emma module": [[218, "module-cctbx.web.emma"]], "cctbx.web.explore_symmetry module": [[219, "module-cctbx.web.explore_symmetry"]], "cctbx.web.frac_cart module": [[220, "module-cctbx.web.frac_cart"]], "cctbx.web.io_utils module": [[221, "module-cctbx.web.io_utils"]], "cctbx.web.iotbx_cif_validate module": [[222, "module-cctbx.web.iotbx_cif_validate"]], "cctbx.web.lattice_symmetry module": [[223, "module-cctbx.web.lattice_symmetry"]], "cctbx.web.libtbx_help module": [[224, "module-cctbx.web.libtbx_help"]], "cctbx.web.multiple_cell module": [[225, "module-cctbx.web.multiple_cell"]], "cctbx.web.phase_o_phrenia module": [[226, "module-cctbx.web.phase_o_phrenia"]], "cctbx.web.replay module": [[227, "module-cctbx.web.replay"]], "cctbx.web.shelx module": [[228, "module-cctbx.web.shelx"]], "cctbx.web.structure_factors module": [[229, "module-cctbx.web.structure_factors"]], "cctbx.web.structure_factors_pdb module": [[230, "module-cctbx.web.structure_factors_pdb"]], "cctbx.web.wyckoff module": [[231, "module-cctbx.web.wyckoff"]], "cctbx.xray package": [[232, "cctbx-xray-package"]], "cctbx.xray.ext module": [[233, "module-cctbx.xray.ext"]], "cctbx.xray.minimization module": [[234, "module-cctbx.xray.minimization"]], "cctbx.xray.observation_types module": [[235, "module-cctbx.xray.observation_types"]], "cctbx.xray.observations package": [[236, "cctbx-xray-observations-package"]], "cctbx.xray.scatterer module": [[237, "module-cctbx.xray.scatterer"]], "cctbx.xray.structure module": [[238, "module-cctbx.xray.structure"]], "cctbx.xray.structure_factors package": [[239, "cctbx-xray-structure-factors-package"]], "cctbx.xray.structure_factors.from_scatterers module": [[240, "module-cctbx.xray.structure_factors.from_scatterers"]], "cctbx.xray.structure_factors.from_scatterers_direct module": [[241, "module-cctbx.xray.structure_factors.from_scatterers_direct"]], "cctbx.xray.structure_factors.from_scatterers_direct_parallel module": [[242, "module-cctbx.xray.structure_factors.from_scatterers_direct_parallel"]], "cctbx.xray.structure_factors.from_scatterers_fft module": [[243, "module-cctbx.xray.structure_factors.from_scatterers_fft"]], "cctbx.xray.structure_factors.global_counters module": [[244, "module-cctbx.xray.structure_factors.global_counters"]], "cctbx.xray.structure_factors.gradient_flags module": [[245, "module-cctbx.xray.structure_factors.gradient_flags"]], "cctbx.xray.structure_factors.gradients module": [[246, "module-cctbx.xray.structure_factors.gradients"]], "cctbx.xray.structure_factors.gradients_base module": [[247, "module-cctbx.xray.structure_factors.gradients_base"]], "cctbx.xray.structure_factors.gradients_direct module": [[248, "module-cctbx.xray.structure_factors.gradients_direct"]], "cctbx.xray.structure_factors.gradients_fft module": [[249, "module-cctbx.xray.structure_factors.gradients_fft"]], "cctbx.xray.structure_factors.manager module": [[250, "module-cctbx.xray.structure_factors.manager"]], "cctbx.xray.structure_factors.misc module": [[251, "module-cctbx.xray.structure_factors.misc"]], "cctbx.xray.target_functors module": [[252, "module-cctbx.xray.target_functors"]], "cctbx.xray.targets package": [[253, "cctbx-xray-targets-package"]], "cctbx.xray.targets.r1 module": [[254, "module-cctbx.xray.targets.r1"]], "cctbx.xray.weighting_schemes module": [[255, "module-cctbx.xray.weighting_schemes"]], "cctbx": [[256, "cctbx"], [261, "cctbx"]], "dxtbx.model": [[257, "dxtbx-model"]], "Table of Contents": [[257, "table-of-contents"], [258, "table-of-contents"], [261, "table-of-contents"], [262, "table-of-contents"], [264, "table-of-contents"], [266, "table-of-contents"], [271, "table-of-contents"], [272, "table-of-contents"], [309, "table-of-contents"], [335, "table-of-contents"]], "dxtbx.model.detector": [[257, "module-dxtbx.model.detector"]], "dxtbx.model.beam": [[257, "module-dxtbx.model.beam"]], "dxtbx.model.scan": [[257, "module-dxtbx.model.scan"]], "dxtbx.model.goniometer": [[257, "module-dxtbx.model.goniometer"]], "dxtbx.model.crystal": [[257, "module-dxtbx.model.crystal"]], "dxtbx.serialize": [[258, "dxtbx-serialize"]], "dxtbx.serialize.load": [[258, "module-dxtbx.serialize.load"]], "dxtbx.serialize.dump": [[258, "dxtbx-serialize-dump"]], "dxtbx.serialize.xds": [[258, "module-dxtbx.serialize.xds"]], "dxtbx package": [[259, "dxtbx-package"]], "CCTBX development history": [[260, "cctbx-development-history"]], "eltbx - Element Toolbox": [[260, "eltbx-element-toolbox"]], "sgtbx - Space Group Toolbox": [[260, "sgtbx-space-group-toolbox"]], "Computational Crystallography Toolbox": [[261, "computational-crystallography-toolbox"]], "Welcome to CCTBX\u2019s documentation!": [[261, "welcome-to-cctbx-s-documentation"]], "High level organization": [[261, "high-level-organization"]], "libtbx": [[261, "libtbx"]], "boost_adaptbx": [[261, "boost-adaptbx"]], "scitbx": [[261, "scitbx"]], "iotbx": [[261, "iotbx"]], "mmtbx": [[261, "mmtbx"], [329, "mmtbx"]], "xfel": [[261, "xfel"], [336, "xfel"]], "smtbx": [[261, "smtbx"]], "dxtbx": [[261, "dxtbx"]], "Tour": [[261, "tour"]], "Tutorials": [[261, "tutorials"]], "Installation": [[261, "installation"]], "Reference Documentation": [[261, "reference-documentation"]], "Links": [[261, "links"]], "Contact": [[261, "contact"]], "Indices and tables": [[261, "indices-and-tables"]], "Installation overview": [[262, "installation-overview"]], "Manually building from sources under Linux and macOS": [[262, "manually-building-from-sources-under-linux-and-macos"]], "Manually building from sources under Windows 2000 or higher": [[262, "manually-building-from-sources-under-windows-2000-or-higher"]], "iotbx - file readers and writers": [[263, "iotbx-file-readers-and-writers"]], "iotbx.cif": [[264, "iotbx-cif"]], "Overview": [[264, "overview"], [266, "overview"], [269, "overview"], [271, "overview"], [272, "overview"]], "Reading a CIF file": [[264, "reading-a-cif-file"]], "Python representation of a CIF file": [[264, "python-representation-of-a-cif-file"]], "Dictionary validation": [[264, "dictionary-validation"]], "Creating a standalone C++ CIF parser": [[264, "creating-a-standalone-c-cif-parser"]], "API documentation": [[264, "api-documentation"], [265, "module-iotbx.file_reader"], [266, "module-iotbx.map_manager"], [268, "api-documentation"], [271, "module-iotbx.shelx"], [272, "module-iotbx.xds.xds_inp"], [282, "module-mmtbx.command_line"], [288, "module-mmtbx.f_model"], [310, "module-mmtbx.pdbtools"], [331, "module-scitbx.array_family.flex"], [332, "module-scitbx.lbfgs"], [333, "module-scitbx.lstbx.normal_eqns"], [334, "api-documentation"]], "iotbx.cif objects": [[264, "iotbx-cif-objects"]], "Accessory classes and functions": [[264, "accessory-classes-and-functions"], [268, "accessory-classes-and-functions"]], "iotbx.file_reader - generic file input": [[265, "iotbx-file-reader-generic-file-input"]], "iotbx.managers": [[266, "iotbx-managers"]], "Parameters:": [[266, "parameters"], [266, "id1"]], "Summary:": [[266, "summary"]], "iotbx.ncs package": [[267, "iotbx-ncs-package"]], "iotbx.ncs.ncs_preprocess module": [[267, "iotbx-ncs-ncs-preprocess-module"]], "iotbx.pdb": [[268, "iotbx-pdb"]], "Input methods and objects": [[268, "input-methods-and-objects"]], "Arguments:": [[268, "arguments"]], "Returns:": [[268, "returns"]], "PDB hierarchy objects": [[268, "pdb-hierarchy-objects"]], "iotbx.pdb.multimer_reconstruction module": [[268, "iotbx-pdb-multimer-reconstruction-module"]], "iotbx.pdb tutorial: pdb_truncate_to_ala": [[269, "iotbx-pdb-tutorial-pdb-truncate-to-ala"]], "Use print and help()!": [[269, "use-print-and-help"]], "v0_getting_started.py": [[269, "v0-getting-started-py"]], "v1_loop_over_atoms.py": [[269, "v1-loop-over-atoms-py"]], "v2_simple.py": [[269, "v2-simple-py"]], "v3_better.py": [[269, "v3-better-py"]], "v4_with_bells_and_whistles.py": [[269, "v4-with-bells-and-whistles-py"]], "Source and PDB files": [[269, "source-and-pdb-files"]], "iotbx.reflection_file_reader - generic reflection file input": [[270, "module-iotbx.reflection_file_reader"]], "iotbx.shelx": [[271, "iotbx-shelx"]], "iotbx.xds": [[272, "iotbx-xds"]], "libtbx - low-level utilities and infrastructure for CCTBX": [[273, "libtbx-low-level-utilities-and-infrastructure-for-cctbx"]], "Basic functionality": [[273, "basic-functionality"]], "libtbx.easy_mp: functions for painless parallelization of Python code": [[274, "libtbx-easy-mp-functions-for-painless-parallelization-of-python-code"]], "pool_map: parallel map() function for Unix/Linux systems": [[274, "pool-map-parallel-map-function-for-unix-linux-systems"]], "parallel_map: parallel map() function for multiple architectures": [[274, "parallel-map-parallel-map-function-for-multiple-architectures"]], "libtbx.program_template: Standard Program Template for CCTBX Programs": [[275, "libtbx-program-template-standard-program-template-for-cctbx-programs"]], "Program Template": [[275, "program-template"]], "mmtbx - macromolecular crystallography": [[276, "mmtbx-macromolecular-crystallography"]], "mmtbx.building package": [[277, "mmtbx-building-package"]], "mmtbx.building.extend_sidechains module": [[277, "module-mmtbx.building.extend_sidechains"]], "mmtbx.building.make_library module": [[277, "module-mmtbx.building.make_library"]], "mmtbx.bulk_solvent package": [[278, "mmtbx-bulk-solvent-package"]], "mmtbx.bulk_solvent.bulk_solvent_and_scaling module": [[278, "module-mmtbx.bulk_solvent.bulk_solvent_and_scaling"]], "mmtbx.bulk_solvent.scaler module": [[278, "module-mmtbx.bulk_solvent.scaler"]], "mmtbx.cablam package": [[279, "mmtbx-cablam-package"]], "mmtbx.cablam.cablam_align module": [[279, "module-mmtbx.cablam.cablam_align"]], "mmtbx.cablam.cablam_fingerprints module": [[279, "module-mmtbx.cablam.cablam_fingerprints"]], "mmtbx.cablam.cablam_math module": [[279, "module-mmtbx.cablam.cablam_math"]], "mmtbx.cablam.cablam_res module": [[279, "module-mmtbx.cablam.cablam_res"]], "mmtbx.cablam.cablam_training module": [[279, "module-mmtbx.cablam.cablam_training"]], "mmtbx.cablam.cablam_validate module": [[279, "module-mmtbx.cablam.cablam_validate"]], "mmtbx.cablam.fingerprints package": [[280, "mmtbx-cablam-fingerprints-package"]], "mmtbx.cablam.fingerprints.antiparallel_beta module": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta"]], "mmtbx.cablam.fingerprints.antiparallel_beta_bridge module": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta_bridge"]], "mmtbx.cablam.fingerprints.how_to module": [[280, "module-mmtbx.cablam.fingerprints.how_to"]], "mmtbx.cablam.fingerprints.parallel_beta module": [[280, "module-mmtbx.cablam.fingerprints.parallel_beta"]], "mmtbx.cablam.fingerprints.regular_helix_definitions module": [[280, "module-mmtbx.cablam.fingerprints.regular_helix_definitions"]], "mmtbx.chemical_components package": [[281, "mmtbx-chemical-components-package"]], "mmtbx.chemical_components.cif_parser module": [[281, "module-mmtbx.chemical_components.cif_parser"]], "mmtbx.command_line package": [[282, "mmtbx-command-line-package"]], "mmtbx.conformation_dependent_library package": [[283, "mmtbx-conformation-dependent-library-package"]], "mmtbx.conformation_dependent_library.altloc_weighting module": [[283, "module-mmtbx.conformation_dependent_library.altloc_weighting"]], "mmtbx.conformation_dependent_library.bond_angle_registry module": [[283, "module-mmtbx.conformation_dependent_library.bond_angle_registry"]], "mmtbx.conformation_dependent_library.cdl_database module": [[283, "module-mmtbx.conformation_dependent_library.cdl_database"]], "mmtbx.conformation_dependent_library.rdl_database module": [[283, "module-mmtbx.conformation_dependent_library.rdl_database"]], "mmtbx.conformation_dependent_library.rotamers module": [[283, "mmtbx-conformation-dependent-library-rotamers-module"]], "mmtbx.conformation_dependent_library.tst_cdl module": [[283, "module-mmtbx.conformation_dependent_library.tst_cdl"]], "mmtbx.conformation_dependent_library.test_interpolation module": [[283, "mmtbx-conformation-dependent-library-test-interpolation-module"]], "mmtbx.conformation_dependent_library.tst_rdl module": [[283, "mmtbx-conformation-dependent-library-tst-rdl-module"]], "mmtbx.conformation_dependent_library.utils module": [[283, "module-mmtbx.conformation_dependent_library.utils"]], "mmtbx.den package": [[284, "mmtbx-den-package"]], "mmtbx.den.plot_weights module": [[284, "module-mmtbx.den.plot_weights"]], "mmtbx.den.refinement module": [[284, "module-mmtbx.den.refinement"]], "mmtbx.density_modification package": [[285, "mmtbx-density-modification-package"]], "mmtbx.disorder package": [[286, "mmtbx-disorder-package"]], "mmtbx.disorder.analyze_model module": [[286, "module-mmtbx.disorder.analyze_model"]], "mmtbx.disorder.backbone module": [[286, "module-mmtbx.disorder.backbone"]], "mmtbx.dynamics package": [[287, "mmtbx-dynamics-package"]], "mmtbx.dynamics.cartesian_dynamics module": [[287, "module-mmtbx.dynamics.cartesian_dynamics"]], "mmtbx.dynamics.constants module": [[287, "module-mmtbx.dynamics.constants"]], "mmtbx.dynamics.ensemble_cd module": [[287, "module-mmtbx.dynamics.ensemble_cd"]], "mmtbx.dynamics.simulated_annealing module": [[287, "module-mmtbx.dynamics.simulated_annealing"]], "mmtbx.f_model": [[288, "mmtbx-f-model"]], "mmtbx.geometry package": [[289, "mmtbx-geometry-package"]], "mmtbx.geometry.altloc module": [[289, "module-mmtbx.geometry.altloc"]], "mmtbx.geometry.asa module": [[289, "module-mmtbx.geometry.asa"]], "mmtbx.geometry.clash module": [[289, "module-mmtbx.geometry.clash"]], "mmtbx.geometry.indexing module": [[289, "module-mmtbx.geometry.indexing"]], "mmtbx.geometry.primitive module": [[289, "mmtbx-geometry-primitive-module"]], "mmtbx.geometry.shared_types module": [[289, "module-mmtbx.geometry.shared_types"]], "mmtbx.geometry.sphere_surface_sampling module": [[289, "module-mmtbx.geometry.sphere_surface_sampling"]], "mmtbx.geometry.topology module": [[289, "module-mmtbx.geometry.topology"]], "mmtbx.geometry.volume module": [[289, "mmtbx-geometry-volume-module"]], "mmtbx.geometry_restraints package": [[290, "mmtbx-geometry-restraints-package"]], "mmtbx.geometry_restraints.c_beta module": [[290, "module-mmtbx.geometry_restraints.c_beta"]], "mmtbx.geometry_restraints.external module": [[290, "module-mmtbx.geometry_restraints.external"]], "mmtbx.geometry_restraints.flags module": [[290, "mmtbx-geometry-restraints-flags-module"]], "mmtbx.geometry_restraints.hbond module": [[290, "mmtbx-geometry-restraints-hbond-module"]], "mmtbx.geometry_restraints.ramachandran module": [[290, "module-mmtbx.geometry_restraints.ramachandran"]], "mmtbx.geometry_restraints.reference module": [[290, "module-mmtbx.geometry_restraints.reference"]], "mmtbx.geometry_restraints.rotamer module": [[290, "mmtbx-geometry-restraints-rotamer-module"]], "mmtbx.hydrogens package": [[291, "mmtbx-hydrogens-package"]], "mmtbx.hydrogens.build_hydrogens module": [[291, "module-mmtbx.hydrogens.build_hydrogens"]], "mmtbx.hydrogens.find module": [[291, "module-mmtbx.hydrogens.find"]], "mmtbx.ias package": [[292, "mmtbx-ias-package"]], "mmtbx.ions package": [[293, "mmtbx-ions-package"]], "mmtbx.ions.build module": [[294, "module-mmtbx.ions.build"]], "mmtbx.ions.environment module": [[295, "module-mmtbx.ions.environment"]], "mmtbx.ions.geometry module": [[296, "module-mmtbx.ions.geometry"]], "mmtbx.ions.halides module": [[297, "module-mmtbx.ions.halides"]], "mmtbx.ions.identify module": [[298, "module-mmtbx.ions.identify"]], "mmtbx.ions.svm package": [[299, "mmtbx-ions-svm-package"]], "mmtbx.ions.svm.dump_sites module": [[300, "module-mmtbx.ions.svm.dump_sites"]], "mmtbx.ions.svm.utils module": [[301, "module-mmtbx.ions.svm.utils"]], "mmtbx.ions.utils module": [[302, "module-mmtbx.ions.utils"]], "mmtbx.kinemage package": [[303, "mmtbx-kinemage-package"]], "mmtbx.kinemage.validation module": [[303, "module-mmtbx.kinemage.validation"]], "mmtbx.ligands package": [[304, "mmtbx-ligands-package"]], "mmtbx.ligands.xtal_screens module": [[304, "module-mmtbx.ligands.xtal_screens"]], "mmtbx.maps package": [[305, "mmtbx-maps-package"]], "mmtbx.maps.composite_omit_map module": [[305, "module-mmtbx.maps.composite_omit_map"]], "mmtbx.maps.fem module": [[305, "module-mmtbx.maps.fem"]], "mmtbx.maps.fobs_minus_fobs_map module": [[305, "module-mmtbx.maps.fobs_minus_fobs_map"]], "mmtbx.maps.kick module": [[305, "module-mmtbx.maps.kick"]], "mmtbx.maps.superpose module": [[305, "module-mmtbx.maps.superpose"]], "mmtbx.maps.utils module": [[305, "module-mmtbx.maps.utils"]], "mmtbx.masks package": [[306, "mmtbx-masks-package"]], "mmtbx.max_lik package": [[307, "mmtbx-max-lik-package"]], "mmtbx.max_lik.max_like_non_uniform module": [[307, "module-mmtbx.max_lik.max_like_non_uniform"]], "mmtbx.max_lik.maxlik module": [[307, "module-mmtbx.max_lik.maxlik"]], "mmtbx.monomer_library package": [[308, "mmtbx-monomer-library-package"]], "mmtbx.monomer_library.bondlength_defaults module": [[308, "module-mmtbx.monomer_library.bondlength_defaults"]], "mmtbx.monomer_library.cif_triage module": [[308, "module-mmtbx.monomer_library.cif_triage"]], "mmtbx.monomer_library.cif_types module": [[308, "module-mmtbx.monomer_library.cif_types"]], "mmtbx.monomer_library.conformation_dependent_restraints module": [[308, "module-mmtbx.monomer_library.conformation_dependent_restraints"]], "mmtbx.monomer_library.conv_v2_v3 module": [[308, "module-mmtbx.monomer_library.conv_v2_v3"]], "mmtbx.monomer_library.correct_hydrogen_geometries module": [[308, "module-mmtbx.monomer_library.correct_hydrogen_geometries"]], "mmtbx.monomer_library.glyco_chiral_values module": [[308, "module-mmtbx.monomer_library.glyco_chiral_values"]], "mmtbx.monomer_library.glyco_utils module": [[308, "module-mmtbx.monomer_library.glyco_utils"]], "mmtbx.monomer_library.hydrogen_restrictions module": [[308, "module-mmtbx.monomer_library.hydrogen_restrictions"]], "mmtbx.monomer_library.idealized_aa module": [[308, "module-mmtbx.monomer_library.idealized_aa"]], "mmtbx.monomer_library.linking_mixins module": [[308, "module-mmtbx.monomer_library.linking_mixins"]], "mmtbx.monomer_library.linking_setup module": [[308, "module-mmtbx.monomer_library.linking_setup"]], "mmtbx.monomer_library.linking_utils module": [[308, "module-mmtbx.monomer_library.linking_utils"]], "mmtbx.monomer_library.pdb_interpretation module": [[308, "module-mmtbx.monomer_library.pdb_interpretation"]], "mmtbx.monomer_library.rna_sugar_pucker_analysis module": [[308, "module-mmtbx.monomer_library.rna_sugar_pucker_analysis"]], "mmtbx.monomer_library.rotamer_utils module": [[308, "module-mmtbx.monomer_library.rotamer_utils"]], "mmtbx.monomer_library.server module": [[308, "module-mmtbx.monomer_library.server"]], "mmtbx.ncs": [[309, "mmtbx-ncs"]], "mmtbx.ncs.ligands module": [[309, "module-mmtbx.ncs.ligands"]], "mmtbx.ncs.ncs module": [[309, "module-mmtbx.ncs.ncs"]], "mmtbx.ncs.restraints module": [[309, "mmtbx-ncs-restraints-module"]], "mmtbx.ncs.ncs_search module": [[309, "module-mmtbx.ncs.ncs_search"]], "mmtbx.ncs.ncs_utils module": [[309, "module-mmtbx.ncs.ncs_utils"]], "mmtbx.pdbtools - model manipulation utilities": [[310, "mmtbx-pdbtools-model-manipulation-utilities"]], "mmtbx.polygon package": [[311, "mmtbx-polygon-package"]], "mmtbx.polygon.output module": [[311, "module-mmtbx.polygon.output"]], "mmtbx.real_space package": [[312, "mmtbx-real-space-package"]], "mmtbx.refinement package": [[313, "mmtbx-refinement-package"]], "mmtbx.refinement.adp_refinement module": [[313, "module-mmtbx.refinement.adp_refinement"]], "mmtbx.refinement.anomalous_scatterer_groups module": [[313, "module-mmtbx.refinement.anomalous_scatterer_groups"]], "mmtbx.refinement.fit_rotamers module": [[313, "mmtbx-refinement-fit-rotamers-module"]], "mmtbx.refinement.flip_peptides module": [[313, "mmtbx-refinement-flip-peptides-module"]], "mmtbx.refinement.geometry_minimization module": [[313, "module-mmtbx.refinement.geometry_minimization"]], "mmtbx.refinement.group module": [[313, "module-mmtbx.refinement.group"]], "mmtbx.refinement.inspect_tardy_trajectory module": [[313, "module-mmtbx.refinement.inspect_tardy_trajectory"]], "mmtbx.refinement.minimization module": [[313, "module-mmtbx.refinement.minimization"]], "mmtbx.refinement.minimization_ncs_constraints module": [[313, "module-mmtbx.refinement.minimization_ncs_constraints"]], "mmtbx.refinement.occupancies module": [[313, "module-mmtbx.refinement.occupancies"]], "mmtbx.refinement.orca module": [[313, "module-mmtbx.refinement.orca"]], "mmtbx.refinement.print_statistics module": [[313, "module-mmtbx.refinement.print_statistics"]], "mmtbx.refinement.refinement_flags module": [[313, "module-mmtbx.refinement.refinement_flags"]], "mmtbx.refinement.rigid_body module": [[313, "module-mmtbx.refinement.rigid_body"]], "mmtbx.refinement.select_best_starting_model module": [[313, "module-mmtbx.refinement.select_best_starting_model"]], "mmtbx.refinement.tardy module": [[313, "module-mmtbx.refinement.tardy"]], "mmtbx.refinement.targets module": [[313, "module-mmtbx.refinement.targets"]], "mmtbx.refinement.weights_params module": [[313, "module-mmtbx.refinement.weights_params"]], "mmtbx.refinement.wx_tardy_pdb module": [[313, "mmtbx-refinement-wx-tardy-pdb-module"]], "mmtbx.refinement.ensemble_refinement package": [[314, "mmtbx-refinement-ensemble-refinement-package"]], "mmtbx.refinement.ensemble_refinement.ensemble_utils module": [[314, "module-mmtbx.refinement.ensemble_refinement.ensemble_utils"]], "mmtbx.refinement.real_space package": [[315, "mmtbx-refinement-real-space-package"]], "mmtbx.refinement.real_space.fit_residue module": [[315, "module-mmtbx.refinement.real_space.fit_residue"]], "mmtbx.refinement.real_space.fit_residues module": [[315, "module-mmtbx.refinement.real_space.fit_residues"]], "mmtbx.refinement.real_space.fit_water module": [[315, "module-mmtbx.refinement.real_space.fit_water"]], "mmtbx.refinement.real_space.individual_sites module": [[315, "module-mmtbx.refinement.real_space.individual_sites"]], "mmtbx.refinement.real_space.rigid_body module": [[315, "module-mmtbx.refinement.real_space.rigid_body"]], "mmtbx.refinement.real_space.weight module": [[315, "module-mmtbx.refinement.real_space.weight"]], "mmtbx.rotamer package": [[316, "mmtbx-rotamer-package"]], "mmtbx.rotamer.graphics module": [[316, "module-mmtbx.rotamer.graphics"]], "mmtbx.rotamer.n_dim_table module": [[316, "module-mmtbx.rotamer.n_dim_table"]], "mmtbx.rotamer.ramachandran_eval module": [[316, "module-mmtbx.rotamer.ramachandran_eval"]], "mmtbx.rotamer.rotamer_eval module": [[316, "module-mmtbx.rotamer.rotamer_eval"]], "mmtbx.rotamer.sidechain_angles module": [[316, "module-mmtbx.rotamer.sidechain_angles"]], "mmtbx.rsr package": [[317, "mmtbx-rsr-package"]], "mmtbx.scaling package": [[318, "mmtbx-scaling-package"]], "mmtbx.scaling.absence_likelihood module": [[318, "module-mmtbx.scaling.absence_likelihood"]], "mmtbx.scaling.absences module": [[318, "module-mmtbx.scaling.absences"]], "mmtbx.scaling.absolute_scaling module": [[318, "module-mmtbx.scaling.absolute_scaling"]], "mmtbx.scaling.basic_analyses module": [[318, "module-mmtbx.scaling.basic_analyses"]], "mmtbx.scaling.data_statistics module": [[318, "module-mmtbx.scaling.data_statistics"]], "mmtbx.scaling.fa_estimation module": [[318, "module-mmtbx.scaling.fa_estimation"]], "mmtbx.scaling.fest module": [[318, "module-mmtbx.scaling.fest"]], "mmtbx.scaling.make_param module": [[318, "module-mmtbx.scaling.make_param"]], "mmtbx.scaling.massage_twin_detwin_data module": [[318, "module-mmtbx.scaling.massage_twin_detwin_data"]], "mmtbx.scaling.matthews module": [[318, "module-mmtbx.scaling.matthews"]], "mmtbx.scaling.outlier_plots module": [[318, "module-mmtbx.scaling.outlier_plots"]], "mmtbx.scaling.outlier_rejection module": [[318, "module-mmtbx.scaling.outlier_rejection"]], "mmtbx.scaling.pair_analyses module": [[318, "module-mmtbx.scaling.pair_analyses"]], "mmtbx.scaling.pre_scale module": [[318, "module-mmtbx.scaling.pre_scale"]], "mmtbx.scaling.random_omit module": [[318, "module-mmtbx.scaling.random_omit"]], "mmtbx.scaling.relative_scaling module": [[318, "module-mmtbx.scaling.relative_scaling"]], "mmtbx.scaling.relative_wilson module": [[318, "module-mmtbx.scaling.relative_wilson"]], "mmtbx.scaling.remove_outliers module": [[318, "module-mmtbx.scaling.remove_outliers"]], "mmtbx.scaling.rip_scale module": [[318, "module-mmtbx.scaling.rip_scale"]], "mmtbx.scaling.sad_scale module": [[318, "module-mmtbx.scaling.sad_scale"]], "mmtbx.scaling.sigmaa_estimation module": [[318, "module-mmtbx.scaling.sigmaa_estimation"]], "mmtbx.scaling.sir_scale module": [[318, "module-mmtbx.scaling.sir_scale"]], "mmtbx.scaling.siras_scale module": [[318, "module-mmtbx.scaling.siras_scale"]], "mmtbx.scaling.ta_alpha_beta_calc module": [[318, "module-mmtbx.scaling.ta_alpha_beta_calc"]], "mmtbx.scaling.thorough_outlier_test module": [[318, "module-mmtbx.scaling.thorough_outlier_test"]], "mmtbx.scaling.twin_analyses module": [[318, "module-mmtbx.scaling.twin_analyses"]], "mmtbx.scaling.twmad_scale module": [[318, "module-mmtbx.scaling.twmad_scale"]], "mmtbx.scaling.xtriage module": [[318, "module-mmtbx.scaling.xtriage"]], "mmtbx.secondary_structure package": [[319, "mmtbx-secondary-structure-package"]], "mmtbx.secondary_structure.base_pairing module": [[319, "mmtbx-secondary-structure-base-pairing-module"]], "mmtbx.secondary_structure.dssp module": [[319, "mmtbx-secondary-structure-dssp-module"]], "mmtbx.secondary_structure.proteins module": [[319, "module-mmtbx.secondary_structure.proteins"]], "mmtbx.secondary_structure.utils module": [[319, "module-mmtbx.secondary_structure.utils"]], "mmtbx.secondary_structure.build package": [[320, "mmtbx-secondary-structure-build-package"]], "mmtbx.solvent package": [[321, "mmtbx-solvent-package"]], "mmtbx.solvent.ensemble_ordered_solvent module": [[321, "module-mmtbx.solvent.ensemble_ordered_solvent"]], "mmtbx.solvent.ordered_solvent module": [[321, "module-mmtbx.solvent.ordered_solvent"]], "mmtbx.tls package": [[322, "mmtbx-tls-package"]], "mmtbx.tls.command_line module": [[322, "module-mmtbx.tls.command_line"]], "mmtbx.tls.ladp module": [[322, "module-mmtbx.tls.ladp"]], "mmtbx.tls.tls_as_xyz module": [[322, "module-mmtbx.tls.tls_as_xyz"]], "mmtbx.tls.tools module": [[322, "module-mmtbx.tls.tools"]], "mmtbx.torsion_restraints package": [[323, "mmtbx-torsion-restraints-package"]], "mmtbx.torsion_restraints.reference_model module": [[323, "mmtbx-torsion-restraints-reference-model-module"]], "mmtbx.torsion_restraints.rotamer_search module": [[323, "mmtbx-torsion-restraints-rotamer-search-module"]], "mmtbx.torsion_restraints.torsion_ncs module": [[323, "mmtbx-torsion-restraints-torsion-ncs-module"]], "mmtbx.torsion_restraints.utils module": [[323, "mmtbx-torsion-restraints-utils-module"]], "mmtbx.twinning package": [[324, "mmtbx-twinning-package"]], "mmtbx.twinning.probabalistic_detwinning module": [[324, "module-mmtbx.twinning.probabalistic_detwinning"]], "mmtbx.twinning.twin_f_model module": [[324, "module-mmtbx.twinning.twin_f_model"]], "mmtbx.twinning.twin_map_utils module": [[324, "mmtbx-twinning-twin-map-utils-module"]], "mmtbx.utils package": [[325, "mmtbx-utils-package"]], "mmtbx.utils.fab_elbow_angle module": [[325, "module-mmtbx.utils.fab_elbow_angle"]], "mmtbx.utils.ncs_utils module": [[325, "mmtbx-utils-ncs-utils-module"]], "mmtbx.utils.rotatable_bonds module": [[325, "module-mmtbx.utils.rotatable_bonds"]], "mmtbx.validation package": [[326, "mmtbx-validation-package"]], "Base classes": [[326, "base-classes"]], "Rotalyze - protein sidechain rotamer analysis": [[326, "rotalyze-protein-sidechain-rotamer-analysis"]], "Ramalyze - Ramachandran plot analysis": [[326, "ramalyze-ramachandran-plot-analysis"]], "Clashscore - all-atom contacts using Reduce and Probe": [[326, "clashscore-all-atom-contacts-using-reduce-and-probe"]], "C-beta deviations": [[326, "c-beta-deviations"]], "mmtbx.validation.restraints module": [[326, "module-mmtbx.validation.restraints"]], "mmtbx.validation.rna_validate module": [[326, "module-mmtbx.validation.rna_validate"]], "mmtbx.validation.analyze_peptides module": [[326, "module-mmtbx.validation.analyze_peptides"]], "mmtbx.validation.experimental module": [[326, "module-mmtbx.validation.experimental"]], "mmtbx.validation.graphics module": [[326, "module-mmtbx.validation.graphics"]], "mmtbx.validation.ligands module": [[326, "module-mmtbx.validation.ligands"]], "mmtbx.validation.model_properties module": [[326, "module-mmtbx.validation.model_properties"]], "mmtbx.validation.sequence module": [[326, "module-mmtbx.validation.sequence"]], "mmtbx.validation.utils module": [[326, "module-mmtbx.validation.utils"]], "mmtbx.validation.waters module": [[326, "module-mmtbx.validation.waters"]], "mmtbx.validation.molprobity package": [[327, "mmtbx-validation-molprobity-package"]], "mmtbx.validation.molprobity.mp_geo module": [[327, "module-mmtbx.validation.molprobity.mp_geo"]], "mmtbx.validation.molprobity.nqh_minimize module": [[327, "module-mmtbx.validation.molprobity.nqh_minimize"]], "mmtbx.wwpdb package": [[328, "mmtbx-wwpdb-package"]], "mmtbx.wwpdb.rcsb_web_services module": [[328, "module-mmtbx.wwpdb.rcsb_web_services"]], "mmtbx.wwpdb.standard_geometry_cif module": [[328, "module-mmtbx.wwpdb.standard_geometry_cif"]], "mmtbx.wwpdb.utils module": [[328, "module-mmtbx.wwpdb.utils"]], "scitbx - general-purpose scientific programming infrastructure": [[330, "scitbx-general-purpose-scientific-programming-infrastructure"]], "scitbx.array_family.flex": [[331, "scitbx-array-family-flex"], [335, "scitbx-array-family-flex"]], "Multidimensional arrays: flex.grid": [[331, "multidimensional-arrays-flex-grid"]], "Working with selections": [[331, "working-with-selections"]], "scitbx.lbfgs": [[332, "scitbx-lbfgs"]], "scitbx.lstbx": [[333, "scitbx-lstbx"]], "scitbx.matrix": [[334, "module-scitbx.matrix"]], "Tour of the cctbx": [[335, "tour-of-the-cctbx"]], "The beach in the box": [[335, "the-beach-in-the-box"]], "At the very bottom": [[335, "at-the-very-bottom"]], "cctbx.array_family.flex": [[335, "cctbx-array-family-flex"]], "A balancing act": [[335, "a-balancing-act"]], "Hybrid systems": [[335, "hybrid-systems"]], "Building bridges": [[335, "building-bridges"]], "Thinking hybrid": [[335, "thinking-hybrid"]], "xfel package": [[337, "xfel-package"]], "xfel.detector_formats module": [[337, "xfel-detector-formats-module"]], "xfel.phil_preferences module": [[337, "module-xfel.phil_preferences"]], "xfel.cftbx package": [[338, "xfel-cftbx-package"]], "xfel.cftbx.detector package": [[339, "xfel-cftbx-detector-package"]], "xfel.cftbx.detector.cspad_cbf_tbx module": [[339, "module-xfel.cftbx.detector.cspad_cbf_tbx"]], "xfel.cftbx.detector.cspad_detector module": [[339, "xfel-cftbx-detector-cspad-detector-module"]], "xfel.cftbx.detector.generic_detector module": [[339, "xfel-cftbx-detector-generic-detector-module"]], "xfel.cftbx.detector.metrology module": [[339, "xfel-cftbx-detector-metrology-module"]], "xfel.cftbx.detector.metrology2phil module": [[339, "module-xfel.cftbx.detector.metrology2phil"]], "xfel.clustering package": [[340, "xfel-clustering-package"]], "xfel.clustering.cluster module": [[340, "module-xfel.clustering.cluster"]], "cluster.Cluster": [[340, "cluster-cluster"]], "xfel.clustering.cluster_groups module": [[340, "module-xfel.clustering.cluster_groups"]], "xfel.clustering.singleframe module": [[340, "module-xfel.clustering.singleframe"]], "singleframe.SingleFrame": [[340, "singleframe-singleframe"]], "xfel.command_line package": [[341, "xfel-command-line-package"]], "xfel.command_line.auto_submit module": [[341, "module-xfel.command_line.auto_submit"]], "xfel.command_line.brehm_diederichs module": [[341, "module-xfel.command_line.brehm_diederichs"]], "xfel.command_line.cbf_average module": [[341, "module-xfel.command_line.cbf_average"]], "xfel.command_line.cluster_42 module": [[341, "xfel-command-line-cluster-42-module"]], "xfel.command_line.cluster_intensity_statistics module": [[341, "xfel-command-line-cluster-intensity-statistics-module"]], "xfel.command_line.cluster_per_frame_wilson module": [[341, "xfel-command-line-cluster-per-frame-wilson-module"]], "xfel.command_line.cluster_unit_cell module": [[341, "xfel-command-line-cluster-unit-cell-module"]], "xfel.command_line.cluster_visualise_orientations module": [[341, "xfel-command-line-cluster-visualise-orientations-module"]], "xfel.command_line.convert_gain_map module": [[341, "module-xfel.command_line.convert_gain_map"]], "xfel.command_line.convert_gain_map_cbf module": [[341, "module-xfel.command_line.convert_gain_map_cbf"]], "xfel.command_line.cxi_apply_metrology module": [[341, "module-xfel.command_line.cxi_apply_metrology"]], "xfel.command_line.cxi_cspad_pinwheel module": [[341, "module-xfel.command_line.cxi_cspad_pinwheel"]], "xfel.command_line.cxi_diff module": [[341, "module-xfel.command_line.cxi_diff"]], "xfel.command_line.cxi_display_metrology module": [[341, "module-xfel.command_line.cxi_display_metrology"]], "xfel.command_line.cxi_generate_circular_gain_mask module": [[341, "module-xfel.command_line.cxi_generate_circular_gain_mask"]], "xfel.command_line.cxi_image2pickle module": [[341, "xfel-command-line-cxi-image2pickle-module"]], "xfel.command_line.cxi_index module": [[341, "module-xfel.command_line.cxi_index"]], "xfel.command_line.cxi_lsf module": [[341, "module-xfel.command_line.cxi_lsf"]], "xfel.command_line.cxi_merge module": [[341, "module-xfel.command_line.cxi_merge"]], "xfel.command_line.cxi_optical2cbfheader module": [[341, "module-xfel.command_line.cxi_optical2cbfheader"]], "xfel.command_line.cxi_pbs module": [[341, "module-xfel.command_line.cxi_pbs"]], "xfel.command_line.cxi_pickle2cbf module": [[341, "module-xfel.command_line.cxi_pickle2cbf"]], "xfel.command_line.cxi_plotcv module": [[341, "module-xfel.command_line.cxi_plotcv"]], "xfel.command_line.cxi_psana module": [[341, "module-xfel.command_line.cxi_psana"]], "xfel.command_line.cxi_pyana module": [[341, "module-xfel.command_line.cxi_pyana"]], "xfel.command_line.cxi_spots module": [[341, "module-xfel.command_line.cxi_spots"]], "xfel.command_line.cxi_stream_to_pickle module": [[341, "module-xfel.command_line.cxi_stream_to_pickle"]], "xfel.command_line.cxi_view module": [[341, "module-xfel.command_line.cxi_view"]], "xfel.command_line.cxi_xmerge module": [[341, "module-xfel.command_line.cxi_xmerge"]], "xfel.command_line.get_next_trial_id module": [[341, "xfel-command-line-get-next-trial-id-module"]], "xfel.command_line.grid_index module": [[341, "xfel-command-line-grid-index-module"]], "xfel.command_line.histogram_finalise module": [[341, "module-xfel.command_line.histogram_finalise"]], "xfel.command_line.list_db_metadata module": [[341, "module-xfel.command_line.list_db_metadata"]], "xfel.command_line.make_mask module": [[341, "module-xfel.command_line.make_mask"]], "xfel.command_line.metrology module": [[341, "module-xfel.command_line.metrology"]], "xfel.command_line.monitor_detectors module": [[341, "module-xfel.command_line.monitor_detectors"]], "xfel.command_line.monitor_trials module": [[341, "module-xfel.command_line.monitor_trials"]], "xfel.command_line.overlay_spectra module": [[341, "module-xfel.command_line.overlay_spectra"]], "xfel.command_line.plot_to_subpixel module": [[341, "module-xfel.command_line.plot_to_subpixel"]], "xfel.command_line.postrefine module": [[341, "module-xfel.command_line.postrefine"]], "xfel.command_line.print_pickle module": [[341, "module-xfel.command_line.print_pickle"]], "xfel.command_line.quadrants module": [[341, "module-xfel.command_line.quadrants"]], "xfel.command_line.radial_average module": [[341, "module-xfel.command_line.radial_average"]], "xfel.command_line.smooth_spectrum module": [[341, "module-xfel.command_line.smooth_spectrum"]], "xfel.command_line.subtract_background module": [[341, "module-xfel.command_line.subtract_background"]], "xfel.command_line.trial_stats module": [[341, "module-xfel.command_line.trial_stats"]], "xfel.command_line.view_pixel_histograms module": [[341, "module-xfel.command_line.view_pixel_histograms"]], "xfel.command_line.xes_finalise module": [[341, "module-xfel.command_line.xes_finalise"]], "xfel.command_line.xes_histograms module": [[341, "module-xfel.command_line.xes_histograms"]], "xfel.cxi package": [[342, "xfel-cxi-package"]], "xfel.cxi.average_spots module": [[342, "module-xfel.cxi.average_spots"]], "xfel.cxi.completeness_plot module": [[342, "xfel-cxi-completeness-plot-module"]], "xfel.cxi.correction_vector_plot module": [[342, "module-xfel.cxi.correction_vector_plot"]], "xfel.cxi.cxi_cc module": [[342, "module-xfel.cxi.cxi_cc"]], "xfel.cxi.display_powder_arcs module": [[342, "module-xfel.cxi.display_powder_arcs"]], "xfel.cxi.display_spots module": [[342, "module-xfel.cxi.display_spots"]], "xfel.cxi.integrate_image_api module": [[342, "module-xfel.cxi.integrate_image_api"]], "xfel.cxi.merging_database module": [[342, "xfel-cxi-merging-database-module"]], "xfel.cxi.merging_database_fs module": [[342, "xfel-cxi-merging-database-fs-module"]], "xfel.cxi.merging_database_sqlite3 module": [[342, "xfel-cxi-merging-database-sqlite3-module"]], "xfel.cxi.strong_zulu module": [[342, "module-xfel.cxi.strong_zulu"]], "xfel.cxi.util module": [[342, "module-xfel.cxi.util"]], "xfel.cxi.cspad_ana package": [[343, "xfel-cxi-cspad-ana-package"]], "xfel.cxi.cspad_ana.average_tbx module": [[343, "module-xfel.cxi.cspad_ana.average_tbx"]], "xfel.cxi.cspad_ana.common_mode module": [[343, "module-xfel.cxi.cspad_ana.common_mode"]], "xfel.cxi.cspad_ana.cspad_tbx module": [[343, "module-xfel.cxi.cspad_ana.cspad_tbx"]], "xfel.cxi.cspad_ana.display_calib module": [[343, "module-xfel.cxi.cspad_ana.display_calib"]], "xfel.cxi.cspad_ana.histogram_finalise module": [[343, "module-xfel.cxi.cspad_ana.histogram_finalise"]], "xfel.cxi.cspad_ana.hitfinder_tbx module": [[343, "module-xfel.cxi.cspad_ana.hitfinder_tbx"]], "xfel.cxi.cspad_ana.mod_average module": [[343, "module-xfel.cxi.cspad_ana.mod_average"]], "xfel.cxi.cspad_ana.mod_average_cbf module": [[343, "xfel-cxi-cspad-ana-mod-average-cbf-module"]], "xfel.cxi.cspad_ana.mod_cbf_hitfind module": [[343, "xfel-cxi-cspad-ana-mod-cbf-hitfind-module"]], "xfel.cxi.cspad_ana.mod_cbf_index module": [[343, "xfel-cxi-cspad-ana-mod-cbf-index-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_daq_status module": [[343, "module-xfel.cxi.cspad_ana.mod_daq_status"]], "xfel.cxi.cspad_ana.mod_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_dump"]], "xfel.cxi.cspad_ana.mod_dump_bitmap module": [[343, "module-xfel.cxi.cspad_ana.mod_dump_bitmap"]], "xfel.cxi.cspad_ana.mod_event_info module": [[343, "module-xfel.cxi.cspad_ana.mod_event_info"]], "xfel.cxi.cspad_ana.mod_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_filter"]], "xfel.cxi.cspad_ana.mod_hdf5 module": [[343, "module-xfel.cxi.cspad_ana.mod_hdf5"]], "xfel.cxi.cspad_ana.mod_hitfind module": [[343, "module-xfel.cxi.cspad_ana.mod_hitfind"]], "xfel.cxi.cspad_ana.mod_illumination_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_illumination_filter"]], "xfel.cxi.cspad_ana.mod_ledge module": [[343, "xfel-cxi-cspad-ana-mod-ledge-module"]], "xfel.cxi.cspad_ana.mod_mar module": [[343, "module-xfel.cxi.cspad_ana.mod_mar"]], "xfel.cxi.cspad_ana.mod_param module": [[343, "module-xfel.cxi.cspad_ana.mod_param"]], "xfel.cxi.cspad_ana.mod_pickle2cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-pickle2cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_pulnix_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_pulnix_dump"]], "xfel.cxi.cspad_ana.mod_radial_average module": [[343, "module-xfel.cxi.cspad_ana.mod_radial_average"]], "xfel.cxi.cspad_ana.mod_spectra module": [[343, "xfel-cxi-cspad-ana-mod-spectra-module"]], "xfel.cxi.cspad_ana.mod_spectra_view module": [[343, "xfel-cxi-cspad-ana-mod-spectra-view-module"]], "xfel.cxi.cspad_ana.mod_view module": [[343, "xfel-cxi-cspad-ana-mod-view-module"]], "xfel.cxi.cspad_ana.mod_xes module": [[343, "module-xfel.cxi.cspad_ana.mod_xes"]], "xfel.cxi.cspad_ana.parse_calib module": [[343, "module-xfel.cxi.cspad_ana.parse_calib"]], "xfel.cxi.cspad_ana.pixel_histograms module": [[343, "module-xfel.cxi.cspad_ana.pixel_histograms"]], "xfel.cxi.cspad_ana.xes_finalise module": [[343, "module-xfel.cxi.cspad_ana.xes_finalise"]], "xfel.cxi.cspad_ana.xes_histograms module": [[343, "module-xfel.cxi.cspad_ana.xes_histograms"]], "xfel.cxi.gfx package": [[344, "xfel-cxi-gfx-package"]], "xfel.cxi.gfx.status_plot module": [[344, "module-xfel.cxi.gfx.status_plot"]], "xfel.cxi.gfx.trials_plot module": [[344, "module-xfel.cxi.gfx.trials_plot"]], "xfel.cxi.gfx.wx_detectors module": [[344, "module-xfel.cxi.gfx.wx_detectors"]], "xfel.cxi.merging package": [[345, "xfel-cxi-merging-package"]], "xfel.cxi.merging.general_fcalc module": [[345, "xfel-cxi-merging-general-fcalc-module"]], "xfel.cxi.merging.phil_validation module": 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"module-xfel.metrology.quadrant"], [348, "module-xfel.metrology.legacy_scale"], [349, "module-xfel.mono_simulation"], [349, "module-xfel.mono_simulation.mono_treatment"]], "adp_aniso_restraints (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.adp_aniso_restraints"]], "cctbx.adp_restraints": [[2, "module-cctbx.adp_restraints"]], "energies_iso (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.energies_iso"]], "adp_similarity_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.adp_similarity_deviation"]], "cctbx.adp_restraints.energies": [[3, "module-cctbx.adp_restraints.energies"]], "energies (class in cctbx.adp_restraints.energies)": [[3, "cctbx.adp_restraints.energies.energies"]], "finalize_target_and_gradients() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.finalize_target_and_gradients"]], "isotropic_adp_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.isotropic_adp_deviation"]], "rigid_bond_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.rigid_bond_deviation"]], "show() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.show"]], "cctbx.adp_restraints.flags": [[4, "module-cctbx.adp_restraints.flags"]], "flags (class in cctbx.adp_restraints.flags)": [[4, "cctbx.adp_restraints.flags.flags"]], "show() (cctbx.adp_restraints.flags.flags method)": [[4, "cctbx.adp_restraints.flags.flags.show"]], "cctbx.adptbx": [[5, "module-cctbx.adptbx"]], "debye_waller_factor_u_star_curvatures() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.debye_waller_factor_u_star_curvatures"]], "debye_waller_factor_u_star_gradients() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.debye_waller_factor_u_star_gradients"]], "intersection() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.intersection"]], "random_rotate_ellipsoid() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_rotate_ellipsoid"]], "random_traceless_symmetry_constrained_b_cart() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_traceless_symmetry_constrained_b_cart"]], "random_u_cart() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_u_cart"]], "cctbx.array_family": [[6, "module-cctbx.array_family"]], "cctbx.array_family.flex": [[7, "module-cctbx.array_family.flex"]], "cctbx.command_line": [[8, "module-cctbx.command_line"]], "cctbx.command_line.brehm_diederichs": [[9, "module-cctbx.command_line.brehm_diederichs"]], "run() (in module cctbx.command_line.brehm_diederichs)": [[9, "cctbx.command_line.brehm_diederichs.run"]], "cctbx.command_line.cod_select_and_pickle": [[10, "module-cctbx.command_line.cod_select_and_pickle"]], "cctbx.command_line.euclidean_model_matching": [[12, "module-cctbx.command_line.euclidean_model_matching"]], "match_record (class in cctbx.command_line.euclidean_model_matching)": [[12, "cctbx.command_line.euclidean_model_matching.match_record"]], "run() (in module cctbx.command_line.euclidean_model_matching)": [[12, "cctbx.command_line.euclidean_model_matching.run"]], "cctbx.command_line.find_reticular_twin_laws": [[13, "module-cctbx.command_line.find_reticular_twin_laws"]], "run() (in module cctbx.command_line.find_reticular_twin_laws)": [[13, "cctbx.command_line.find_reticular_twin_laws.run"]], "cctbx.command_line.form_factor_query": [[14, "module-cctbx.command_line.form_factor_query"]], "run() (in module cctbx.command_line.form_factor_query)": [[14, "cctbx.command_line.form_factor_query.run"]], "getsize() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.GetSize"]], "getsize() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.GetSize"]], "cctbx.command_line.precession_view": [[15, "module-cctbx.command_line.precession_view"]], "draw_filled_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_filled_circle"]], "draw_filled_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_filled_circle"]], "draw_line() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_line"]], "draw_line() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_line"]], "draw_open_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_open_circle"]], "draw_open_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_open_circle"]], "draw_text() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_text"]], "draw_text() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_text"]], "frac2int() (in module cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.frac2int"]], "get_scale_factor() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.get_scale_factor"]], "get_scale_factor() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.get_scale_factor"]], "paint() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.paint"]], "render_pil (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_pil"]], "render_postscript (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_postscript"]], "run() (in module cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.run"]], "cctbx.command_line.space_group_info": [[16, "module-cctbx.command_line.space_group_info"]], "run() (in module cctbx.command_line.space_group_info)": [[16, "cctbx.command_line.space_group_info.run"]], "cctbx.command_line.structure_factor_timings": [[17, "module-cctbx.command_line.structure_factor_timings"]], "read_structure() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.read_structure"]], "run() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.run"]], "timings() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.timings"]], "cctbx.command_line.subgroups": [[18, "module-cctbx.command_line.subgroups"]], "run() (in module cctbx.command_line.subgroups)": [[18, "cctbx.command_line.subgroups.run"]], "cctbx.command_line.version": [[19, "module-cctbx.command_line.version"]], "run() (in module cctbx.command_line.version)": [[19, "cctbx.command_line.version.run"]], "cctbx.command_line.wavelength_units": [[20, "module-cctbx.command_line.wavelength_units"]], "raise_usage() (in module cctbx.command_line.wavelength_units)": [[20, "cctbx.command_line.wavelength_units.raise_usage"]], "run() (in module cctbx.command_line.wavelength_units)": [[20, "cctbx.command_line.wavelength_units.run"]], "cctbx.covariance": [[22, "module-cctbx.covariance"]], "as_cif_block() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_cif_block"]], "as_pdb_remark_290() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_pdb_remark_290"]], "as_py_code() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_py_code"]], "as_reference_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_reference_setting"]], "as_str() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_str"]], "assert_min_distance_sym_equiv() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.assert_min_distance_sym_equiv"]], "asu_mappings() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.asu_mappings"]], "asu_mappings() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.asu_mappings"]], "average_b_cart() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.average_b_cart"]], "average_u_cart() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.average_u_cart"]], "best_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.best_cell"]], "build_miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.build_miller_set"]], "calculate_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_angles"]], "calculate_dihedrals (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_dihedrals"]], "calculate_distances (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_distances"]], "cctbx.crystal": [[23, "module-cctbx.crystal"]], "cell_equivalent_p1() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.cell_equivalent_p1"]], "change_basis() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.change_basis"]], "change_basis() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_basis"]], "change_of_basis_op_to_best_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_best_cell"]], "change_of_basis_op_to_inverse_hand() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_inverse_hand"]], "change_of_basis_op_to_minimum_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_minimum_cell"]], "change_of_basis_op_to_niggli_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_niggli_cell"]], "change_of_basis_op_to_primitive_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_primitive_setting"]], "change_of_basis_op_to_reference_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_reference_setting"]], "cluster_erosion() (in module cctbx.crystal)": [[23, "cctbx.crystal.cluster_erosion"]], "correct_special_position() (in module cctbx.crystal)": [[23, "cctbx.crystal.correct_special_position"]], "customized_copy() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.customized_copy"]], "dihedral_angle_def (class in cctbx.crystal)": [[23, "cctbx.crystal.dihedral_angle_def"]], "direct_space_asu() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.direct_space_asu"]], "distance_based_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.distance_based_clustering"]], "distances_info (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.distances_info"]], "expand_to_p1() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.expand_to_p1"]], "gridding() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.gridding"]], "have_sym (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.have_sym"]], "i_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.i_seq"]], "i_seqs() (cctbx.crystal.sym_pair method)": [[23, "cctbx.crystal.sym_pair.i_seqs"]], "incremental_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.incremental_clustering"]], "incremental_pairs() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.incremental_pairs"]], "inverse_hand() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.inverse_hand"]], "is_compatible_unit_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_compatible_unit_cell"]], "is_empty() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_empty"]], "is_identical_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_identical_symmetry"]], "is_incomplete() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_incomplete"]], "is_nonsense() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_nonsense"]], "is_patterson_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_patterson_symmetry"]], "is_similar_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_similar_symmetry"]], "j_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.j_seq"]], "join_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.join_symmetry"]], "miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.miller_set"]], "min_distance_sym_equiv() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.min_distance_sym_equiv"]], "minimum_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.minimum_cell"]], "next() (cctbx.crystal.calculate_dihedrals method)": [[23, "cctbx.crystal.calculate_dihedrals.next"]], "niggli_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.niggli_cell"]], "non_crystallographic_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.non_crystallographic_symmetry"]], "pair_asu_table (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.pair_asu_table"]], "pair_asu_table() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.pair_asu_table"]], "pair_generator() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.pair_generator"]], "patterson_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.patterson_symmetry"]], "primitive_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.primitive_setting"]], "reflection_intensity_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.reflection_intensity_symmetry"]], "rt_mx_ji (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.rt_mx_ji"]], "select_crystal_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.select_crystal_symmetry"]], "show_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.show_angles"]], "show_dihedral_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.show_dihedral_angles"]], "show_distances (class in cctbx.crystal)": [[23, "cctbx.crystal.show_distances"]], "show_summary() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.show_summary"]], "site_cluster_analysis() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_cluster_analysis"]], "site_symmetry() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry"]], "site_symmetry_table() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry_table"]], "space_group() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group"]], "space_group_info() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group_info"]], "space_group_number() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group_number"]], "special_position_settings (class in cctbx.crystal)": [[23, "cctbx.crystal.special_position_settings"]], "special_position_settings() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.special_position_settings"]], "subtract_continuous_allowed_origin_shifts() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.subtract_continuous_allowed_origin_shifts"]], "sym_equiv_sites() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.sym_equiv_sites"]], "sym_pair (class in cctbx.crystal)": [[23, "cctbx.crystal.sym_pair"]], "symmetry (class in cctbx.crystal)": [[23, "cctbx.crystal.symmetry"]], "u_star_tolerance() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.u_star_tolerance"]], "unit_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.unit_cell"]], "unit_crystal_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.unit_crystal_symmetry"]], "xray_structure() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.xray_structure"]], "latticecharacter (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter"]], "metriccriteria (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria"]], "all() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.all"]], "apply_sign_correction() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.apply_sign_correction"]], "best() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best"]], "best_bravais__() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best_bravais__"]], "cctbx.crystal.burzlaff_zimmermann_dewolff": [[24, "module-cctbx.crystal.burzlaff_zimmermann_dewolff"]], "character_tests() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.character_tests"]], "counterexamples() (in module cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.counterexamples"]], "equal() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal"]], "equal_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal_penalty"]], "penalty_scores() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.penalty_scores"]], "run() (in module cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.run"]], "show_summary() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.show_summary"]], "show_summary_labelit_format() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.show_summary_labelit_format"]], "zero() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.zero"]], "zero_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.zero_penalty"]], "cctbx.crystal.close_packing": [[25, "module-cctbx.crystal.close_packing"]], "hexagonal_sampling() (in module cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.hexagonal_sampling"]], "setup_hexagonal_sampling (class in cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.setup_hexagonal_sampling"]], "cctbx.crystal.coordination_sequences": [[26, "module-cctbx.crystal.coordination_sequences"]], "find_node() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.find_node"]], "get_kriber_coseq_file() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.get_kriber_coseq_file"]], "node (class in cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.node"]], "show_terms() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.show_terms"]], "simple_and_slow() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.simple_and_slow"]], "add_buffer() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.add_buffer"]], "as_float_asu() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.as_float_asu"]], "cctbx.crystal.direct_space_asu": [[27, "module-cctbx.crystal.direct_space_asu"]], "direct_space_asu (class in cctbx.crystal.direct_space_asu)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu"]], "minimum_covering_sphere() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.minimum_covering_sphere"]], "non_crystallographic_asu_mappings() (in module cctbx.crystal.direct_space_asu)": [[27, "cctbx.crystal.direct_space_asu.non_crystallographic_asu_mappings"]], "build_simple_two_way_bond_sets() (in module cctbx.crystal.distance_based_connectivity)": [[28, "cctbx.crystal.distance_based_connectivity.build_simple_two_way_bond_sets"]], "cctbx.crystal.distance_based_connectivity": [[28, "module-cctbx.crystal.distance_based_connectivity"]], "all_cells() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.all_cells"]], "alternative_find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell"]], "cb_op() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.cb_op"]], "cctbx.crystal.find_best_cell": [[29, "module-cctbx.crystal.find_best_cell"]], "exercise() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise"]], "exercise_alternative() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise_alternative"]], "find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.find_best_cell"]], "find_it() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.find_it"]], "order_check() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.order_check"]], "return_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_best_cell"]], "return_best_xs() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_best_xs"]], "return_change_of_basis_op_to_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_change_of_basis_op_to_best_cell"]], "symmetry() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.symmetry"]], "cb_ops_in_niggli_setting() (cctbx.crystal.reindex.reindexing_operators method)": [[30, "cctbx.crystal.reindex.reindexing_operators.cb_ops_in_niggli_setting"]], "cctbx.crystal.reindex": [[30, "module-cctbx.crystal.reindex"]], "combined_cb_ops() (cctbx.crystal.reindex.reindexing_operators method)": [[30, "cctbx.crystal.reindex.reindexing_operators.combined_cb_ops"]], "reindexing_operators (class in cctbx.crystal.reindex)": [[30, "cctbx.crystal.reindex.reindexing_operators"]], "basis_type (class in cctbx.crystal_orientation)": [[31, "cctbx.crystal_orientation.basis_type"]], "cctbx.crystal_orientation": [[31, "module-cctbx.crystal_orientation"]], "direct (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.direct"]], "reciprocal (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.reciprocal"]], "cctbx.development": [[32, "module-cctbx.development"]], "cctbx.development.cns_density_modification": [[33, "module-cctbx.development.cns_density_modification"]], "do_dirty_work() (in module cctbx.development.cns_density_modification)": [[33, "cctbx.development.cns_density_modification.do_dirty_work"]], "run() (in module cctbx.development.cns_density_modification)": [[33, "cctbx.development.cns_density_modification.run"]], "cctbx.development.debug_utils": [[34, "module-cctbx.development.debug_utils"]], "get_test_space_group_symbols() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.get_test_space_group_symbols"]], "loop_space_groups() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.loop_space_groups"]], "parse_options_loop_space_groups() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.parse_options_loop_space_groups"]], "random_origin_shift() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.random_origin_shift"]], "cctbx.development.direct_or_fft": [[35, "module-cctbx.development.direct_or_fft"]], "dummy_miller_set() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_miller_set"]], "dummy_structure() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_structure"]], "get_times() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.get_times"]], "run() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.run"]], "run_call_back() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.run_call_back"]], "cctbx.development.electron_density_sampling": [[36, "module-cctbx.development.electron_density_sampling"]], "run() (in module cctbx.development.electron_density_sampling)": [[36, "cctbx.development.electron_density_sampling.run"]], "timings() (in module cctbx.development.electron_density_sampling)": [[36, "cctbx.development.electron_density_sampling.timings"]], "mathformmx33() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormMx33"]], "mathformvec3() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormVec3"]], "mathform_adp() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathForm_adp"]], "cctbx.development.fmt_utils": [[37, "module-cctbx.development.fmt_utils"]], "dot6fdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot"]], "dot6fdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot_list"]], "dot6g_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6g_list"]], "dot6gdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot"]], "dot6gdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot_list"]], "xtal6g() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.xtal6g"]], "xtal6g_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.xtal6g_list"]], "cctbx.development.make_cns_input": [[38, "module-cctbx.development.make_cns_input"]], "coordinates() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.coordinates"]], "exercise() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.exercise"]], "parameter_nbonds (class in cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.parameter_nbonds"]], "parameter_nonb (class in cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.parameter_nonb"]], "run() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.run"]], "run_call_back() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.run_call_back"]], "script_predict_methods_comparison() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_predict_methods_comparison"]], "script_vdw_energy() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_vdw_energy"]], "script_xray_gradients() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_xray_gradients"]], "topology() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.topology"]], "tst_run_requiring_cns() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.tst_run_requiring_cns"]], "write() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.write"]], "xray_anomalous() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_anomalous"]], "xray_declare() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_declare"]], "xray_generate() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_generate"]], "xray_gradients() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_gradients"]], "xray_mapresolution() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_mapresolution"]], "xray_method() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_method"]], "xray_predict() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_predict"]], "xray_reflection() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_reflection"]], "xray_structure() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_structure"]], "xray_symmetry() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_symmetry"]], "xray_unit_cell() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_unit_cell"]], "cctbx.development.make_settings": [[39, "module-cctbx.development.make_settings"]], "run() (in module cctbx.development.make_settings)": [[39, "cctbx.development.make_settings.run"]], "build_scatterers() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.build_scatterers"]], "cctbx.development.random_structure": [[40, "module-cctbx.development.random_structure"]], "have_suitable_hetero_distance() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.have_suitable_hetero_distance"]], "loop() (cctbx.development.random_structure.wyckoff_pair_generator method)": [[40, "cctbx.development.random_structure.wyckoff_pair_generator.loop"]], "random_elements() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_elements"]], "random_modify_adp_and_adp_flags() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_adp_and_adp_flags"]], "random_modify_adp_and_adp_flags_2() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_adp_and_adp_flags_2"]], "random_modify_fdp() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_fdp"]], "random_modify_fp() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_fp"]], "random_modify_occupancy() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_occupancy"]], "random_modify_parameters() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_parameters"]], "random_modify_site() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_site"]], "random_modify_site() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_site"]], "random_modify_u_iso() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_iso"]], "random_modify_u_star() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_star"]], "random_site() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_site"]], "random_sites() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_sites"]], "wyckoff_pair_generator (class in cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.wyckoff_pair_generator"]], "xray_structure (class in cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.xray_structure"]], "fix() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.FIX"]], "hklf() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.HKLF"]], "nofix() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.NOFIX"]], "sfac_disp_unit() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.SFAC_DISP_UNIT"]], "atoms() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.atoms"]], "calculate_cell_content() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.calculate_cell_content"]], "cctbx.development.run_shelx": [[41, "module-cctbx.development.run_shelx"]], "check_anisou() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_anisou"]], "check_r1() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_r1"]], "exercise() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.exercise"]], "pre_check() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.pre_check"]], "run() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run"]], "run_call_back() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run_call_back"]], "run_shelx() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run_shelx"]], "atoms() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.atoms"]], "cctbx.development.run_shelx76": [[42, "module-cctbx.development.run_shelx76"]], "exercise() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.exercise"]], "run() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run"]], "run_call_back() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run_call_back"]], "run_shelx76() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run_shelx76"]], "sfac_unit() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.sfac_unit"]], "write_shelx76_ls() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.write_shelx76_ls"]], "cctbx.development.space_group_option_parser": [[43, "module-cctbx.development.space_group_option_parser"]], "loop_over_space_groups() (cctbx.development.space_group_option_parser.space_group_processed_options method)": [[43, "cctbx.development.space_group_option_parser.space_group_processed_options.loop_over_space_groups"]], "process() (cctbx.development.space_group_option_parser.space_group_option_parser method)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.process"]], "processed_options_type (cctbx.development.space_group_option_parser.space_group_option_parser attribute)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.processed_options_type"]], "space_group_option_parser (class in cctbx.development.space_group_option_parser)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser"]], "space_group_processed_options (class in cctbx.development.space_group_option_parser)": [[43, "cctbx.development.space_group_option_parser.space_group_processed_options"]], "space_group_sets (cctbx.development.space_group_option_parser.space_group_option_parser attribute)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.space_group_sets"]], "add() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.add"]], "cctbx.development.structure_factor_utils": [[44, "module-cctbx.development.structure_factor_utils"]], "check_correlation() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_correlation"]], "check_phase_restrictions() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_phase_restrictions"]], "check_regression() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_regression"]], "collector (class in cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.collector"]], "report() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.report"]], "cctbx.dmtbx": [[45, "module-cctbx.dmtbx"]], "triplet_generator() (in module cctbx.dmtbx)": [[45, "cctbx.dmtbx.triplet_generator"]], "cctbx.eltbx": [[46, "module-cctbx.eltbx"]], "atomic_number() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number"]], "atomic_number_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number_list"]], "cctbx.eltbx.attenuation_coefficient": [[47, "module-cctbx.eltbx.attenuation_coefficient"]], "chemlex() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.chemlex"]], "get_table() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.get_table"]], "nist_elements (class in cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements"]], "symbol() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.symbol"]], "symbol_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.symbol_list"]], "cctbx.eltbx.chemical_elements": [[48, "module-cctbx.eltbx.chemical_elements"]], "cctbx.eltbx.covalent_radii": [[49, "module-cctbx.eltbx.covalent_radii"]], "cctbx.eltbx.development": [[50, "module-cctbx.eltbx.development"]], "cctbx.eltbx.development.combine_fits": [[51, "module-cctbx.eltbx.development.combine_fits"]], "main() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.main"]], "pick_nicest_fit() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.pick_nicest_fit"]], "reset_max_error() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.reset_max_error"]], "cctbx.eltbx.development.create_n_gaussian_raw_cpp": [[52, "module-cctbx.eltbx.development.create_n_gaussian_raw_cpp"]], "identifier() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.identifier"]], "run() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.run"]], "write_fit_group() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_fit_group"]], "write_header() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_header"]], "write_labels() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_labels"]], "write_module_info() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_module_info"]], "write_table() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_table"]], "write_tail() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_tail"]], "cctbx.eltbx.development.e_scattering_plots": [[53, "module-cctbx.eltbx.development.e_scattering_plots"]], "run() (in module cctbx.eltbx.development.e_scattering_plots)": [[53, "cctbx.eltbx.development.e_scattering_plots.run"]], "cctbx.eltbx.development.format_gaussian_fits": [[54, "module-cctbx.eltbx.development.format_gaussian_fits"]], "cross_check() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.cross_check"]], "expected_labels() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.expected_labels"]], "labeled_fit (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.labeled_fit"]], "main() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.main"]], "read_pickled_fits (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.read_pickled_fits"]], "run() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.run"]], "cctbx.eltbx.development.hydrogen_plots": [[55, "module-cctbx.eltbx.development.hydrogen_plots"]], "fit_input (class in cctbx.eltbx.development.hydrogen_plots)": [[55, "cctbx.eltbx.development.hydrogen_plots.fit_input"]], "run() (in module cctbx.eltbx.development.hydrogen_plots)": [[55, "cctbx.eltbx.development.hydrogen_plots.run"]], "cctbx.eltbx.development.itvc_approx": [[56, "module-cctbx.eltbx.development.itvc_approx"]], "main() (in module cctbx.eltbx.development.itvc_approx)": [[56, "cctbx.eltbx.development.itvc_approx.main"]], "run() (in module cctbx.eltbx.development.itvc_approx)": [[56, "cctbx.eltbx.development.itvc_approx.run"]], "cctbx.eltbx.development.itvc_cross_validation": [[57, "module-cctbx.eltbx.development.itvc_cross_validation"]], "main() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.main"]], "run() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.run"]], "show_differences_if_any() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.show_differences_if_any"]], "cctbx.eltbx.development.itvc_fits": [[58, "module-cctbx.eltbx.development.itvc_fits"]], "main() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.main"]], "run() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.run"]], "run_and_time() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.run_and_time"]], "cctbx.eltbx.development.itvc_section61_io": [[60, "module-cctbx.eltbx.development.itvc_section61_io"]], "enter_block() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_block"]], "enter_entry() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_entry"]], "read_table6111() (in module cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.read_table6111"]], "table6111 (class in cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111"]], "table6111_entry (class in cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111_entry"]], "cctbx.eltbx.development.kissel_fits": [[61, "module-cctbx.eltbx.development.kissel_fits"]], "main() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.main"]], "run() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.run"]], "run_and_time() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.run_and_time"]], "cctbx.eltbx.development.kissel_io": [[62, "module-cctbx.eltbx.development.kissel_io"]], "itvc_sampling_selection() (cctbx.eltbx.development.kissel_io.table method)": [[62, "cctbx.eltbx.development.kissel_io.table.itvc_sampling_selection"]], "main() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.main"]], "read_table() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.read_table"]], "table (class in cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.table"]], "cctbx.eltbx.development.rez_rez_grant": [[63, "module-cctbx.eltbx.development.rez_rez_grant"]], "run() (in module cctbx.eltbx.development.rez_rez_grant)": [[63, "cctbx.eltbx.development.rez_rez_grant.run"]], "build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.build_edge_list"]], "cctbx.eltbx.distance_based_connectivity": [[64, "module-cctbx.eltbx.distance_based_connectivity"]], "tst_build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.tst_build_edge_list"]], "cctbx.eltbx.e_scattering": [[65, "module-cctbx.eltbx.e_scattering"]], "ito_vol_c_2011_table_4_3_2_2_elements() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_elements"]], "ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian"]], "cctbx.eltbx.formula": [[66, "module-cctbx.eltbx.formula"]], "formula (class in cctbx.eltbx.formula)": [[66, "cctbx.eltbx.formula.formula"]], "sorted_as_c_h_then_by_increasing_atomic_number() (cctbx.eltbx.formula.formula method)": [[66, "cctbx.eltbx.formula.formula.sorted_as_c_h_then_by_increasing_atomic_number"]], "cctbx.eltbx.fp_fdp": [[67, "module-cctbx.eltbx.fp_fdp"]], "cctbx.eltbx.gaussian_fit": [[68, "module-cctbx.eltbx.gaussian_fit"]], "decremental_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.decremental_fits"]], "fit_parameters (class in 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"cctbx.examples.structure_factor_derivatives_3.structure_factor.d_target_d_params"]], "d_target_d_params() (cctbx.examples.structure_factor_derivatives_3.structure_factors method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factors.d_target_d_params"]], "df_d_params() (cctbx.examples.structure_factor_derivatives_3.structure_factor method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factor.df_d_params"]], "f() (cctbx.examples.structure_factor_derivatives_3.structure_factor method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factor.f"]], "f() (cctbx.examples.structure_factor_derivatives_3.structure_factors method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factors.f"]], "fs() (cctbx.examples.structure_factor_derivatives_3.structure_factors method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factors.fs"]], "gradients (class in cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.gradients"]], "pack_gradients() (in module cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.pack_gradients"]], "scatterer_as_list() (in module cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.scatterer_as_list"]], "scatterer_from_list() (in module cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.scatterer_from_list"]], "structure_factor (class in cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factor"]], "structure_factors (class in cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factors"]], "cctbx.examples.structure_factor_derivatives_4": [[122, "module-cctbx.examples.structure_factor_derivatives_4"]], "d2_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2_target_d_params"]], "d2_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params"]], "d2_target_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2_target_d_params_diag"]], "d2_target_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params_diag"]], "d2_target_d_params_diag_cpp() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params_diag_cpp"]], "d2f_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2f_d_params"]], "d2f_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2f_d_params_diag"]], "d_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d_target_d_params"]], "d_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d_target_d_params"]], "df_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.df_d_params"]], "f() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.f"]], "f() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.f"]], "fs() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.fs"]], "structure_factor (class in cctbx.examples.structure_factor_derivatives_4)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor"]], "structure_factors (class in cctbx.examples.structure_factor_derivatives_4)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors"]], "cctbx.examples.sub_group_graph": [[123, "module-cctbx.examples.sub_group_graph"]], "run() (in module cctbx.examples.sub_group_graph)": [[123, "cctbx.examples.sub_group_graph.run"]], "cctbx.examples.symops_530": [[124, "module-cctbx.examples.symops_530"]], "run() (in module cctbx.examples.symops_530)": [[124, "cctbx.examples.symops_530.run"]], "cctbx.examples.trigonal_r_vs_tetragonal_i": [[125, "module-cctbx.examples.trigonal_r_vs_tetragonal_i"]], "run() (in module cctbx.examples.trigonal_r_vs_tetragonal_i)": [[125, "cctbx.examples.trigonal_r_vs_tetragonal_i.run"]], "cctbx.examples.unit_cell_minimizers": [[126, "module-cctbx.examples.unit_cell_minimizers"]], "functional() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.functional"]], "gradients() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.gradients"]], "gradients() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.gradients"]], "hessian() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.hessian"]], "hessian() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.hessian"]], "refinery (class in cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.refinery"]], "residual() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.residual"]], "run() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.run"]], "run_lbfgs_raw() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.run_lbfgs_raw"]], "run_lbfgsb() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.run_lbfgsb"]], "show_fit() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.show_fit"]], "unit_cell() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.unit_cell"]], "callback_after_step() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.callback_after_step"]], "cctbx.examples.unit_cell_refinement": [[127, "module-cctbx.examples.unit_cell_refinement"]], "compute_functional_and_gradients() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.compute_functional_and_gradients"]], "gradients() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.gradients"]], "refinery (class in cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.refinery"]], "residual() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.residual"]], "run() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.run"]], "show_fit() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.show_fit"]], "unit_cell() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.unit_cell"]], "calculate_mean_intensities() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.calculate_mean_intensities"]], "cctbx.french_wilson": [[129, "module-cctbx.french_wilson"]], "f_w_binning() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.f_w_binning"]], "french_wilson_scale() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.french_wilson_scale"]], "fw_acentric() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.fw_acentric"]], "fw_centric() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.fw_centric"]], "get_bin_centers() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_bin_centers"]], "get_mean_intensity() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_mean_intensity"]], "interpolate() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.interpolate"]], "show_rejected_summary() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.show_rejected_summary"]], "cctbx.geometry": [[130, "module-cctbx.geometry"]], "add_if_not_duplicated() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.chirality_proxy_registry method)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.parallelity_proxy_registry method)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.planarity_proxy_registry method)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry.add_if_not_duplicated"]], "angle_delta_deg() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_delta_deg"]], "angle_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_proxy_registry"]], "append_custom_proxy() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.append_custom_proxy"]], "bond_simple_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry"]], "cctbx.geometry_restraints": [[131, "module-cctbx.geometry_restraints"]], "chirality_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry"]], "dihedral_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry"]], "discard_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.discard_table"]], "initialize_table() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.initialize_table"]], "initialize_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.initialize_table"]], "is_any_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_any_proxy_set"]], "is_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_proxy_set"]], "lookup_i_proxy() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.lookup_i_proxy"]], "lookup_i_proxy() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.lookup_i_proxy"]], "pair_proxies (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.pair_proxies"]], "parallelity_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry"]], "planarity_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry"]], "process() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.process"]], "process() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.process"]], "process() (cctbx.geometry_restraints.chirality_proxy_registry method)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry.process"]], "process() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.process"]], "process() (cctbx.geometry_restraints.parallelity_proxy_registry method)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry.process"]], "process() (cctbx.geometry_restraints.planarity_proxy_registry method)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry.process"]], "proxy_registry_base (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.proxy_registry_base"]], "proxy_registry_process_result (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.proxy_registry_process_result"]], "resid_to_pymol() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.resid_to_pymol"]], "sigma_as_weight() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.sigma_as_weight"]], "weight_as_sigma() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.weight_as_sigma"]], "angle_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations"]], "angle_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_weighted"]], "angle_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_z"]], "bond_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations"]], "bond_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_weighted"]], "bond_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_z"]], "cctbx.geometry_restraints.energies": [[132, "module-cctbx.geometry_restraints.energies"]], "chirality_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.chirality_deviations"]], "dihedral_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.dihedral_deviations"]], "energies (class in cctbx.geometry_restraints.energies)": [[132, "cctbx.geometry_restraints.energies.energies"]], "get_angle_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_angle_outliers"]], "get_bond_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_bond_outliers"]], "get_chirality_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_chirality_outliers"]], "get_dihedral_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_dihedral_outliers"]], "get_filtered_n_angle_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_angle_proxies"]], "get_filtered_n_bond_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_bond_proxies"]], "get_filtered_n_dihedral_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_dihedral_proxies"]], "get_filtered_n_planarity_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_planarity_proxies"]], "nonbonded_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.nonbonded_deviations"]], "nonbonded_distances() (cctbx.geometry_restraints.energies.energies 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"apply_shifts() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.apply_shifts"]], "cctbx.geometry_restraints.lbfgs": [[134, "module-cctbx.geometry_restraints.lbfgs"]], "compute_functional_and_gradients() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.compute_functional_and_gradients"]], "compute_target() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.compute_target"]], "empty (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.empty"]], "lbfgs (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs"]], "add_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_angles_in_place"]], "add_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_chi_torsion_restraints_in_place"]], "add_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_dihedrals_in_place"]], "add_new_bond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_bond_restraints_in_place"]], "add_new_hbond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_hbond_restraints_in_place"]], "add_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_parallelities_in_place"]], "add_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_planarities_in_place"]], "add_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_reference_coordinate_restraints_in_place"]], "adopt_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_den_manager"]], "adopt_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_coordinate_restraints_in_place"]], "adopt_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_dihedral_manager"]], "append_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.append_reference_coordinate_restraints_in_place"]], "cctbx.geometry_restraints.manager": [[135, "module-cctbx.geometry_restraints.manager"]], "construct_non_crystallographic_conserving_bonds_and_angles() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.construct_non_crystallographic_conserving_bonds_and_angles"]], "construct_tardy_tree() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.construct_tardy_tree"]], "create_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.create_den_manager"]], "discard_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.discard_symmetry"]], "energies_sites() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.energies_sites"]], "format_distances_for_error_message() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.format_distances_for_error_message"]], "get_all_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_angle_proxies"]], "get_all_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_bond_proxies"]], "get_angle_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_angle_proxies_without_user_supplied"]], "get_bond_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_bond_proxies_without_user_supplied"]], "get_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_c_beta_torsion_proxies"]], "get_chi_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_chi_torsion_proxies"]], "get_cif_link_entries() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_cif_link_entries"]], "get_covalent_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_angle_proxies"]], "get_covalent_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_bond_proxies"]], "get_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies"]], "get_dihedral_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies_without_user_supplied"]], "get_hbond_proxies_iseqs() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_hbond_proxies_iseqs"]], "get_n_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_angle_proxies"]], "get_n_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_bond_proxies"]], "get_n_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_c_beta_torsion_proxies"]], "get_n_chi_torsion_proixes() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_chi_torsion_proixes"]], "get_n_den_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_den_proxies"]], "get_n_hangle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hangle_proxies"]], "get_n_hbond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hbond_proxies"]], "get_n_parallelity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_parallelity_bp_proxies"]], "get_n_planarity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_bp_proxies"]], "get_n_planarity_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_proxies"]], "get_n_ramachandran_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_ramachandran_proxies"]], "get_n_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_coordinate_proxies"]], "get_n_reference_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_dihedral_proxies"]], "get_n_stacking_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_stacking_proxies"]], "get_parallelity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_parallelity_proxies_without_user_supplied"]], "get_planarity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_planarity_proxies_without_user_supplied"]], "get_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_reference_coordinate_proxies"]], "get_struct_conn_mmcif() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_struct_conn_mmcif"]], "get_user_supplied_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_user_supplied_restraints"]], "harmonic_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.harmonic_restraints"]], "is_bonded_atoms() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.is_bonded_atoms"]], "manager (class in cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.manager"]], "new_included_bonded_atoms() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.new_included_bonded_atoms"]], "new_including_isolated_sites() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.new_including_isolated_sites"]], "nonbonded_model_distances() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.nonbonded_model_distances"]], "pair_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.pair_proxies"]], "reduce_for_tardy() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reduce_for_tardy"]], "remove_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_angles_in_place"]], "remove_c_beta_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_c_beta_torsion_restraints_in_place"]], "remove_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chi_torsion_restraints_in_place"]], "remove_chiralities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chiralities_in_place"]], "remove_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_dihedrals_in_place"]], "remove_ncs_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ncs_dihedrals_in_place"]], "remove_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_parallelities_in_place"]], "remove_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_planarities_in_place"]], "remove_ramachandran_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ramachandran_in_place"]], "remove_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_coordinate_restraints_in_place"]], "remove_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedral_manager"]], "remove_reference_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedrals_in_place"]], "remove_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_secondary_structure_restraints"]], "remove_user_supplied_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_user_supplied_restraints_in_place"]], "replace_site_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.replace_site_symmetry"]], "reset_internals() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reset_internals"]], "rigid_clusters_due_to_dihedrals_and_planes() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.rigid_clusters_due_to_dihedrals_and_planes"]], "select() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.select"]], "set_external_energy_function() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_external_energy_function"]], "set_ramachandran_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_ramachandran_restraints"]], "set_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_secondary_structure_restraints"]], "shift_sites_cart() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.shift_sites_cart"]], "show_sorted() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.show_sorted"]], "simple_edge_list() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.simple_edge_list"]], "sites_cart_used_for_pair_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.sites_cart_used_for_pair_proxies"]], "sync_reference_dihedral_with_ncs() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.sync_reference_dihedral_with_ncs"]], "ta_harmonic_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.ta_harmonic_restraints"]], "update_atom_nonbonded_type() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_atom_nonbonded_type"]], "update_dihedral_ncs_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_dihedral_ncs_restraints"]], "update_plain_pair_sym_table() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_plain_pair_sym_table"]], "update_ramachandran_restraints_phi_psi_targets() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_ramachandran_restraints_phi_psi_targets"]], "write_geo_file() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.write_geo_file"]], "cctbx.macro_mol": [[137, "module-cctbx.macro_mol"]], "adjust_cosine() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.adjust_cosine"]], "amore_alpha_beta_gamma (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma"]], "amore_alpha_beta_gamma_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_as_matrix"]], "amore_alpha_beta_gamma_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_from_matrix"]], "amore_alpha_beta_gamma_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_normalize"]], "amore_kappa_l_m_n (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n"]], "amore_kappa_l_m_n_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_as_matrix"]], "amore_kappa_l_m_n_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_from_matrix"]], "amore_kappa_l_m_n_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_normalize"]], "ccp4_alpha_beta_gamma_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs"]], "ccp4_alpha_beta_gamma_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc"]], "ccp4_phi_omega_kappa_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs"]], "ccp4_phi_omega_kappa_fcalc_fobs_params_to_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs_params_to_matrix"]], "ccp4_phi_omega_kappa_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc"]], "ccp4_phi_omega_kappa_fobs_fcalc_matrix_to_params() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc_matrix_to_params"]], "cctbx.macro_mol.rotation_parameters": [[138, "module-cctbx.macro_mol.rotation_parameters"]], "cns_axis_x_axis_y_axis_z_axis_kappa (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa"]], "cns_psi_phi_kappa (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa"]], "cns_theta1_theta2_theta3 (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3"]], "cns_theta_123_as_p2m() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_123_as_p2m"]], "cns_theta_123_from_p2m() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_123_from_p2m"]], "cns_theta_plus_theta2_theta_minus (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus"]], "converter_base (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.converter_base"]], "degree_as_radians() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.degree_as_radians"]], "degree_from_radians() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.degree_from_radians"]], "det() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.det"]], "fmod_positive() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.fmod_positive"]], "generic_polar_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.generic_polar_normalize"]], "get_converter_by_docstring() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converter_by_docstring"]], "get_converters() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converters"]], "index1d() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.index1d"]], "matrix33 (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.matrix_to_params"]], "normalize() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.normalize"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.params_to_matrix"]], "preprocess_angles() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.preprocess_angles"]], "safe_atan2() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.safe_atan2"]], "trace() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.trace"]], "all() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all"]], "all_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_site_cluster_analysis"]], "all_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_with_effective_resolution"]], "append_fixed_site() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.append_fixed_site"]], "as_cobjectzyx() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.as_CObjectZYX"]], "assert_equal() (cctbx.maptbx.positivity_constrained_density_modification method)": [[139, "cctbx.maptbx.positivity_constrained_density_modification.assert_equal"]], "assert_same_gridding() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.assert_same_gridding"]], "atom_curves (class in cctbx.maptbx)": [[139, "cctbx.maptbx.atom_curves"]], "atom_radius_as_central_peak_width() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.atom_radius_as_central_peak_width"]], "bcr_approx() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.bcr_approx"]], "boxes (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes"]], "boxes_by_dimension (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes_by_dimension"]], "cc_peak() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.cc_peak"]], "cctbx.maptbx": [[139, "module-cctbx.maptbx"]], "ccv() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.ccv"]], "change_space_group() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.change_space_group"]], "cluster_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.cluster_height_fraction"]], "cluster_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.cluster_height_fraction"]], "cluster_site_info (class in cctbx.maptbx)": [[139, "cctbx.maptbx.cluster_site_info"]], "crystal_gridding (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding"]], "crystal_gridding_tags (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding_tags"]], "crystal_symmetry() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.crystal_symmetry"]], "d99 (class in cctbx.maptbx)": [[139, "cctbx.maptbx.d99"]], "d_min() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.d_min"]], "d_min_corner() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.d_min_corner"]], "d_min_from_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.d_min_from_map"]], "discard_last() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.discard_last"]], "effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.effective_resolution"]], "effective_resolution() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.effective_resolution"]], "exact_density() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density"]], "exact_density_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density_at_r"]], "exact_gradient_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_gradient_at_r"]], "fixed_site_indices() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.fixed_site_indices"]], "form_factor() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.form_factor"]], "general_positions_only() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.general_positions_only"]], "general_positions_only() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.general_positions_only"]], "get_diff_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_diff_score_towards_periodic"]], "get_edge_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_edge_score_towards_periodic"]], "get_relative_cc() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_relative_cc"]], "get_resolution_where_significant_data_present() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_resolution_where_significant_data_present"]], "get_xray_structure() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.get_xray_structure"]], "heights() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.heights"]], "image() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image"]], "image_from_3d() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_3d"]], "image_from_miller_indices() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_miller_indices"]], "integrand() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.integrand"]], "interpolate() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.interpolate"]], "is_bounded_by_constant() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_bounded_by_constant"]], "is_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_periodic"]], "loc_res() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.loc_res"]], "local_scale (class in cctbx.maptbx)": [[139, "cctbx.maptbx.local_scale"]], "mandatory_factors() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.mandatory_factors"]], "map_accumulator() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_accumulator"]], "map_coefficients_to_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_coefficients_to_map"]], "map_peak_3d_as_2d() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_peak_3d_as_2d"]], "map_to_map_coefficients() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_to_map_coefficients"]], "map_values_along_line_connecting_two_points() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_values_along_line_connecting_two_points"]], "mask() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.mask"]], "max_clusters() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_clusters"]], "max_clusters() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_clusters"]], "max_grid_height() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_grid_height"]], "max_peaks() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_peaks"]], "max_prime() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.max_prime"]], "min_cross_distance() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.min_cross_distance"]], "min_cross_distance() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cross_distance"]], "min_cubicle_edge() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cubicle_edge"]], "min_distance_sym_equiv() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_distance_sym_equiv"]], "n_grid_points() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.n_grid_points"]], "n_real() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.n_real"]], "next() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next"]], "next_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next_site_cluster_analysis"]], "next_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next_with_effective_resolution"]], "one_gaussian_approximation() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.one_gaussian_approximation"]], "one_gaussian_exact() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.one_gaussian_exact"]], "peak_cluster_analysis (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_cluster_analysis"]], "peak_cutoff() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.peak_cutoff"]], "peak_list (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_list"]], "peak_list() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.peak_list"]], "peak_list_indices() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.peak_list_indices"]], "peak_search() (cctbx.maptbx.crystal_gridding_tags method)": [[139, "cctbx.maptbx.crystal_gridding_tags.peak_search"]], "peak_search_level() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.peak_search_level"]], "peak_search_parameters (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_search_parameters"]], "peak_volume_estimate() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.peak_volume_estimate"]], "positivity_constrained_density_modification (class in cctbx.maptbx)": [[139, "cctbx.maptbx.positivity_constrained_density_modification"]], "principal_axes_of_inertia() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.principal_axes_of_inertia"]], "region_density_correlation() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.region_density_correlation"]], "relative_sd_on_edges() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.relative_sd_on_edges"]], "resolution_factor() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.resolution_factor"]], "sharpen2() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sharpen2"]], "shift_origin_if_needed() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.shift_origin_if_needed"]], "show() (cctbx.maptbx.d99 method)": [[139, "cctbx.maptbx.d99.show"]], "show() (cctbx.maptbx.spherical_variance_around_point method)": [[139, "cctbx.maptbx.spherical_variance_around_point.show"]], "significant_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.significant_height_fraction"]], "significant_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.significant_height_fraction"]], "site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.site_cluster_analysis"]], "sites() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.sites"]], "smooth_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.smooth_map"]], "space_group() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.space_group"]], "space_group_info() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.space_group_info"]], "special_position_settings() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.special_position_settings"]], "spherical_variance_around_point (class in cctbx.maptbx)": [[139, "cctbx.maptbx.spherical_variance_around_point"]], "sphericity_by_heuristics() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sphericity_by_heuristics"]], "statistics (class in cctbx.maptbx)": [[139, "cctbx.maptbx.statistics"]], "symmetry_flags() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.symmetry_flags"]], "tags() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.tags"]], "tags() (cctbx.maptbx.crystal_gridding_tags method)": [[139, "cctbx.maptbx.crystal_gridding_tags.tags"]], "truncate() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.truncate"]], "unit_cell() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.unit_cell"]], "value_at_closest_grid_point() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.value_at_closest_grid_point"]], "hn() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hn"]], "hw() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hw"]], "q_x() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Q_X"]], "cctbx.maptbx.mem": [[140, "module-cctbx.maptbx.mem"]], "is_converged() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.is_converged"]], "iterations() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.iterations"]], "map_coefficients() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.map_coefficients"]], "normalize_start_map() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.normalize_start_map"]], "r_factor() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.r_factor"]], "run (class in cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.run"]], "scale() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.scale"]], "show() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.show"]], "show_map_stat() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.show_map_stat"]], "update_metrics() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.update_metrics"]], "write_mtz_file() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.write_mtz_file"]], "cctbx.maptbx.real_space_refinement_simple": [[142, "module-cctbx.maptbx.real_space_refinement_simple"]], "compute_functional_and_gradients() (cctbx.maptbx.real_space_refinement_simple.lbfgs method)": [[142, "cctbx.maptbx.real_space_refinement_simple.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization method)": [[142, "cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization.compute_functional_and_gradients"]], "lbfgs (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.lbfgs"]], "local_standard_deviations_gradients() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_gradients"]], "local_standard_deviations_target() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target"]], "local_standard_deviations_target_per_site() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target_per_site"]], "magnification_anisotropic_minimization (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization"]], "cctbx.masks": [[144, "module-cctbx.masks"]], "show() (cctbx.masks.vdw_radii method)": [[144, "cctbx.masks.vdw_radii.show"]], "vdw_radii (class in cctbx.masks)": [[144, "cctbx.masks.vdw_radii"]], "vdw_radii_from_xray_structure() (in module cctbx.masks)": [[144, "cctbx.masks.vdw_radii_from_xray_structure"]], "basis_of_mirror_plane_with_normal() (in module cctbx.math_module)": [[145, "cctbx.math_module.basis_of_mirror_plane_with_normal"]], "cctbx.math_module": [[145, "module-cctbx.math_module"]], "cctbx.merging": [[146, "module-cctbx.merging"]], "algorithm2 (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.algorithm2"]], "cctbx.merging.brehm_diederichs": [[147, "module-cctbx.merging.brehm_diederichs"]], "compute_functional_and_gradients() (cctbx.merging.brehm_diederichs.minimize method)": [[147, "cctbx.merging.brehm_diederichs.minimize.compute_functional_and_gradients"]], "compute_functional_and_gradients() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.compute_functional_and_gradients"]], "curvatures() (cctbx.merging.brehm_diederichs.minimize method)": [[147, "cctbx.merging.brehm_diederichs.minimize.curvatures"]], "functional_only() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.functional_only"]], "generate_comparison_selections() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_comparison_selections"]], "generate_reindex_sets() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_reindex_sets"]], "generate_twin_operators() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_twin_operators"]], "minimize (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize"]], "minimize_divide (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide"]], "mp_reassemble() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.mp_reassemble"]], "one_lattice_slice() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.one_lattice_slice"]], "plus_minus() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.plus_minus"]], "reassemble() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.reassemble"]], "report() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.report"]], "run() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.run"]], "run_core_algorithm() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.run_core_algorithm"]], "run_multiprocess() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.run_multiprocess"]], "test_reassembly() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.test_reassembly"]], "adopt_set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.adopt_set"]], "all_selection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.all_selection"]], "amplitude_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_normalisations"]], "amplitude_normalisations() (cctbx.miller.set method)": [[148, "cctbx.miller.set.amplitude_normalisations"]], "amplitude_quasi_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_quasi_normalisations"]], "amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitudes"]], "analyze_intensity_statistics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.analyze_intensity_statistics"]], "anomalous_completeness() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_completeness"]], "anomalous_differences() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_differences"]], "anomalous_flag() (cctbx.miller.set method)": [[148, "cctbx.miller.set.anomalous_flag"]], "anomalous_probability_plot() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_probability_plot"]], "anomalous_signal() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_signal"]], "apply_change_of_basis() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_change_of_basis"]], "apply_debye_waller_factors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_debye_waller_factors"]], "apply_scaling() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_scaling"]], "apply_shelxl_extinction_correction() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_shelxl_extinction_correction"]], "arg() (cctbx.miller.array method)": [[148, "cctbx.miller.array.arg"]], "array (class in cctbx.miller)": [[148, "cctbx.miller.array"]], "array() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.array"]], "array() (cctbx.miller.set method)": [[148, "cctbx.miller.set.array"]], "array_info (class in cctbx.miller)": [[148, "cctbx.miller.array_info"]], "as_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_amplitude_array"]], "as_anomalous_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_anomalous_array"]], "as_anomalous_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.as_anomalous_set"]], "as_cif_block() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_cif_block"]], "as_cif_simple() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_cif_simple"]], "as_double() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_double"]], "as_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_intensity_array"]], "as_map_manager() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_map_manager"]], "as_mtz_dataset() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_mtz_dataset"]], "as_non_anomalous_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_non_anomalous_array"]], "as_non_anomalous_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.as_non_anomalous_set"]], "as_phases_phs() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_phases_phs"]], "as_xray_observations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_xray_observations"]], "at_first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.at_first_index"]], "auto_anomalous() (cctbx.miller.set method)": [[148, "cctbx.miller.set.auto_anomalous"]], "average_bijvoet_mates() (cctbx.miller.array method)": [[148, "cctbx.miller.array.average_bijvoet_mates"]], "average_neighbors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.average_neighbors"]], "bijvoet_ratios() (cctbx.miller.array method)": [[148, "cctbx.miller.array.bijvoet_ratios"]], "binner (class in cctbx.miller)": [[148, "cctbx.miller.binner"]], "binner() (cctbx.miller.set method)": [[148, "cctbx.miller.set.binner"]], "build_set() (in module cctbx.miller)": [[148, "cctbx.miller.build_set"]], "cc_anom() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_anom"]], "cc_one_half() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_one_half"]], "cc_one_half_sigma_tau() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_one_half_sigma_tau"]], "cctbx.miller": [[148, "module-cctbx.miller"]], "centric_flags() (cctbx.miller.set method)": [[148, "cctbx.miller.set.centric_flags"]], "change_basis() (cctbx.miller.array method)": [[148, "cctbx.miller.array.change_basis"]], "change_basis() (cctbx.miller.set method)": [[148, "cctbx.miller.set.change_basis"]], "change_symmetry() (cctbx.miller.array method)": [[148, "cctbx.miller.array.change_symmetry"]], "clear_binner() (cctbx.miller.set method)": [[148, "cctbx.miller.set.clear_binner"]], "combine() (cctbx.miller.array method)": [[148, "cctbx.miller.array.combine"]], "common_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.common_set"]], "common_sets() (cctbx.miller.set method)": [[148, "cctbx.miller.set.common_sets"]], "complete_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.complete_array"]], "complete_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.complete_set"]], "complete_with() (cctbx.miller.array method)": [[148, "cctbx.miller.array.complete_with"]], "complete_with_bin_average() (cctbx.miller.array method)": [[148, "cctbx.miller.array.complete_with_bin_average"]], "completeness() (cctbx.miller.set method)": [[148, "cctbx.miller.set.completeness"]], "concatenate() (cctbx.miller.array method)": [[148, "cctbx.miller.array.concatenate"]], "concatenate() (cctbx.miller.set method)": [[148, "cctbx.miller.set.concatenate"]], "conjugate() (cctbx.miller.array method)": [[148, "cctbx.miller.array.conjugate"]], "convert_to_non_anomalous_if_ratio_pairs_lone_less_than() (cctbx.miller.array method)": [[148, "cctbx.miller.array.convert_to_non_anomalous_if_ratio_pairs_lone_less_than"]], "copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.copy"]], "copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.copy"]], "correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.correlation"]], "count_and_fraction_in_bins() (cctbx.miller.array method)": [[148, "cctbx.miller.array.count_and_fraction_in_bins"]], "crystal_gridding() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_gridding"]], "crystal_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_symmetry"]], "crystal_symmetry_is_compatible_with_symmetry_from_file (class in cctbx.miller)": [[148, "cctbx.miller.crystal_symmetry_is_compatible_with_symmetry_from_file"]], "crystal_symmetry_is_compatible_with_symmetry_from_file() (cctbx.miller.array method)": [[148, "cctbx.miller.array.crystal_symmetry_is_compatible_with_symmetry_from_file"]], "customized_copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.customized_copy"]], "customized_copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.customized_copy"]], "d_max_min() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_max_min"]], "d_min() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_min"]], "d_min_along_a_b_c_star() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_min_along_a_b_c_star"]], "d_min_from_fsc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.d_min_from_fsc"]], "d_spacings() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_spacings"]], "d_star_cubed() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_star_cubed"]], "d_star_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_star_sq"]], "data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.data"]], "data_at_first_index() (cctbx.miller.array method)": [[148, "cctbx.miller.array.data_at_first_index"]], "debye_waller_factors() (cctbx.miller.set method)": [[148, "cctbx.miller.set.debye_waller_factors"]], "deep_copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.deep_copy"]], "deep_copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.deep_copy"]], "delete_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.delete_index"]], "delete_indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.delete_indices"]], "detwin_data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.detwin_data"]], "direct_summation_at_point() (cctbx.miller.array method)": [[148, "cctbx.miller.array.direct_summation_at_point"]], "disagreeable_reflections() (cctbx.miller.array method)": [[148, "cctbx.miller.array.disagreeable_reflections"]], "discard_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.discard_sigmas"]], "double_step_filtration() (cctbx.miller.array method)": [[148, "cctbx.miller.array.double_step_filtration"]], "eliminate_sys_absent() (cctbx.miller.array method)": [[148, "cctbx.miller.array.eliminate_sys_absent"]], "ellipsoidal_resolutions_and_indices_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_resolutions_and_indices_by_sigma"]], "ellipsoidal_truncation_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_truncation_by_sigma"]], "enforce_positive_amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_amplitudes"]], "enforce_positive_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_sigmas"]], "epsilons() (cctbx.miller.set method)": [[148, "cctbx.miller.set.epsilons"]], "expand_to_p1() (cctbx.miller.array method)": [[148, "cctbx.miller.array.expand_to_p1"]], "expand_to_p1() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1"]], "expand_to_p1_iselection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1_iselection"]], "export_as_cns_hkl() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_cns_hkl"]], "export_as_scalepack_unmerged() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_scalepack_unmerged"]], "export_as_shelx_hklf() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_shelx_hklf"]], "f_as_f_sq() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_as_f_sq"]], "f_obs_f_calc_fan_outlier_selection() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_obs_f_calc_fan_outlier_selection"]], "f_obs_minus_f_calc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_obs_minus_f_calc"]], "f_obs_minus_xray_structure_f_calc() (cctbx.miller.set method)": [[148, "cctbx.miller.set.f_obs_minus_xray_structure_f_calc"]], "f_sq_as_f() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_sq_as_f"]], "fft_map (class in cctbx.miller)": [[148, "cctbx.miller.fft_map"]], "fft_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fft_map"]], "first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.first_index"]], "french_wilson() (cctbx.miller.array method)": [[148, "cctbx.miller.array.french_wilson"]], "from_cif() (cctbx.miller.array class method)": [[148, "cctbx.miller.array.from_cif"]], "fsc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fsc"]], "g_function() (cctbx.miller.array method)": [[148, "cctbx.miller.array.g_function"]], "generate_bijvoet_mates() (cctbx.miller.array method)": [[148, "cctbx.miller.array.generate_bijvoet_mates"]], "generate_bivoet_mates() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_bivoet_mates"]], "generate_r_free_flags() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags"]], "generate_r_free_flags_basic() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_basic"]], "generate_r_free_flags_on_lattice_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_on_lattice_symmetry"]], "half_dataset_anomalous_correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.half_dataset_anomalous_correlation"]], "has_twinning() (cctbx.miller.array method)": [[148, "cctbx.miller.array.has_twinning"]], "hemisphere_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemisphere_acentrics"]], "hemispheres_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemispheres_acentrics"]], "hoppe_gassmann_modification() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hoppe_gassmann_modification"]], "i_over_sig_i() (cctbx.miller.array method)": [[148, "cctbx.miller.array.i_over_sig_i"]], "index_span() (cctbx.miller.set method)": [[148, "cctbx.miller.set.index_span"]], "indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.indices"]], "info() (cctbx.miller.array method)": [[148, "cctbx.miller.array.info"]], "intensities() (cctbx.miller.array method)": [[148, "cctbx.miller.array.intensities"]], "intensity_quasi_normalisations() (cctbx.miller.array method)": [[148, 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(cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_amplitude_array"]], "is_xray_data_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_data_array"]], "is_xray_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_intensity_array"]], "is_xray_reconstructed_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_reconstructed_amplitude_array"]], "local_overlap_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_overlap_map"]], "local_standard_deviation_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_standard_deviation_map"]], "log_binning() (cctbx.miller.set method)": [[148, "cctbx.miller.set.log_binning"]], "lone_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_set"]], "lone_sets() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_sets"]], "make_up_hl_coeffs() (cctbx.miller.array method)": [[148, 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"sigmas_are_sensible() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigmas_are_sensible"]], "sin_theta_over_lambda_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sin_theta_over_lambda_sq"]], "size() (cctbx.miller.array method)": [[148, "cctbx.miller.array.size"]], "size() (cctbx.miller.set method)": [[148, "cctbx.miller.set.size"]], "slice() (cctbx.miller.set method)": [[148, "cctbx.miller.set.slice"]], "sort() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sort"]], "sort_permutation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sort_permutation"]], "sort_permutation() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sort_permutation"]], "statistical_mean() (cctbx.miller.array method)": [[148, "cctbx.miller.array.statistical_mean"]], "structure_factors_from_asu_map() (cctbx.miller.set method)": [[148, "cctbx.miller.set.structure_factors_from_asu_map"]], "structure_factors_from_map() (cctbx.miller.set method)": [[148, 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"cctbx.miller.reindexing.assistant.inv_perms"]], "lattice_group (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.lattice_group"]], "miller_indices (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.miller_indices"]], "perms (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.perms"]], "show_summary() (cctbx.miller.reindexing.assistant method)": [[150, "cctbx.miller.reindexing.assistant.show_summary"]], "cctbx.multipolar": [[151, "module-cctbx.multipolar"]], "add_scatterer() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterer"]], "add_scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterers"]], "apply_symmetry() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.apply_symmetry"]], "apply_symmetry() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.apply_symmetry"]], "cctbx.neutron": [[152, "module-cctbx.neutron"]], "multiplicity() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.multiplicity"]], "scatterer (class in cctbx.neutron)": [[152, "cctbx.neutron.scatterer"]], "scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.scatterers"]], "show_scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.show_scatterers"]], "show_summary() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.show_summary"]], "special_position_indices() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.special_position_indices"]], "structure (class in cctbx.neutron)": [[152, "cctbx.neutron.structure"]], "structure_factors() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.structure_factors"]], "update_weight() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.update_weight"]], "weight() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.weight"]], "cctbx.omz": [[153, "module-cctbx.omz"]], "b_update() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.b_update"]], "cctbx.omz.bfgs": [[154, "module-cctbx.omz.bfgs"]], "get() (cctbx.omz.bfgs.memory_element method)": [[154, "cctbx.omz.bfgs.memory_element.get"]], "h0_scaling() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.h0_scaling"]], "h_update() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.h_update"]], "hg_two_loop_recursion() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.hg_two_loop_recursion"]], "memory_element (class in cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.memory_element"]], "rho (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.rho"]], "s (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.s"]], "y (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.y"]], "c_obs (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.c_obs"]], "cctbx.omz.cif_refine": [[155, "module-cctbx.omz.cif_refine"]], "edge_list (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.edge_list"]], "extract_from_cif_files (class in cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files"]], "init_slots_with_none() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.init_slots_with_none"]], "non_hydrogen_iselection (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.non_hydrogen_iselection"]], "non_hydrogen_selection (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.non_hydrogen_selection"]], "process() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.process"]], "process_geom_bond() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.process_geom_bond"]], "report_fraction_of_negative_observations_if_any() (in module cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.report_fraction_of_negative_observations_if_any"]], "run() (in module cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.run"]], "xray_structure (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.xray_structure"]], "cctbx.omz.cod_refine": [[156, "module-cctbx.omz.cod_refine"]], "get_master_phil() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.get_master_phil"]], "process() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.process"]], "process_continue() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.process_continue"]], "remove_tmp_files() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.remove_tmp_files"]], "run() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run"]], "run_shelx76() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_shelx76"]], "run_shelxl() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_shelxl"]], "run_smtbx_ls() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_smtbx_ls"]], "shelxl_weights() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.shelxl_weights"]], "shelxl_weights_a_b() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.shelxl_weights_a_b"]], "show_cc_r1() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.show_cc_r1"]], "c_obs (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.c_obs"]], "cctbx.omz.cod_select_and_pickle": [[157, "module-cctbx.omz.cod_select_and_pickle"]], "cod_data (class in cctbx.omz.cod_select_and_pickle)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data"]], "cod_id (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.cod_id"]], "edge_list (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.edge_list"]], "f_obs_and_f_calc_agree_well() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.f_obs_and_f_calc_agree_well"]], "have_bad_sigmas() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_bad_sigmas"]], "have_close_contacts() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_close_contacts"]], "have_redundant_data() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_redundant_data"]], "have_shelxl_compatible_scattering_types() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_shelxl_compatible_scattering_types"]], "have_sys_absent() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_sys_absent"]], "have_zero_occupancies() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_zero_occupancies"]], "is_useful() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.is_useful"]], "non_hydrogen_iselection (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.non_hydrogen_iselection"]], "non_hydrogen_selection (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.non_hydrogen_selection"]], "quick_info() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.quick_info"]], "run() (in module cctbx.omz.cod_select_and_pickle)": [[157, "cctbx.omz.cod_select_and_pickle.run"]], "xray_structure (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.xray_structure"]], "approx_curvs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.approx_curvs"]], "approx_quads (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.approx_quads"]], "build_bfgs_memory() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.build_bfgs_memory"]], "calc_shelxl_wght_ls() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.calc_shelxl_wght_ls"]], "calc_weights_if_needed() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.calc_weights_if_needed"]], "callback_after_step() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.callback_after_step"]], "cctbx.omz.dev": [[158, "module-cctbx.omz.dev"]], "check_strong_wolfe() (cctbx.omz.dev.xfgc_info method)": [[158, "cctbx.omz.dev.xfgc_info.check_strong_wolfe"]], "classic_lbfgs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.classic_lbfgs"]], "compute_functional_and_gradients() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_functional_and_gradients"]], "compute_step() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step"]], "compute_step_just_grads() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_just_grads"]], "compute_step_using_curvs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_using_curvs"]], "curv_est_factor (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.curv_est_factor"]], "curv_est_shift() (cctbx.omz.dev.shift_limit_pair method)": [[158, "cctbx.omz.dev.shift_limit_pair.curv_est_shift"]], "curvs (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.curvs"]], "d_min (cctbx.omz.dev.dynamic_shift_limit_u_iso attribute)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso.d_min"]], "delta_estimation_minus_cos() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.delta_estimation_minus_cos"]], "developmental_algorithms() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.developmental_algorithms"]], "dynamic_shift_limit_site (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site"]], "dynamic_shift_limit_u_iso (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso"]], "format_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.format_rms_info"]], "funcl (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.funcl"]], "get() (cctbx.omz.dev.shift_limit_pair method)": [[158, "cctbx.omz.dev.shift_limit_pair.get"]], "get_active_infos() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_active_infos"]], "get_f_calc() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_calc"]], "get_f_cbs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_cbs"]], "get_master_phil() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.get_master_phil"]], "get_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_rms_info"]], "grads (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.grads"]], "is_iterate (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.is_iterate"]], "lbfgs_emulation() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.lbfgs_emulation"]], "line_search() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.line_search"]], "neg (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.neg"]], "pack_variables() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.pack_variables"]], "pair() (cctbx.omz.dev.dynamic_shift_limit_site method)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site.pair"]], "pair() (cctbx.omz.dev.dynamic_shift_limit_u_iso method)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso.pair"]], "plot_samples() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples"]], "plot_samples_ix() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples_ix"]], "pos (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.pos"]], "r1_factor() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.r1_factor"]], "refinement (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.refinement"]], "run_refinement() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.run_refinement"]], "setup_bulk_solvent_correction() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.setup_bulk_solvent_correction"]], "shift_limit_pair (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.shift_limit_pair"]], "show_dests() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.show_dests"]], "show_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.show_rms_info"]], "sign0() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.sign0"]], "update_dests_using_bfgs_formula() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.update_dests_using_bfgs_formula"]], "update_fgc() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.update_fgc"]], "width (cctbx.omz.dev.dynamic_shift_limit_site attribute)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site.width"]], "x (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.x"]], "xfgc_info (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.xfgc_info"]], "cctbx.omz.eval_iso_vs_refined": [[159, "module-cctbx.omz.eval_iso_vs_refined"]], "eval_logs() (in module cctbx.omz.eval_iso_vs_refined)": [[159, "cctbx.omz.eval_iso_vs_refined.eval_logs"]], "run() (in module cctbx.omz.eval_iso_vs_refined)": [[159, "cctbx.omz.eval_iso_vs_refined.run"]], "cctbx.omz.pdb_dev": [[160, "module-cctbx.omz.pdb_dev"]], "process() (in module cctbx.omz.pdb_dev)": [[160, "cctbx.omz.pdb_dev.process"]], "run() (in module cctbx.omz.pdb_dev)": [[160, "cctbx.omz.pdb_dev.run"]], "cctbx.omz.tardy_adaptor": [[161, "module-cctbx.omz.tardy_adaptor"]], "e_pot() (cctbx.omz.tardy_adaptor.potential_object method)": [[161, "cctbx.omz.tardy_adaptor.potential_object.e_pot"]], "potential_object (class in cctbx.omz.tardy_adaptor)": [[161, "cctbx.omz.tardy_adaptor.potential_object"]], "sample_e_pot() (in module cctbx.omz.tardy_adaptor)": [[161, "cctbx.omz.tardy_adaptor.sample_e_pot"]], "adjust_fraction() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.adjust_fraction"]], "assign_r_free_flags_by_shells() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_r_free_flags_by_shells"]], "assign_random_r_free_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_random_r_free_flags"]], "cctbx.r_free_utils": [[162, "module-cctbx.r_free_utils"]], "export_r_free_flags_for_ccp4() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.export_r_free_flags_for_ccp4"]], "export_r_free_flags_for_shelx() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.export_r_free_flags_for_shelx"]], "extend_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.extend_flags"]], "get_r_free_as_bool() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_as_bool"]], "get_r_free_stats() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_stats"]], "looks_like_ccp4_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.looks_like_ccp4_flags"]], "remediate_mismatches() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.remediate_mismatches"]], "cctbx.run_examples": [[163, "module-cctbx.run_examples"]], "run() (in module cctbx.run_examples)": [[163, "cctbx.run_examples.run"]], "cctbx.run_tests": [[164, "module-cctbx.run_tests"]], "run() (in module cctbx.run_tests)": [[164, "cctbx.run_tests.run"]], "any_compatible_crystal_symmetry() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_crystal_symmetry"]], "any_compatible_unit_cell() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_unit_cell"]], "any_generator_set (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.any_generator_set"]], "any_generator_set() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_generator_set"]], "as_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.as_reference_setting"]], "brick() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.brick"]], "cctbx.sgtbx": [[165, "module-cctbx.sgtbx"]], "change_basis() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_basis"]], "change_hand() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_hand"]], "change_of_basis_op_to() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to"]], "change_of_basis_op_to_other_hand() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_other_hand"]], "change_of_basis_op_to_primitive_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_primitive_setting"]], "change_of_basis_op_to_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_reference_setting"]], "cif_symmetry_code() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.cif_symmetry_code"]], "compare_cb_op_as_hkl() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.compare_cb_op_as_hkl"]], "constant (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.constant"]], "direct_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.direct_space_asu"]], "empty (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.empty"]], "get() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.get"]], "group() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.group"]], "i_vars (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.i_vars"]], "is_allowed_origin_shift() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_allowed_origin_shift"]], "is_equivalent() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.is_equivalent"]], "is_identity() (cctbx.sgtbx.special_op_simplified_term method)": [[165, "cctbx.sgtbx.special_op_simplified_term.is_identity"]], "is_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_reference_setting"]], "le_page_1982_delta_details (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.le_page_1982_delta_details"]], "multipliers (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.multipliers"]], "number_of_continuous_allowed_origin_shifts() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.number_of_continuous_allowed_origin_shifts"]], "primitive_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.primitive_setting"]], "reciprocal_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reciprocal_space_asu"]], "reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reference_setting"]], "reference_space_group_infos() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.reference_space_group_infos"]], "reflection_intensity_equivalent_groups() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reflection_intensity_equivalent_groups"]], "registry (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.registry"]], "shelx_fvar_encoding() (cctbx.sgtbx.special_op_simplified method)": [[165, "cctbx.sgtbx.special_op_simplified.shelx_fvar_encoding"]], "show_summary() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.show_summary"]], "site_symmetry_ops_j (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.site_symmetry_ops_j"]], "space_group_info (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.space_group_info"]], "special_op_simplified (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplified"]], "special_op_simplified_term (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplified_term"]], "special_op_simplifier() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplifier"]], "structure_seminvariants() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.structure_seminvariants"]], "subtract_continuous_allowed_origin_shifts() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.subtract_continuous_allowed_origin_shifts"]], "symbol_and_number() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.symbol_and_number"]], "symmetry_equivalent_pair_interactions (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions"]], "terms (cctbx.sgtbx.special_op_simplified attribute)": [[165, "cctbx.sgtbx.special_op_simplified.terms"]], "type() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.type"]], "vec3_rat_from_str() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.vec3_rat_from_str"]], "wyckoff_table() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.wyckoff_table"]], "bravais_lattice (class in cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice"]], "cctbx.sgtbx.bravais_types": [[166, "module-cctbx.sgtbx.bravais_types"]], "crystal_family_symbols (cctbx.sgtbx.bravais_types.bravais_lattice attribute)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice.crystal_family_symbols"]], "exercise() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.exercise"]], "tst_bravais_types() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.tst_bravais_types"]], "best_partition_representatives() (cctbx.sgtbx.cosets.left_decomposition_point_groups_only method)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only.best_partition_representatives"]], "cctbx.sgtbx.cosets": [[167, "module-cctbx.sgtbx.cosets"]], "clear_up_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.clear_up_cosets"]], "construct_nice_cb_op() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.construct_nice_cb_op"]], "double_cosets (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_cosets"]], "double_unique() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_unique"]], "have_duplicates() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.have_duplicates"]], "is_in_coset() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_coset"]], "is_in_list_of_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_list_of_cosets"]], "is_subgroup() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.is_subgroup"]], "left_decomposition (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition"]], "left_decomposition_point_groups_only (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only"]], "partition_t (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.partition_t"]], "run() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.run"]], "show() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.show"]], "show() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.show"]], "sort_cosets() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.sort_cosets"]], "test_double_coset_decomposition() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.test_double_coset_decomposition"]], "test_lattice_translation_aware_left_decomposition() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.test_lattice_translation_aware_left_decomposition"]], "add_buffer() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_buffer"]], "add_plane() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_plane"]], "add_planes() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_planes"]], "box_max() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_max"]], "box_min() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_min"]], "cctbx.sgtbx.direct_space_asu": [[168, "module-cctbx.sgtbx.direct_space_asu"]], "change_basis() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.change_basis"]], "define_metric() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.define_metric"]], "direct_space_asu (class in cctbx.sgtbx.direct_space_asu)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.extract_all_cuts"]], "in_which_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.in_which_cuts"]], "is_inside() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.is_inside"]], "shape_only() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_only"]], "shape_vertices() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_vertices"]], "show_comprehensive_summary() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.show_comprehensive_summary"]], "show_summary() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.show_summary"]], "analyze_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.analyze_redundancies"]], "cctbx.sgtbx.direct_space_asu.check_redundancies": [[169, "module-cctbx.sgtbx.direct_space_asu.check_redundancies"]], "check_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_asu"]], "check_compatibility_with_sampling_grid() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_compatibility_with_sampling_grid"]], "check_multiplicities() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_multiplicities"]], "color_server (class in cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.color_server"]], "colored_grid_point (class in cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.colored_grid_point"]], "compare_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.compare_redundancies"]], "grid_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.grid_asu"]], "iround() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.iround"]], "next() (cctbx.sgtbx.direct_space_asu.check_redundancies.color_server method)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.color_server.next"]], "recolor_grid_points() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.recolor_grid_points"]], "rt_mx_analysis() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_mx_analysis"]], "rt_plus_unit_shifts() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_plus_unit_shifts"]], "rt_times_grid_point() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_times_grid_point"]], "sample_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.sample_asu"]], "slice() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.slice"]], "sort_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.sort_redundancies"]], "str_ev() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.str_ev"]], "test_all() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.test_all"]], "u_index_as_r_index() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.u_index_as_r_index"]], "as_float_cut_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.as_float_cut_plane"]], "as_xyz() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.as_xyz"]], "as_xyz() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.as_xyz"]], "base_symbol() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.base_symbol"]], "c (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.c"]], "cctbx.sgtbx.direct_space_asu.cut_plane": [[170, "module-cctbx.sgtbx.direct_space_asu.cut_plane"]], "change_basis() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.change_basis"]], "change_basis() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.change_basis"]], "cut (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut"]], "cut_expr (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.cut_expr"]], "cut_expr_ops (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expr_ops"]], "cut_expression (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression"]], "evaluate() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.evaluate"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.extract_all_cuts"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.extract_all_cuts"]], "get_point_in_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.get_point_in_plane"]], "has_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.has_cuts"]], "inclusive (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.inclusive"]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.is_inside"]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.is_inside"]], "lcm_of_denominators() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.lcm_of_denominators"]], "lhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.lhs"]], "n (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.n"]], "one() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.one"]], "op (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.op"]], "rhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.rhs"]], "strip() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.strip"]], "add() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.add"]], "all_cut_points() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.all_cut_points"]], "all_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.all_points"]], "asu (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.asu"]], "asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.asu_polygons"]], "cctbx.sgtbx.direct_space_asu.facet_analysis": [[171, "module-cctbx.sgtbx.direct_space_asu.facet_analysis"]], "collect_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.collect_cuts"]], "consolidated_edges_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points"]], "cut_point_positions() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.cut_point_positions"]], "cut_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.cut_points"]], "depth1_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.depth1_cuts"]], "edge_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.edge_inclusive_flag"]], "edge_position() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_position"]], "edge_segment (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment"]], "edge_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points"]], "eliminate_outside_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.eliminate_outside_vertices"]], "end_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.end_points"]], "extract_polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.extract_polygon_vertices"]], "face_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_polygons"]], "face_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_vertices"]], "get_all_edge_segments() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_edge_segments"]], "get_all_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_all_segments"]], "get_all_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_vertices"]], "get_edge_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_edge_vertices"]], "get_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_segments"]], "intersection() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.intersection"]], "is_one_of() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.is_one_of"]], "join_edge() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_edge"]], "join_point() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_point"]], "line_sample_point() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.line_sample_point"]], "list (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.list"]], "polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.polygon_vertices"]], "sense_of_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.sense_of_polygon"]], "shape_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.shape_vertices"]], "show_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.show_points"]], "sort_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.sort_cut_points"]], "sorted_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.sorted_cut_points"]], "trace_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.trace_polygon"]], "verify_asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.verify_asu_polygons"]], "verify_edge_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.verify_edge_segments"]], "vertex (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.vertex"]], "vertex_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.vertex_inclusive_flag"]], "asu_01() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_01"]], "asu_02() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_02"]], "asu_03() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_03"]], "asu_04() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_04"]], "asu_05() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_05"]], "asu_06() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_06"]], "asu_07() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_07"]], "asu_08() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_08"]], "asu_09() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_09"]], "asu_10() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_10"]], "asu_11() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_11"]], "asu_12() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_12"]], "asu_13() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_13"]], "asu_14() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_14"]], "asu_15() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_15"]], "asu_16() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_16"]], "asu_17() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_17"]], "cctbx.sgtbx.direct_space_asu.plane_group_reference_table": [[172, "module-cctbx.sgtbx.direct_space_asu.plane_group_reference_table"]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.get_asu"]], "asu_show_() (in module cctbx.sgtbx.direct_space_asu.proto)": [[173, "cctbx.sgtbx.direct_space_asu.proto.asu_show_"]], "cctbx.sgtbx.direct_space_asu.proto": [[173, "module-cctbx.sgtbx.direct_space_asu.proto"]], "base_symbol_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.base_symbol_cpp"]], "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table": [[174, "module-cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table"]], "make_md5() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.make_md5"]], "out_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.out_cpp"]], "run() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.run"]], "show_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.show_cpp"]], "apply_change_of_basis() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.apply_change_of_basis"]], "asu_001() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_001"]], "asu_002() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_002"]], "asu_003() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_003"]], "asu_004() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_004"]], "asu_005() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_005"]], "asu_006() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_006"]], "asu_007() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_007"]], "asu_008() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_008"]], "asu_009() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_009"]], "asu_010() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_010"]], "asu_011() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_011"]], "asu_012() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_012"]], "asu_013() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_013"]], "asu_014() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_014"]], "asu_015() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_015"]], "asu_016() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_016"]], "asu_017() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_017"]], "asu_018() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_018"]], "asu_019() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_019"]], "asu_020() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_020"]], "asu_021() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_021"]], "asu_022() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_022"]], "asu_023() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_023"]], "asu_024() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_024"]], "asu_025() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_025"]], "asu_026() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_026"]], "asu_027() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_027"]], "asu_028() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_028"]], "asu_029() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_029"]], "asu_030() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_030"]], "asu_031() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_031"]], "asu_032() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_032"]], "asu_033() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_033"]], "asu_034() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_034"]], "asu_035() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_035"]], "asu_036() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_036"]], "asu_037() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_037"]], "asu_038() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_038"]], "asu_039() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_039"]], "asu_040() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_040"]], "asu_041() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_041"]], "asu_042() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_042"]], "asu_043() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_043"]], "asu_044() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_044"]], "asu_045() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_045"]], "asu_046() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_046"]], "asu_047() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_047"]], "asu_048() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_048"]], "asu_049() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_049"]], "asu_050() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_050"]], "asu_051() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_051"]], "asu_052() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_052"]], "asu_053() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_053"]], "asu_054() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_054"]], "asu_055() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_055"]], "asu_056() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_056"]], "asu_057() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_057"]], "asu_058() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_058"]], "asu_059() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_059"]], "asu_060() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_060"]], "asu_061() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_061"]], "asu_062() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_062"]], "asu_063() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_063"]], "asu_064() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_064"]], "asu_065() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_065"]], "asu_066() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_066"]], "asu_067() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_067"]], "asu_068() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_068"]], "asu_069() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_069"]], "asu_070() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_070"]], "asu_071() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_071"]], "asu_072() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_072"]], "asu_073() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_073"]], "asu_074() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_074"]], "asu_075() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_075"]], "asu_076() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_076"]], "asu_077() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_077"]], "asu_078() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_078"]], "asu_079() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_079"]], "asu_080() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_080"]], "asu_081() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_081"]], "asu_082() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_082"]], "asu_083() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_083"]], "asu_084() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_084"]], "asu_085() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_085"]], "asu_086() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_086"]], "asu_087() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_087"]], "asu_088() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_088"]], "asu_089() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_089"]], "asu_090() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_090"]], "asu_091() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_091"]], "asu_092() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_092"]], "asu_093() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_093"]], "asu_094() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_094"]], "asu_095() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_095"]], "asu_096() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_096"]], "asu_097() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_097"]], "asu_098() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_098"]], "asu_099() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_099"]], "asu_100() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_100"]], "asu_101() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_101"]], "asu_102() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_102"]], "asu_103() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_103"]], "asu_104() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_104"]], "asu_105() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_105"]], "asu_106() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_106"]], "asu_107() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_107"]], "asu_108() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_108"]], "asu_109() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_109"]], "asu_110() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_110"]], "asu_111() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_111"]], "asu_112() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_112"]], "asu_113() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_113"]], "asu_114() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_114"]], "asu_115() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_115"]], "asu_116() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_116"]], "asu_117() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_117"]], "asu_118() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_118"]], "asu_119() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_119"]], "asu_120() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_120"]], "asu_121() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_121"]], "asu_122() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_122"]], "asu_123() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_123"]], "asu_124() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_124"]], "asu_125() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_125"]], "asu_126() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_126"]], "asu_127() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_127"]], "asu_128() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_128"]], "asu_129() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_129"]], "asu_130() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_130"]], "asu_131() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_131"]], "asu_132() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_132"]], "asu_133() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_133"]], "asu_134() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_134"]], "asu_135() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_135"]], "asu_136() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_136"]], "asu_137() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_137"]], "asu_138() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_138"]], "asu_139() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_139"]], "asu_140() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_140"]], "asu_141() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_141"]], "asu_142() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_142"]], "asu_143() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_143"]], "asu_144() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_144"]], "asu_145() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_145"]], "asu_146() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_146"]], "asu_147() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_147"]], "asu_148() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_148"]], "asu_149() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_149"]], "asu_150() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_150"]], "asu_151() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_151"]], "asu_152() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_152"]], "asu_153() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_153"]], "asu_154() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_154"]], "asu_155() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_155"]], "asu_156() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_156"]], "asu_157() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_157"]], "asu_158() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_158"]], "asu_159() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_159"]], "asu_160() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_160"]], "asu_161() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_161"]], "asu_162() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_162"]], "asu_163() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_163"]], "asu_164() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_164"]], "asu_165() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_165"]], "asu_166() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_166"]], "asu_167() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_167"]], "asu_168() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_168"]], "asu_169() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_169"]], "asu_170() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_170"]], "asu_171() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_171"]], "asu_172() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_172"]], "asu_173() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_173"]], "asu_174() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_174"]], "asu_175() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_175"]], "asu_176() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_176"]], "asu_177() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_177"]], "asu_178() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_178"]], "asu_179() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_179"]], "asu_180() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_180"]], "asu_181() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_181"]], "asu_182() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_182"]], "asu_183() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_183"]], "asu_184() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_184"]], "asu_185() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_185"]], "asu_186() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_186"]], "asu_187() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_187"]], "asu_188() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_188"]], "asu_189() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_189"]], "asu_190() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_190"]], "asu_191() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_191"]], "asu_192() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_192"]], "asu_193() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_193"]], "asu_194() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_194"]], "asu_195() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_195"]], "asu_196() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_196"]], "asu_197() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_197"]], "asu_198() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_198"]], "asu_199() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_199"]], "asu_200() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_200"]], "asu_201() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_201"]], "asu_202() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_202"]], "asu_203() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_203"]], "asu_204() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_204"]], "asu_205() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_205"]], "asu_206() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_206"]], "asu_207() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_207"]], "asu_208() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_208"]], "asu_209() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_209"]], "asu_210() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_210"]], "asu_211() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_211"]], "asu_212() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_212"]], "asu_213() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_213"]], "asu_214() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_214"]], "asu_215() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_215"]], "asu_216() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_216"]], "asu_217() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_217"]], "asu_218() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_218"]], "asu_219() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_219"]], "asu_220() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_220"]], "asu_221() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_221"]], "asu_222() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_222"]], "asu_223() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_223"]], "asu_224() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_224"]], "asu_225() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_225"]], "asu_226() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_226"]], "asu_227() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_227"]], "asu_228() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_228"]], "asu_229() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_229"]], "asu_230() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_230"]], "cctbx.sgtbx.direct_space_asu.reference_table": [[175, "module-cctbx.sgtbx.direct_space_asu.reference_table"]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.get_asu"]], "cctbx.sgtbx.direct_space_asu.short_cuts": [[176, "module-cctbx.sgtbx.direct_space_asu.short_cuts"]], "algebraic() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.algebraic"]], "cctbx.sgtbx.harker": [[177, "module-cctbx.sgtbx.harker"]], "count() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.count"]], "distance() (cctbx.sgtbx.harker.plane_cartesian method)": [[177, "cctbx.sgtbx.harker.plane_cartesian.distance"]], "dot3() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.dot3"]], "min_distance() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.min_distance"]], "mod_positive3() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.mod_positive3"]], "operation() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.operation"]], "plane_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_cartesian"]], "plane_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_fractional"]], "planes_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_cartesian"]], "planes_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_fractional"]], "test() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test"]], "test_call_back() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test_call_back"]], "cctbx.sgtbx.lattice_symmetry": [[178, "module-cctbx.sgtbx.lattice_symmetry"]], "change_input_to_minimum_cell() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.change_input_to_minimum_cell"]], "change_of_basis_op_to_best_cell() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.change_of_basis_op_to_best_cell"]], "derive_result_group_list() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.derive_result_group_list"]], "lattice_group_info() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.lattice_group_info"]], "metric_subgroups (class in cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups"]], "metric_supergroup() (in module cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_supergroup"]], "show() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show"]], "show_groups() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show_groups"]], "show_input() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show_input"]], "cctbx.sgtbx.literal_description": [[179, "module-cctbx.sgtbx.literal_description"]], "cosets_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.cosets_form"]], "labelit_check_pdb_symmetry_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_form"]], "labelit_check_pdb_symmetry_short() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_short"]], "literal_description (class in cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.literal_description"]], "long_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.long_form"]], "select() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.select"]], "str_ev() (in module cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.str_ev"]], "cctbx.sgtbx.plane_groups": [[180, "module-cctbx.sgtbx.plane_groups"]], "assemble_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.assemble_symops"]], "build_it() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.build_it"]], "cctbx.sgtbx.pointgroup_tools": [[181, "module-cctbx.sgtbx.pointgroup_tools"]], "compare_abs_lists() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.compare_abs_lists"]], "compatible_symmetries() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.compatible_symmetries"]], "coset_lookup() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.coset_lookup"]], "edge_object (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object"]], "find_absent_indices() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.find_absent_indices"]], "find_compatible_space_groups (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups"]], "find_left_over_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.find_left_over_symops"]], "full_sys_abs_mask() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.full_sys_abs_mask"]], "get_maximal_subgroup() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.get_maximal_subgroup"]], "get_space_groups_compatible_with_likely_point_group() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.get_space_groups_compatible_with_likely_point_group"]], "get_symops_from_supergroup_that_are_not_in_subgroup() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.get_symops_from_supergroup_that_are_not_in_subgroup"]], "graphviz_pg_graph() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.graphviz_pg_graph"]], "make_and_place_nodes_and_connections() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.make_and_place_nodes_and_connections"]], "make_sys_abs_list() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.make_sys_abs_list"]], "node_object (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.node_object"]], "point_group_graph (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph"]], "reference_setting_choices() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.reference_setting_choices"]], "remove_point_group_and_its_super_groups_from_graph() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.remove_point_group_and_its_super_groups_from_graph"]], "return_likely_sg_and_cell() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.return_likely_sg_and_cell"]], "return_next_index() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_index"]], "return_next_left_over_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_left_over_set"]], "return_next_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_set"]], "return_next_sg() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_sg"]], "return_unused() (cctbx.sgtbx.pointgroup_tools.edge_object method)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object.return_unused"]], "return_used() (cctbx.sgtbx.pointgroup_tools.edge_object method)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object.return_used"]], "reverse_dict() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.reverse_dict"]], "show() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.show"]], "show() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.show"]], "show() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.show"]], "space_group_graph_from_cell_and_sg (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg"]], "sub_super_point_group_relations (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations"]], "as_hkl() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.as_hkl"]], "cb_op_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.cb_op_as_rational"]], "cctbx.sgtbx.rational_matrices_point_groups": [[182, "module-cctbx.sgtbx.rational_matrices_point_groups"]], "change_basis() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.change_basis"]], "compare_groups() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.compare_groups"]], "construct_rational_point_group() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.construct_rational_point_group"]], "expand() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.expand"]], "is_in_group() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.is_in_group"]], "rat_rot_group (class in cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group"]], "rt_mx_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rt_mx_as_rational"]], "run() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.run"]], "show() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.show"]], "tst_compare() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_compare"]], "tst_groups() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_groups"]], "as_hkl() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.as_hkl"]], "build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.build_reticular_twin_laws"]], "cb_op_as_rational() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cb_op_as_rational"]], "cctbx.sgtbx.reticular_pg_tools": [[183, "module-cctbx.sgtbx.reticular_pg_tools"]], "change_basis() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.change_basis"]], "compare_groups() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.compare_groups"]], "construct_rational_point_group() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.construct_rational_point_group"]], "cosets() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cosets"]], "expand() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.expand"]], "extra_operators() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.extra_operators"]], "is_in_group() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.is_in_group"]], "is_reticular_polyholohedral() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_reticular_polyholohedral"]], "is_subgroup() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_subgroup"]], "rat_rot_group (class in cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group"]], "recurring_operators() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.recurring_operators"]], "rt_mx_as_rational() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.rt_mx_as_rational"]], "run() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.run"]], "show() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.show"]], "tst_build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_build_reticular_twin_laws"]], "tst_compare() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_compare"]], "tst_groups() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_groups"]], "cctbx.sgtbx.reticular_twin_laws": [[184, "module-cctbx.sgtbx.reticular_twin_laws"]], "construct_twin_laws() (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws.construct_twin_laws"]], "exercise() (in module cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.exercise"]], "make_new_xs() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.make_new_xs"]], "metric_r() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.metric_r"]], "ret_twin_law_info (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info"]], "reticular_twin_laws (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws"]], "show() (cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info method)": [[184, "cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info.show"]], "show() (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws.show"]], "symmetry_safe_sublattice_xs (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs"]], "cctbx.sgtbx.show_cosets": [[185, "module-cctbx.sgtbx.show_cosets"]], "run() (in module cctbx.sgtbx.show_cosets)": [[185, "cctbx.sgtbx.show_cosets.run"]], "cctbx.sgtbx.sub_lattice_tools": [[186, "module-cctbx.sgtbx.sub_lattice_tools"]], "compare_lattice (class in cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice"]], "divisor() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.divisor"]], "exercise() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.exercise"]], "find_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples"]], "find_triples_slowly() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples_slowly"]], "generate_cb_op_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_cb_op_up_to_order"]], "generate_inverse_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_inverse_matrix_up_to_order"]], "generate_matrix() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix"]], "generate_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix_up_to_order"]], "make_list_of_target_xs_up_to_order (class in cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order"]], "make_new_cell_and_symmetry() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.make_new_cell_and_symmetry"]], "make_new_xs() (cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order method)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order.make_new_xs"]], "make_permutations() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_permutations"]], "make_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_triples"]], "rt_mx_as_rational() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.rt_mx_as_rational"]], "show_basic_info() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.show_basic_info"]], "show_solution() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.show_solution"]], "sort_triple() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.sort_triple"]], "tst_centered_cells() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_centered_cells"]], "tst_compare() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_compare"]], "tst_make_bigger_cell() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_make_bigger_cell"]], "tst_sublattice() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_sublattice"]], "anomalous_reflection_intensity_primitive_cell() (in module cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.anomalous_reflection_intensity_primitive_cell"]], "cctbx.sgtbx.subgroups": [[187, "module-cctbx.sgtbx.subgroups"]], "groups_parent_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_parent_setting"]], "groups_primitive_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_primitive_setting"]], "show() (in module cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.show"]], "subgroups (class in cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.subgroups"]], "cctbx.sgtbx.symbol_confidence": [[188, "module-cctbx.sgtbx.symbol_confidence"]], "level() (in module cctbx.sgtbx.symbol_confidence)": [[188, "cctbx.sgtbx.symbol_confidence.level"]], "cctbx.sgtbx.sys_abs_equiv": [[189, "module-cctbx.sgtbx.sys_abs_equiv"]], "cctbx.source_generators": [[190, "module-cctbx.source_generators"]], "cctbx.source_generators.eltbx": [[191, "module-cctbx.source_generators.eltbx"]], "cctbx.source_generators.eltbx.generate_henke_cpp": [[192, "module-cctbx.source_generators.eltbx.generate_henke_cpp"]], "collect_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_points"]], "collect_tab_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_tab_points"]], "collect_tables() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_tables"]], "compare_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.compare_points"]], "print_ftp_info() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_ftp_info"]], "print_header() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_header"]], "print_henke_cpp() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_henke_cpp"]], "print_table_block() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_table_block"]], "run() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.run"]], "cctbx.source_generators.eltbx.generate_sasaki_cpp": [[193, "module-cctbx.source_generators.eltbx.generate_sasaki_cpp"]], "check_first_last() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table.check_first_last"]], "collect_tables() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.collect_tables"]], "combine_tables() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.combine_tables"]], "print_ftp_info() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_ftp_info"]], "print_header() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_header"]], "print_sasaki_cpp() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_sasaki_cpp"]], "print_table_block() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_table_block"]], "run() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.run"]], "sasaki_table (class in cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table"]], "table_references (class in cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.table_references"]], "validate() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table.validate"]], "cctbx.source_generators.flex_fwd_h": [[194, "module-cctbx.source_generators.flex_fwd_h"]], "run() (in module cctbx.source_generators.flex_fwd_h)": [[194, "cctbx.source_generators.flex_fwd_h.run"]], "cctbx.statistics": [[195, "module-cctbx.statistics"]], "cumulative_intensity_distribution (class in cctbx.statistics)": [[195, "cctbx.statistics.cumulative_intensity_distribution"]], "empty (class in cctbx.statistics)": [[195, "cctbx.statistics.empty"]], "sys_absent_intensity_distribution (class in cctbx.statistics)": [[195, "cctbx.statistics.sys_absent_intensity_distribution"]], "wilson_plot (class in cctbx.statistics)": [[195, "cctbx.statistics.wilson_plot"]], "xy_plot_info() (cctbx.statistics.cumulative_intensity_distribution method)": [[195, "cctbx.statistics.cumulative_intensity_distribution.xy_plot_info"]], "xy_plot_info() (cctbx.statistics.sys_absent_intensity_distribution method)": [[195, "cctbx.statistics.sys_absent_intensity_distribution.xy_plot_info"]], "xy_plot_info() (cctbx.statistics.wilson_plot method)": [[195, "cctbx.statistics.wilson_plot.xy_plot_info"]], "accepted (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.accepted"]], "cctbx.symmetry_search": [[196, "module-cctbx.symmetry_search"]], "centring_translation_peak_sites() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.centring_translation_peak_sites"]], "change_origin() (cctbx.symmetry_search.possible_symmetry method)": [[196, "cctbx.symmetry_search.possible_symmetry.change_origin"]], "compute_functional_and_gradients() (cctbx.symmetry_search.shift_refinement method)": [[196, "cctbx.symmetry_search.shift_refinement.compute_functional_and_gradients"]], "cross_correlation_cutoff_for_centring (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_cutoff_for_centring"]], "cross_correlation_peaks() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_peaks"]], "find_centring_translations() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_centring_translations"]], "find_space_group() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_space_group"]], "fmt3vec (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.fmt3vec"]], "grid_resolution_factor (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.grid_resolution_factor"]], "misfit() (cctbx.symmetry_search.symmetrised_shifted_structure_factors method)": [[196, "cctbx.symmetry_search.symmetrised_shifted_structure_factors.misfit"]], "phi_sym_acceptance_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_acceptance_cutoff"]], "phi_sym_rejection_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_rejection_cutoff"]], "possible_point_group_generators() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.possible_point_group_generators"]], "possible_symmetry (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.possible_symmetry"]], "rejected (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.rejected"]], "set_components_of_global_origin() (cctbx.symmetry_search.possible_symmetry method)": [[196, "cctbx.symmetry_search.possible_symmetry.set_components_of_global_origin"]], "shift_refinement (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.shift_refinement"]], "structure_factor_symmetry (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.structure_factor_symmetry"]], "symmetrised_shifted_structure_factors (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.symmetrised_shifted_structure_factors"]], "symmetrised_structure_factors() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.symmetrised_structure_factors"]], "unsure (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.unsure"]], "cctbx.translation_search": [[197, "module-cctbx.translation_search"]], "unit_cell (class in cctbx.uctbx)": [[198, "cctbx.uctbx.unit_cell"]], "cctbx.uctbx.determine_unit_cell": [[199, "module-cctbx.uctbx.determine_unit_cell"]], "as_gruber_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_gruber_matrix"]], "as_niggli_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_niggli_matrix"]], "as_sym_mat3() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_sym_mat3"]], "as_unit_cell() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_unit_cell"]], "b2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b2_action"]], "b2_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b2_action"]], "b3_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b3_action"]], "b3_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b3_action"]], "b4_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b4_action"]], "b4_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b4_action"]], "b5_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b5_action"]], "b5_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b5_action"]], "cb_update() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.cb_update"]], "cctbx.uctbx.gruber_1973": [[200, "module-cctbx.uctbx.gruber_1973"]], "def_gt_0() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.def_gt_0"]], "def_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.def_test"]], "entier() (in module cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.entier"]], "fast_minimum_reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction"]], "iteration_limit() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.iteration_limit"]], "minimum_reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.minimum_reduction"]], "n1_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n1_action"]], "n2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n2_action"]], "n3_false_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n3_false_action"]], "n3_false_action() (cctbx.uctbx.gruber_1973.minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.minimum_reduction.n3_false_action"]], "n3_true_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n3_true_action"]], "n_iterations() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n_iterations"]], "r_inv() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.r_inv"]], "reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.reduction"]], "significant_change_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.significant_change_test"]], "step() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.step"]], "step() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.step"]], "type() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.type"]], "cctbx.uctbx.gruber_1973_table_1": [[201, "module-cctbx.uctbx.gruber_1973_table_1"]], "get_mk2_sets() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_mk2_sets"]], "get_type_conditions() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_type_conditions"]], "type_conditions (class in cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.type_conditions"]], "a1_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a1_action"]], "a2_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a2_action"]], "a3_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a3_action"]], "a4_action() (cctbx.uctbx.krivy_gruber_1976.minimum_reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.minimum_reduction.a4_action"]], "a4_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a4_action"]], "a5_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a5_action"]], "a6_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a6_action"]], "a7_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a7_action"]], "a8_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a8_action"]], "cctbx.uctbx.krivy_gruber_1976": [[202, "module-cctbx.uctbx.krivy_gruber_1976"]], "minimum_reduction (class in cctbx.uctbx.krivy_gruber_1976)": [[202, "cctbx.uctbx.krivy_gruber_1976.minimum_reduction"]], "reduction (class in cctbx.uctbx.krivy_gruber_1976)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction"]], "step() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.step"]], "as_gruber_matrix() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_gruber_matrix"]], "as_niggli_matrix() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_niggli_matrix"]], "as_sym_mat3() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_sym_mat3"]], "as_unit_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_unit_cell"]], "cb_update() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.cb_update"]], "cctbx.uctbx.reduction_base": [[203, "module-cctbx.uctbx.reduction_base"]], "change_of_basis_op() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.change_of_basis_op"]], "def_gt_0() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.def_gt_0"]], "def_test() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.def_test"]], "eps_eq() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_eq"]], "eps_eq() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.eps_eq"]], "eps_gt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_gt"]], "eps_lt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_lt"]], "gruber_parameterization (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization"]], "is_buerger_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_buerger_cell"]], "is_niggli_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_niggli_cell"]], "iteration_limit() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.iteration_limit"]], "iteration_limit_exceeded": [[203, "cctbx.uctbx.reduction_base.iteration_limit_exceeded"]], "meets_main_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_main_conditions"]], "meets_primary_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_primary_conditions"]], "minimum_reduction_mixin (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin"]], "n1_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n1_action"]], "n2_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n2_action"]], "n3_false_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n3_false_action"]], "n3_true_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n3_true_action"]], "n_iterations() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n_iterations"]], "r_inv() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.r_inv"]], "reduction_base (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.reduction_base"]], "significant_change_test() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.significant_change_test"]], "type() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.type"]], "cctbx.web": [[204, "module-cctbx.web"]], "cctbx.web.all_axes": [[205, "module-cctbx.web.all_axes"]], "interpret_form_data() (in module cctbx.web.all_axes)": [[205, "cctbx.web.all_axes.interpret_form_data"]], "run() (in module cctbx.web.all_axes)": [[205, "cctbx.web.all_axes.run"]], "cctbx.web.asu_gallery": [[206, "module-cctbx.web.asu_gallery"]], "html_head_title() (in module cctbx.web.asu_gallery)": [[206, "cctbx.web.asu_gallery.html_head_title"]], "cctbx.web.asu_gallery.guide_to_notation": [[207, "module-cctbx.web.asu_gallery.guide_to_notation"]], "write_html() (in module cctbx.web.asu_gallery.guide_to_notation)": [[207, "cctbx.web.asu_gallery.guide_to_notation.write_html"]], "asu_as_jvx() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.asu_as_jvx"]], "basis_vector_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.basis_vector_geometry"]], "cartesian_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.cartesian_polygon"]], "cctbx.web.asu_gallery.jv_asu": [[208, "module-cctbx.web.asu_gallery.jv_asu"]], "edge_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.edge_geometry"]], "get_diagonal_extend() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_diagonal_extend"]], "get_edge_vectors() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_edge_vectors"]], "get_min_fractional() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_min_fractional"]], "orthogonalizer (class in cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.orthogonalizer"]], "run() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.run"]], "select_color() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.select_color"]], "shrink_edge() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_edge"]], "shrink_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_polygon"]], "unit_cell_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.unit_cell_geometry"]], "vertex_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.vertex_geometry"]], "add() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add"]], "add() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.add"]], "add_point_group_type() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add_point_group_type"]], "cctbx.web.asu_gallery.jv_index": [[209, "module-cctbx.web.asu_gallery.jv_index"]], "crystal_system_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table"]], "format_html() (cctbx.web.asu_gallery.jv_index.crystal_system_table method)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.plane_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.format_html"]], "hermann_mauguin() (cctbx.web.asu_gallery.jv_index.point_group_symbols method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols.hermann_mauguin"]], "number() (cctbx.web.asu_gallery.jv_index.point_group_symbols method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols.number"]], "plane_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table"]], "point_group_symbols (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols"]], "point_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table"]], "symbol_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table"]], "table_format_html() (in module cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.table_format_html"]], "write_html() (in module cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.write_html"]], "append() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.append"]], "append() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.append"]], "append() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.append"]], "bracketed_link() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.bracketed_link"]], "cctbx.web.asu_gallery.jvx": [[210, "module-cctbx.web.asu_gallery.jvx"]], "extend() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.extend"]], "face (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.face"]], "faceset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.faceSet"]], "geometry (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.geometry"]], "head() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.head"]], "hide_points() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.hide_points"]], "html_loader() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.html_loader"]], "index() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.index"]], "jvx() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.geometry method)": [[210, "cctbx.web.asu_gallery.jvx.geometry.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.jvx"]], "jvx_item_colors() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.jvx_item_colors"]], "line (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.line"]], "lineset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.lineSet"]], "make_point() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.make_point"]], "point (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.point"]], "pointset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.pointSet"]], "run() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.run"]], "size() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.size"]], "size() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.size"]], "size() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.size"]], "tail() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.tail"]], "cctbx.web.asu_gallery.web_links": [[211, "module-cctbx.web.asu_gallery.web_links"]], "cctbx.web.browse_settings": [[212, "module-cctbx.web.browse_settings"]], "interpret_form_data() (in module cctbx.web.browse_settings)": [[212, "cctbx.web.browse_settings.interpret_form_data"]], "run() (in module cctbx.web.browse_settings)": [[212, "cctbx.web.browse_settings.run"]], "formaterror": [[213, "cctbx.web.cgi_utils.FormatError"], [265, "iotbx.file_reader.FormatError"]], "base() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.base"]], "cctbx.web.cgi_utils": [[213, "module-cctbx.web.cgi_utils"]], "coordinates_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.coordinates_from_form"]], "empty (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.empty"]], "file() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.file"]], "inp_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.inp_from_form"]], "script() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.script"]], "server_info (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.server_info"]], "cctbx.web.change_basis": [[214, "module-cctbx.web.change_basis"]], "display_r() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_r"]], "display_rt() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_rt"]], "fmt_nums() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.fmt_nums"]], "interpret_form_data() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.interpret_form_data"]], "number_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.number_from_string"]], "nums_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.nums_from_string"]], "p_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.p_from_string"]], "raise_uninterpretable() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.raise_uninterpretable"]], "rt_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.rt_from_string"]], "run() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.run"]], "w_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.w_from_string"]], "xyz_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.xyz_from_string"]], "cctbx.web.change_hand": [[215, "module-cctbx.web.change_hand"]], "interpret_form_data() (in module cctbx.web.change_hand)": [[215, "cctbx.web.change_hand.interpret_form_data"]], "run() (in module cctbx.web.change_hand)": [[215, "cctbx.web.change_hand.run"]], "cctbx.web.change_setting": [[216, "module-cctbx.web.change_setting"]], "interpret_form_data() (in module cctbx.web.change_setting)": [[216, "cctbx.web.change_setting.interpret_form_data"]], "run() (in module cctbx.web.change_setting)": [[216, "cctbx.web.change_setting.run"]], "cctbx.web.dispatcher": [[217, "module-cctbx.web.dispatcher"]], "run() (in module cctbx.web.dispatcher)": [[217, "cctbx.web.dispatcher.run"]], "cctbx.web.emma": [[218, "module-cctbx.web.emma"]], "crystal_symmetry() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.crystal_symmetry"]], "get_next() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_next"]], "get_space_group_info() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_space_group_info"]], "get_unit_cell() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_unit_cell"]], "interpret_form_data() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_form_data"]], "interpret_generic_coordinate_line() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_generic_coordinate_line"]], "model_is_too_large() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.model_is_too_large"]], "pdb_file_to_emma_model() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.pdb_file_to_emma_model"]], "run() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.run"]], "run_implementation() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.run_implementation"]], "sdb_file_to_emma_model() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.sdb_file_to_emma_model"]], "web_to_models (class in cctbx.web.emma)": [[218, "cctbx.web.emma.web_to_models"]], "cctbx.web.explore_symmetry": [[219, "module-cctbx.web.explore_symmetry"]], "expand_shelx_latt() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.expand_shelx_latt"]], "interpret_form_data() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.interpret_form_data"]], "rt_mx_analysis() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.rt_mx_analysis"]], "rt_mx_analysis_header() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.rt_mx_analysis_header"]], "run() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.run"]], "show_group_generic() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.show_group_generic"]], "show_symbols() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.show_symbols"]], "str_ev() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.str_ev"]], "cctbx.web.frac_cart": [[220, "module-cctbx.web.frac_cart"]], "interpret_form_data() (in module cctbx.web.frac_cart)": [[220, "cctbx.web.frac_cart.interpret_form_data"]], "run() (in module cctbx.web.frac_cart)": [[220, "cctbx.web.frac_cart.run"]], "cctbx.web.io_utils": [[221, "module-cctbx.web.io_utils"]], "interpret_coordinate_line() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_coordinate_line"]], "interpret_skip_columns() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_skip_columns"]], "read_scatterer() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.read_scatterer"]], "show_input_symbol() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.show_input_symbol"]], "special_position_settings_from_inp() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.special_position_settings_from_inp"]], "structure_from_inp() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.structure_from_inp"]], "structure_from_inp_pdb() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.structure_from_inp_pdb"]], "cctbx.web.iotbx_cif_validate": [[222, "module-cctbx.web.iotbx_cif_validate"]], "interpret_form_data() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.interpret_form_data"]], "run() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.run"]], "run_implementation() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.run_implementation"]], "cctbx.web.lattice_symmetry": [[223, "module-cctbx.web.lattice_symmetry"]], "interpret_form_data() (in module cctbx.web.lattice_symmetry)": [[223, "cctbx.web.lattice_symmetry.interpret_form_data"]], "run() (in module cctbx.web.lattice_symmetry)": [[223, "cctbx.web.lattice_symmetry.run"]], "cctbx.web.libtbx_help": [[224, "module-cctbx.web.libtbx_help"]], "interpret_form_data() (in module cctbx.web.libtbx_help)": [[224, "cctbx.web.libtbx_help.interpret_form_data"]], "run() (in module cctbx.web.libtbx_help)": [[224, "cctbx.web.libtbx_help.run"]], "linkexploresymmetry() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.LinkExploreSymmetry"]], "cctbx.web.multiple_cell": [[225, "module-cctbx.web.multiple_cell"]], "escape() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.escape"]], "run() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.run"]], "cctbx.web.phase_o_phrenia": [[226, "module-cctbx.web.phase_o_phrenia"]], "inp_as_xray_structures() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.inp_as_xray_structures"]], "interpret_form_data() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.interpret_form_data"]], "run() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.run"]], "sdb_files_as_xray_structures() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.sdb_files_as_xray_structures"]], "cctbx.web.replay": [[227, "module-cctbx.web.replay"]], "empty (class in cctbx.web.replay)": [[227, "cctbx.web.replay.empty"]], "run() (in module cctbx.web.replay)": [[227, "cctbx.web.replay.run"]], "cctbx.web.shelx": [[228, "module-cctbx.web.shelx"]], "interpret_form_data() (in module cctbx.web.shelx)": [[228, "cctbx.web.shelx.interpret_form_data"]], "run() (in module cctbx.web.shelx)": [[228, "cctbx.web.shelx.run"]], "cctbx.web.structure_factors": [[229, "module-cctbx.web.structure_factors"]], "interpret_form_data() (in module cctbx.web.structure_factors)": [[229, "cctbx.web.structure_factors.interpret_form_data"]], "run() (in module cctbx.web.structure_factors)": [[229, "cctbx.web.structure_factors.run"]], "cctbx.web.structure_factors_pdb": [[230, "module-cctbx.web.structure_factors_pdb"]], "interpret_form_data() (in module cctbx.web.structure_factors_pdb)": [[230, "cctbx.web.structure_factors_pdb.interpret_form_data"]], "run() (in module cctbx.web.structure_factors_pdb)": [[230, "cctbx.web.structure_factors_pdb.run"]], "cctbx.web.wyckoff": [[231, "module-cctbx.web.wyckoff"]], "interpret_form_data() (in module cctbx.web.wyckoff)": [[231, "cctbx.web.wyckoff.interpret_form_data"]], "run() (in module cctbx.web.wyckoff)": [[231, "cctbx.web.wyckoff.run"]], "cctbx.xray": [[232, "module-cctbx.xray"]], "cctbx.xray.ext": [[233, "module-cctbx.xray.ext"]], "add_gradients() (in module cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.add_gradients"]], "apply_shifts() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.apply_shifts"]], "callback_after_step() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.callback_after_step"]], "cctbx.xray.minimization": [[234, "module-cctbx.xray.minimization"]], "compute_functional_and_gradients() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.compute_functional_and_gradients"]], "compute_target() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.compute_target"]], "functional() (cctbx.xray.minimization.occupancy_penalty_exp method)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp.functional"]], "gradient() (cctbx.xray.minimization.occupancy_penalty_exp method)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp.gradient"]], "lbfgs (class in cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.lbfgs"]], "occupancy_penalty_exp (class in cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp"]], "amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.amplitude"]], "any (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.any"]], "cctbx.xray.observation_types": [[235, "module-cctbx.xray.observation_types"]], "intensity (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.intensity"]], "reconstructed_amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.reconstructed_amplitude"]], "cctbx.xray.observations": [[236, "module-cctbx.xray.observations"]], "customized_copy() (in module cctbx.xray.observations)": [[236, "cctbx.xray.observations.customized_copy"]], "anomalous_scatterer_group (class in cctbx.xray.scatterer)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group"]], "cctbx.xray.scatterer": [[237, "module-cctbx.xray.scatterer"]], "copy_to_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.copy_to_scatterers_in_place"]], "extract_from_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.extract_from_scatterers_in_place"]], "labels_refine() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.labels_refine"]], "scatterer (class in cctbx.xray.scatterer)": [[237, "cctbx.xray.scatterer.scatterer"]], "select() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.select"]], "show_summary() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.show_summary"]], "add_scatterer() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterer"]], "add_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterers"]], "adjust_occupancy() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_occupancy"]], "adjust_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_u_iso"]], "all_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.all_selection"]], "apply_rigid_body_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift"]], "apply_rigid_body_shift_obj() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift_obj"]], "apply_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_shift"]], "apply_special_position_ops_d_target_d_site() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_special_position_ops_d_target_d_site"]], "apply_symmetry_sites() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_symmetry_sites"]], "apply_symmetry_u_stars() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_symmetry_u_stars"]], "as_cif_block() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_cif_block"]], "as_cif_simple() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_cif_simple"]], "as_emma_model() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_emma_model"]], "as_pdb_file() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_pdb_file"]], "as_py_code() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_py_code"]], "asu_mappings() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asu_mappings"]], "asymmetric_unit_in_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asymmetric_unit_in_p1"]], "atomic_weights() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.atomic_weights"]], "b_iso_min_max_mean() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_min_max_mean"]], "b_iso_or_b_equiv() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_or_b_equiv"]], "by_index_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.by_index_selection"]], "cctbx.xray.structure": [[238, "module-cctbx.xray.structure"]], "center_of_mass() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.center_of_mass"]], "change_basis() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.change_basis"]], "change_hand() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.change_hand"]], "closest_distances() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.closest_distances"]], "concatenate() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.concatenate"]], "concatenate_inplace() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.concatenate_inplace"]], "conservative_pair_proxies (class in cctbx.xray.structure)": [[238, "cctbx.xray.structure.conservative_pair_proxies"]], "conservative_pair_proxies() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.conservative_pair_proxies"]], "convert_to_anisotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_anisotropic"]], "convert_to_isotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_isotropic"]], "coordinate_degrees_of_freedom_counts() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.coordinate_degrees_of_freedom_counts"]], "crystal_density() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_density"]], "crystal_symmetry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_symmetry"]], "cubic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.cubic_unit_cell_around_centered_scatterers"]], "customized_copy() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.customized_copy"]], "deep_copy_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.deep_copy_scatterers"]], "difference_vectors_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.difference_vectors_cart"]], "discard_scattering_type_registry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.discard_scattering_type_registry"]], "distances() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.distances"]], "element_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.element_selection"]], "erase_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.erase_scatterers"]], "expand_to_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.expand_to_p1"]], "extract_u_cart_plus_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.extract_u_cart_plus_u_iso"]], "extract_u_iso_or_u_equiv() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.extract_u_iso_or_u_equiv"]], "f_000() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.f_000"]], "from_cif() (cctbx.xray.structure.structure class method)": [[238, "cctbx.xray.structure.structure.from_cif"]], "from_shelx() (cctbx.xray.structure.structure class method)": [[238, "cctbx.xray.structure.structure.from_shelx"]], "grads_and_curvs_target_simple() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.grads_and_curvs_target_simple"]], "guess_scattering_type_is_a_mixture_of_xray_and_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_is_a_mixture_of_xray_and_neutron"]], "guess_scattering_type_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_neutron"]], "hd_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.hd_selection"]], "intersection_of_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.intersection_of_scatterers"]], "is_positive_definite_u() 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(iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.keys"]], "loop (class in iotbx.cif.model)": [[264, "iotbx.cif.model.loop"]], "miller_arrays_as_cif_block (class in iotbx.cif)": [[264, "iotbx.cif.miller_arrays_as_cif_block"]], "model() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.model"]], "n_columns() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.n_columns"]], "n_rows() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.n_rows"]], "name() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.name"]], "order() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.order"]], "reader (class in iotbx.cif)": [[264, "iotbx.cif.reader"]], "save (class in iotbx.cif.model)": [[264, "iotbx.cif.model.save"]], "show() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.show"]], "show() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.show"]], "show() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.show"]], "show() (iotbx.cif.model.save method)": [[264, "iotbx.cif.model.save.show"]], "show_errors() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.show_errors"]], "size() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.size"]], "sort() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.sort"]], "sort() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.sort"]], "sort() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.sort"]], "update() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.update"]], "update_column() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.update_column"]], "validate() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.validate"]], "any_file() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file"]], "any_file_fast() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file_fast"]], "any_file_fast_input (class in iotbx.file_reader)": [[265, 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property)": [[265, "iotbx.file_reader.any_file_input.file_name"]], "file_object (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_object"]], "file_server (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_server"]], "file_type (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_type"]], "find_closest_base_name() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.find_closest_base_name"]], "get_wildcard_string() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_string"]], "get_wildcard_strings() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_strings"]], "group_files (class in iotbx.file_reader)": [[265, "iotbx.file_reader.group_files"]], "guess_file_type() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.guess_file_type"]], "iotbx.file_reader": [[265, "module-iotbx.file_reader"]], "set_file_type() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.set_file_type"]], "show_summary() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.show_summary"]], "sort_by_file_type() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.sort_by_file_type"]], "splitext() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.splitext"]], "strip_shelx_format_extension() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.strip_shelx_format_extension"]], "try_all_types() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.try_all_types"]], "absolute_center_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.absolute_center_cart"]], "absolute_rt_info() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.absolute_rt_info"]], "add_crystal_symmetry_to_model_if_necessary() (iotbx.map_model_manager.map_model_manager method)": 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method)": [[266, "iotbx.map_model_manager.map_model_manager.add_model_by_id"]], "add_ncs_object() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.add_ncs_object"]], "add_to_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_to_info"]], "add_tuples_int() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.add_tuples_int"]], "apply_aniso_b_cart_to_f_array_info() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_aniso_b_cart_to_f_array_info"]], "apply_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_mask"]], "apply_mask_to_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_map"]], "apply_mask_to_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_maps"]], "apply_ncs_to_dv_results() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_ncs_to_dv_results"]], "apply_rt() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.apply_rt"]], "apply_spectral_scaling() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_spectral_scaling"]], "as_full_size_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.as_full_size_map"]], "as_map_model_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.as_map_model_manager"]], "as_map_model_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_map_model_manager"]], "as_map_model_manager() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.as_map_model_manager"]], "as_map_model_manager_with_resampled_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_map_model_manager_with_resampled_maps"]], "as_match_map_model_ncs() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_match_map_model_ncs"]], "binary_filter() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.binary_filter"]], "box_all_maps_around_density_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_density_and_shift_origin"]], "box_all_maps_around_mask_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_mask_and_shift_origin"]], "box_all_maps_around_model_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_model_and_shift_origin"]], "box_all_maps_around_unique_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_unique_and_shift_origin"]], "box_all_maps_with_bounds_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_with_bounds_and_shift_origin"]], "cart_to_grid_units() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cart_to_grid_units"]], "cc_to_other_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cc_to_other_map_manager"]], "check_model_and_set_to_match_map_if_necessary() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.check_model_and_set_to_match_map_if_necessary"]], "check_stop_file() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.check_stop_file"]], "choose_best_set() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.choose_best_set"]], "convert_tlso_group_info_to_lists() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.convert_tlso_group_info_to_lists"]], "counts() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.counts"]], "create_fine_spacing_array() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_fine_spacing_array"]], "create_map_manager_with_value_list() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_map_manager_with_value_list"]], "create_mask_around_atoms() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_atoms"]], "create_mask_around_atoms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_atoms"]], "create_mask_around_density() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_density"]], "create_mask_around_density() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_density"]], "create_mask_around_edges() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_edges"]], "create_mask_around_edges() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_edges"]], "create_mask_with_map_data() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_with_map_data"]], "create_masked_copies_of_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_masked_copies_of_maps"]], "create_spherical_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_spherical_mask"]], "crystal_symmetry() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.crystal_symmetry"]], "crystal_symmetry() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.crystal_symmetry"]], "customized_copy() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.customized_copy"]], "customized_copy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.customized_copy"]], "cutoff_values() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.cutoff_values"]], "deep_copy() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.deep_copy"]], "deep_copy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.deep_copy"]], "deep_copy() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.deep_copy"]], "delete_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.delete_mask"]], "density_at_model_sites() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.density_at_model_sites"]], "density_at_sites_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.density_at_sites_cart"]], "dummy_map_manager() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.dummy_map_manager"]], "duplicate_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.duplicate_id"]], "duplicate_map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, 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module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_average_scale_factors"]], "get_boxes_to_tile_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_boxes_to_tile_map"]], "get_cb_resseq_to_skip() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_cb_resseq_to_skip"]], "get_center_of_box_frac() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_center_of_box_frac"]], "get_coordinate_shift() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.get_coordinate_shift"]], "get_counts_and_histograms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_counts_and_histograms"]], "get_density_along_line() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_density_along_line"]], "get_diffs_for_matching_target_and_model() 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"iotbx.shelx.crystal_symmetry_from_ins": [[271, "module-iotbx.shelx.crystal_symmetry_from_ins"]], "iotbx.shelx.hklf": [[271, "module-iotbx.shelx.hklf"]], "iotbx.shelx.lexer": [[271, "module-iotbx.shelx.lexer"]], "iotbx.shelx.parsers": [[271, "module-iotbx.shelx.parsers"]], "iotbx.shelx.tokens": [[271, "module-iotbx.shelx.tokens"]], "iotbx.shelx.write_ins": [[271, "module-iotbx.shelx.write_ins"]], "iotbx.shelx.writer": [[271, "module-iotbx.shelx.writer"]], "issue_merohedral_twinning() (iotbx.shelx.parsers.instruction_parser method)": [[271, "iotbx.shelx.parsers.instruction_parser.issue_merohedral_twinning"]], "lex_scatterer() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.lex_scatterer"]], "miller_array_export_as_shelx_hklf() (in module iotbx.shelx.hklf)": [[271, "iotbx.shelx.hklf.miller_array_export_as_shelx_hklf"]], "name (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.name"]], "number (iotbx.shelx.tokens.residue_token attribute)": [[271, "iotbx.shelx.tokens.residue_token.number"]], "parse() (iotbx.shelx.parsers.crystal_symmetry_parser method)": [[271, "iotbx.shelx.parsers.crystal_symmetry_parser.parse"]], "parse() (iotbx.shelx.parsers.parser method)": [[271, "iotbx.shelx.parsers.parser.parse"]], "parse_restraints() (iotbx.shelx.parsers.restraint_parser method)": [[271, "iotbx.shelx.parsers.restraint_parser.parse_restraints"]], "parse_smtbx_refinement_model() (in module iotbx.shelx)": [[271, "iotbx.shelx.parse_smtbx_refinement_model"]], "parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.parser"]], "plus_minus (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.plus_minus"]], "plus_minus (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.plus_minus"]], "process_occupancies_depending_on_free_variable() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.process_occupancies_depending_on_free_variable"]], "process_possible_constrained_occupancy() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.process_possible_constrained_occupancy"]], "process_possible_u_iso_constraints() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.process_possible_u_iso_constraints"]], "reader (class in iotbx.shelx.hklf)": [[271, "iotbx.shelx.hklf.reader"]], "residue_number (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.residue_number"]], "residue_number (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.residue_number"]], "residue_token (class in iotbx.shelx.tokens)": [[271, "iotbx.shelx.tokens.residue_token"]], "restraint_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.restraint_parser"]], "restraint_types (iotbx.shelx.parsers.restraint_parser attribute)": [[271, "iotbx.shelx.parsers.restraint_parser.restraint_types"]], "shelx_commands (iotbx.shelx.lexer.command_stream attribute)": [[271, "iotbx.shelx.lexer.command_stream.shelx_commands"]], "shelxd() (in module iotbx.shelx.write_ins)": [[271, "iotbx.shelx.write_ins.shelxd"]], "symm_space (iotbx.shelx.lexer.command_stream attribute)": [[271, "iotbx.shelx.lexer.command_stream.symm_space"]], "symmetry (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.symmetry"]], "variable_decoder (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.variable_decoder"]], "wavelength_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.wavelength_parser"]], "wavelengths() (iotbx.shelx.hklf.reader method)": [[271, "iotbx.shelx.hklf.reader.wavelengths"]], "as_miller_array() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.as_miller_array"]], "as_miller_arrays() (iotbx.xds.integrate_hkl.reader method)": [[272, "iotbx.xds.integrate_hkl.reader.as_miller_arrays"]], "as_miller_arrays() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.as_miller_arrays"]], "batch_as_miller_array() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.batch_as_miller_array"]], "column_index() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.column_index"]], "crystal_symmetry() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.crystal_symmetry"]], "find_version() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.find_version"]], "get_rhs() (in module iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.get_rhs"]], "iotbx.xds.integrate_hkl": [[272, "module-iotbx.xds.integrate_hkl"]], "iotbx.xds.read_ascii": [[272, "module-iotbx.xds.read_ascii"]], "iotbx.xds.spot_xds": [[272, "module-iotbx.xds.spot_xds"]], "iotbx.xds.xds_inp": [[272, "module-iotbx.xds.xds_inp"]], "iotbx.xds.xparm": [[272, "module-iotbx.xds.xparm"]], "is_integrate_hkl_file() (iotbx.xds.integrate_hkl.reader static method)": [[272, "iotbx.xds.integrate_hkl.reader.is_integrate_hkl_file"]], "is_xds_inp_file() (iotbx.xds.xds_inp.reader static method)": [[272, "iotbx.xds.xds_inp.reader.is_xds_inp_file"]], "is_xparm_file() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.is_xparm_file"]], "miller_set() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.miller_set"]], "parse_lines() (iotbx.xds.xds_inp.reader method)": [[272, "iotbx.xds.xds_inp.reader.parse_lines"]], "parse_version_1_tokens() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.parse_version_1_tokens"]], "parse_version_2_tokens() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.parse_version_2_tokens"]], "read_file() (iotbx.xds.integrate_hkl.reader method)": [[272, "iotbx.xds.integrate_hkl.reader.read_file"]], "read_file() (iotbx.xds.spot_xds.reader method)": [[272, "iotbx.xds.spot_xds.reader.read_file"]], "read_file() (iotbx.xds.xds_inp.reader method)": [[272, "iotbx.xds.xds_inp.reader.read_file"]], "read_file() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.read_file"]], "reader (class in iotbx.xds.integrate_hkl)": [[272, "iotbx.xds.integrate_hkl.reader"]], "reader (class in iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.reader"]], "reader (class in iotbx.xds.spot_xds)": [[272, "iotbx.xds.spot_xds.reader"]], "reader (class in iotbx.xds.xds_inp)": [[272, "iotbx.xds.xds_inp.reader"]], "reader (class in iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.reader"]], "show() (iotbx.xds.xparm.writer method)": [[272, "iotbx.xds.xparm.writer.show"]], "write() (in module iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.write"]], "write_file() (iotbx.xds.spot_xds.writer method)": [[272, "iotbx.xds.spot_xds.writer.write_file"]], "write_file() (iotbx.xds.xparm.writer method)": [[272, "iotbx.xds.xparm.writer.write_file"]], "writer (class in iotbx.xds.spot_xds)": [[272, "iotbx.xds.spot_xds.writer"]], "writer (class in iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.writer"]], "autotype (class in libtbx)": [[273, "libtbx.AutoType"]], "add_if_missing() (libtbx.group_args method)": [[273, "libtbx.group_args.add_if_missing"]], "adopt_init_args() (in module libtbx)": [[273, "libtbx.adopt_init_args"]], "adopt_optional_init_args() (in module libtbx)": [[273, "libtbx.adopt_optional_init_args"]], "copy() (libtbx.group_args method)": [[273, "libtbx.group_args.copy"]], "dict_with_default_0 (class in libtbx)": [[273, "libtbx.dict_with_default_0"]], "group_args (class in libtbx)": [[273, "libtbx.group_args"]], "libtbx": [[273, "module-libtbx"]], "merge() (libtbx.group_args method)": [[273, "libtbx.group_args.merge"]], "mutable (class in libtbx)": [[273, "libtbx.mutable"]], "slots_getstate_setstate (class in libtbx)": [[273, "libtbx.slots_getstate_setstate"]], "slots_getstate_setstate_default_initializer (class in libtbx)": [[273, "libtbx.slots_getstate_setstate_default_initializer"]], "unpicklable (class in libtbx)": [[273, "libtbx.unpicklable"]], "detect_problem() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.detect_problem"]], "enable_multiprocessing_if_possible() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.enable_multiprocessing_if_possible"]], "get_processes() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.get_processes"]], "parallel_map() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.parallel_map"]], "pool_map() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.pool_map"]], "programtemplate (class in libtbx.program_template)": [[275, "libtbx.program_template.ProgramTemplate"]], "__init__() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.__init__"]], "clean_up() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.clean_up"]], "custom_init() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.custom_init"]], "get_results() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.get_results"]], "run() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.run"]], "validate() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.validate"]], "dfc (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.DFC"]], "fc (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FC"]], "filled (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FILLED"]], "fo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FO"]], "mfo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.MFO"]], "anomalous (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous"]], "anomalous_residual (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous_residual"]], "create_target_functors() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.create_target_functors"]], "error() (mmtbx.map_names method)": [[276, "mmtbx.map_names.error"]], "f_obs_filled (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.f_obs_filled"]], "fmodel_neutron (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_neutron"]], "fmodel_neutron() (mmtbx.fmodels method)": [[276, "id0"]], "fmodel_xray (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_xray"]], "fmodel_xray() (mmtbx.fmodels method)": [[276, "id1"]], "fmodels (class in mmtbx)": [[276, "mmtbx.fmodels"]], "format() (mmtbx.map_names method)": [[276, "mmtbx.map_names.format"]], "k (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.k"]], "map_names (class in mmtbx)": [[276, "mmtbx.map_names"]], "ml_map (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.ml_map"]], "mmtbx": [[276, "module-mmtbx"]], "n (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.n"]], "neutron_refinement (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.neutron_refinement"]], "neutron_scattering_dict (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.neutron_scattering_dict"]], "phaser_sad_llg (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.phaser_sad_llg"]], "prepare_target_functors_for_minimization() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.prepare_target_functors_for_minimization"]], "pseudo_deep_copy() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.pseudo_deep_copy"]], "resolution_filter() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.resolution_filter"]], "show_comprehensive() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_comprehensive"]], "show_short() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_short"]], "show_targets() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_targets"]], "target_and_gradients() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_and_gradients"]], "target_functions_are_invariant_under_allowed_origin_shifts() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functions_are_invariant_under_allowed_origin_shifts"]], "target_functor_result_neutron() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functor_result_neutron"]], "target_functor_result_xray() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functor_result_xray"]], "update() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update"]], "update_all_scales() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update_all_scales"]], "update_xray_structure() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update_xray_structure"]], "xray_scattering_dict (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.xray_scattering_dict"]], "align_model() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.align_model"]], "anneal() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.anneal"]], "apply_final() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.apply_final"]], "as_multi_model_hierarchy() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.as_multi_model_hierarchy"]], "atom_group_as_hierarchy() (in module mmtbx.building)": [[277, "mmtbx.building.atom_group_as_hierarchy"]], "atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_fofc_map_level"]], "atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_two_fofc_map_level"]], "atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_outside_density"]], "box_build_refine_base (class in mmtbx.building)": [[277, "mmtbx.building.box_build_refine_base"]], "cc_model_map() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.cc_model_map"]], "chain_id (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.chain_id"]], "conformation_scorer (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer"]], "correct_sequence() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.correct_sequence"]], "density_at_atom() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.density_at_atom"]], "ensembler (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.ensembler"]], "examine_model() (mmtbx.building.make_library.extract_related_models method)": [[277, "mmtbx.building.make_library.extract_related_models.examine_model"]], "extend_and_refine (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_and_refine"]], "extend_protein_model() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_protein_model"]], "extend_residue() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_residue"]], "extract_and_superpose() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_and_superpose"]], "extract_iselection() (in module mmtbx.building)": [[277, "mmtbx.building.extract_iselection"]], "extract_peptide_fragments_by_sequence() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_peptide_fragments_by_sequence"]], "extract_related_models (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_related_models"]], "fetch_similar_pdb_ids() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.fetch_similar_pdb_ids"]], "find_similar_chains() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.find_similar_chains"]], "fit_residue_in_box() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.fit_residue_in_box"]], "fraction_of_nearby_grid_points_above_cutoff() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.fraction_of_nearby_grid_points_above_cutoff"]], "generate_sidechain_clusters() (in module mmtbx.building)": [[277, "mmtbx.building.generate_sidechain_clusters"]], "geometry_minimization() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.geometry_minimization"]], "get_difference_maps() (in module mmtbx.building)": [[277, "mmtbx.building.get_difference_maps"]], "get_model_map_stats() (in module mmtbx.building)": [[277, "mmtbx.building.get_model_map_stats"]], "get_nearby_water_selection() (in module mmtbx.building)": [[277, "mmtbx.building.get_nearby_water_selection"]], "get_non_hydrogen_atom_indices() (in module mmtbx.building)": [[277, "mmtbx.building.get_non_hydrogen_atom_indices"]], "get_selected_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.get_selected_sites"]], "get_window_around_residue() (in module mmtbx.building)": [[277, "mmtbx.building.get_window_around_residue"]], "identity (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.identity"]], "is_stub_residue() (in module mmtbx.building)": [[277, "mmtbx.building.is_stub_residue"]], "iter_residue_groups() (in module mmtbx.building)": [[277, "mmtbx.building.iter_residue_groups"]], "join_hierarchies() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.join_hierarchies"]], "load_all_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_all_models_in_directory"]], "load_pdb_models() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_pdb_models"]], "load_related_models_from_pdb() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_from_pdb"]], "load_related_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_in_directory"]], "local_density_quality (class in mmtbx.building)": [[277, "mmtbx.building.local_density_quality"]], "max_fofc_value() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.max_fofc_value"]], "mean_density_at_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.mean_density_at_sites"]], "mmtbx.building": [[277, "module-mmtbx.building"]], "mmtbx.building.extend_sidechains": [[277, "module-mmtbx.building.extend_sidechains"]], "mmtbx.building.make_library": [[277, "module-mmtbx.building.make_library"]], "number_of_atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_below_fofc_map_level"]], "number_of_atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_below_two_fofc_map_level"]], "number_of_atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_outside_density"]], "only_residue() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.only_residue"]], "pdb_hierarchy (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.pdb_hierarchy"]], "prefilter (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.prefilter"]], "real_space_refine() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.real_space_refine"]], "realign() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.realign"]], "refit_residues() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.refit_residues"]], "related_chain (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.related_chain"]], "remove_sidechain_atoms() (in module mmtbx.building)": [[277, "mmtbx.building.remove_sidechain_atoms"]], "reprocess_pdb() (in module mmtbx.building)": [[277, "mmtbx.building.reprocess_pdb"]], "reset() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.reset"]], "residue_density_quality() (in module mmtbx.building)": [[277, "mmtbx.building.residue_density_quality"]], "residues_are_adjacent() (in module mmtbx.building)": [[277, "mmtbx.building.residues_are_adjacent"]], "restrain_atoms() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.restrain_atoms"]], "results() (mmtbx.building.make_library.extract_related_models method)": [[277, "mmtbx.building.make_library.extract_related_models.results"]], "run_real_space_annealing() (in module mmtbx.building)": [[277, "mmtbx.building.run_real_space_annealing"]], "selection_by_symmetry() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.selection_by_symmetry"]], "show_atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.show_atoms_outside_density"]], "show_chain_resseq_ranges() (in module mmtbx.building)": [[277, "mmtbx.building.show_chain_resseq_ranges"]], "source_info (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.source_info"]], "update() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.update"]], "update_coordinates() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_coordinates"]], "update_original_coordinates() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_original_coordinates"]], "update_sites_from_pdb_atoms() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_sites_from_pdb_atoms"]], "anisotropic_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.anisotropic_scaling"]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.apply_back_trace_of_overall_exp_scale_matrix"]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_back_trace_of_overall_exp_scale_matrix"]], "apply_overall_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_overall_scale"]], "b_cart() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.b_cart"]], "b_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.b_sols"]], "bulk_solvent_and_scales (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales"]], "bulk_solvent_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.bulk_solvent_scaling"]], "estimate_scale_k1() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.estimate_scale_k1"]], "format_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.format_scale_matrix"]], "format_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.format_scale_matrix"]], "get_k_total() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.get_k_total"]], "is_converged() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_converged"]], "is_flags_good() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_flags_good"]], "k_anisotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_anisotropic"]], "k_anisotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_anisotropic"]], "k_isotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_isotropic"]], "k_isotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_isotropic"]], "k_mask_grid_search() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_mask_grid_search"]], "k_masks() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_masks"]], "k_masks() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_masks"]], "k_sol_b_sol_b_cart_minimizer() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.k_sol_b_sol_b_cart_minimizer"]], "k_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_sols"]], "kb_range() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.kb_range"]], "ksol_bsol_result (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.ksol_bsol_result"]], "mmtbx.bulk_solvent": [[278, "module-mmtbx.bulk_solvent"]], "mmtbx.bulk_solvent.bulk_solvent_and_scaling": [[278, "module-mmtbx.bulk_solvent.bulk_solvent_and_scaling"]], "mmtbx.bulk_solvent.scaler": [[278, "module-mmtbx.bulk_solvent.scaler"]], "moving_average() (in module mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.moving_average"]], "overall_isotropic_kb_estimate() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.overall_isotropic_kb_estimate"]], "populate_bin_to_individual_k_mask_linear_interpolation() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.populate_bin_to_individual_k_mask_linear_interpolation"]], "r_all() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.r_all"]], "r_all() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_all"]], "r_factor() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.r_factor"]], "r_factor() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_factor"]], "r_work() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_work"]], "run (class in mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.run"]], "run_simple() (in module mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.run_simple"]], "set_k_isotropic_exp() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.set_k_isotropic_exp"]], "show() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.show"]], "smooth() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.smooth"]], "tmp (class in mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.tmp"]], "try_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.try_scale"]], "u_star() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.u_star"]], "aligncablammeasures (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures"]], "capseudos() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.CApseudos"]], "copseudodihedrals() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.COpseudodihedrals"]], "findsimilarcablamregions (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions"]], "add_bond() (mmtbx.cablam.cablam_fingerprints.residue method)": [[279, "mmtbx.cablam.cablam_fingerprints.residue.add_bond"]], "add_probe_data() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.add_probe_data"]], "add_residue() (mmtbx.cablam.cablam_fingerprints.motif method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif.add_residue"]], "add_target_atom() (mmtbx.cablam.cablam_fingerprints.bond method)": [[279, "mmtbx.cablam.cablam_fingerprints.bond.add_target_atom"]], "add_to_instance() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.add_to_instance"]], "analyze_pdb() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb"]], "analyze_pdb_ca() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb_ca"]], "analyze_pdb_gui() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb_gui"]], "assign_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.assign_sec_struc"]], "bond (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.bond"]], "build_superposition() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.build_superposition"]], "ca_measures() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.ca_measures"]], "cablam_align_wrapper() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.cablam_align_wrapper"]], "cablam_key() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.cablam_key"]], "cablam_measures() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.cablam_measures"]], "cablam_multicrit_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.cablam_multicrit_kin"]], "cablam_residues (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.cablam_residues"]], "cablam_validation (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.cablam_validation"]], "check_for_motif() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.check_for_motif"]], "check_prolines() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.check_prolines"]], "check_protein() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.check_protein"]], "check_resname() (mmtbx.cablam.cablam_fingerprints.residue method)": [[279, "mmtbx.cablam.cablam_fingerprints.residue.check_resname"]], "condense_simple_aligned_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.condense_simple_aligned_regions"]], "consecutive() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.consecutive"]], "construct_linked_residues() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.construct_linked_residues"]], "cross() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.cross"]], "csv_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.csv_header"]], "csv_print() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.csv_print"]], "do_move() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.do_move"]], "dot() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.dot"]], "fail_cis_or_trans_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_cis_or_trans_check"]], "fail_forbidden_bond_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_forbidden_bond_check"]], "fail_index_match() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_index_match"]], "fail_required_bond_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_required_bond_check"]], "fail_residue_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_residue_check"]], "fails_cis_check() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.fails_cis_check"]], "fetch_ca_expectations() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_ca_expectations"]], "fetch_cis_trans_proline() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_cis_trans_proline"]], "fetch_fingerprints() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fetch_fingerprints"]], "fetch_motifs() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_motifs"]], "fetch_peptide_expectations() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_peptide_expectations"]], "find_all_residue_stats() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_all_residue_stats"]], "find_ca_outliers() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_ca_outliers"]], "find_partial_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_partial_sec_struc"]], "find_peptide_outliers() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_peptide_outliers"]], "find_whole_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_whole_sec_struc"]], "firstalt() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.firstalt"]], "get_all_labels() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.get_all_labels"]], "get_chain_selection() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.get_chain_selection"]], "get_continuous_segments() (mmtbx.cablam.cablam_align.cablam_residues method)": [[279, "mmtbx.cablam.cablam_align.cablam_residues.get_continuous_segments"]], "get_measures() (mmtbx.cablam.cablam_align.findsimilarcablamregions method)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions.get_measures"]], "getatomxyz() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.getatomxyz"]], "give_ca_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_ca_kin"]], "give_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_kin"]], "give_points() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_points"]], "give_text() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_text"]], "has_all_measures() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.has_all_measures"]], "helix_or_sheet() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.helix_or_sheet"]], "helix_or_sheet_res() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.helix_or_sheet_res"]], "id_to_str() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.id_to_str"]], "id_with_resname() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.id_with_resname"]], "interpretation() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.interpretation"]], "is_complete() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.is_complete"]], "kin_frame() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_frame"]], "kin_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_header"]], "kin_print() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print"]], "kin_print_by_instance() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_by_instance"]], "kin_print_by_instance_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_by_instance_header"]], "kin_print_probe() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe"]], "kin_print_probe_annote() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe_annote"]], "kin_print_probe_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe_header"]], "linked_residue (class in mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.linked_residue"]], "make_pickle() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.make_pickle"]], "make_probe_data() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.make_probe_data"]], "mmtbx.cablam": [[279, "module-mmtbx.cablam"]], "mmtbx.cablam.cablam_align": [[279, "module-mmtbx.cablam.cablam_align"]], "mmtbx.cablam.cablam_fingerprints": [[279, "module-mmtbx.cablam.cablam_fingerprints"]], "mmtbx.cablam.cablam_math": [[279, "module-mmtbx.cablam.cablam_math"]], "mmtbx.cablam.cablam_res": [[279, "module-mmtbx.cablam.cablam_res"]], "mmtbx.cablam.cablam_training": [[279, "module-mmtbx.cablam.cablam_training"]], "mmtbx.cablam.cablam_validate": [[279, "module-mmtbx.cablam.cablam_validate"]], "motif (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.motif"]], "motif_chunk (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk"]], "motif_guess (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_guess"]], "motif_instance (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance"]], "motif_value (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_value"]], "mp_id() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.mp_id"]], "not_enough_pdbs() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.not_enough_pdbs"]], "old_kin_print_probe_annote() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.old_kin_print_probe_annote"]], "omegacalc() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.omegacalc"]], "oneline() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.oneline"]], "oneline_header() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.oneline_header"]], "perpdist() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.perpdist"]], "perptersect() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.perptersect"]], "phipsi() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.phipsi"]], "print_aligned_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_aligned_regions"]], "print_cablam_markup_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_cablam_markup_kin"]], "print_helix_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_helix_record"]], "print_helix_sheet_records() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_helix_sheet_records"]], "print_pdb_with_new_helix_sheet_records() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_pdb_with_new_helix_sheet_records"]], "print_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_record"]], "print_region() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_region"]], "print_sheet_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_sheet_record"]], "print_simple_similar_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_simple_similar_regions"]], "print_threeten_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_threeten_record"]], "printtocsv() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.printtocsv"]], "printtokin() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.printtokin"]], "prune_alts() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.prune_alts"]], "prunerestype() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.prunerestype"]], "removelinks() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.removelinks"]], "res_seq_by_instance() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.res_seq_by_instance"]], "residue (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.residue"]], "run() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.run"]], "run() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.run"]], "run() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.run"]], "seq_dist() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.seq_dist"]], "setup() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.setup"]], "simple_align_measures() (mmtbx.cablam.cablam_align.findsimilarcablamregions method)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions.simple_align_measures"]], "skipcheck() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.skipcheck"]], "stripb() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.stripB"]], "target_atom (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.target_atom"]], "taucalc() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.taucalc"]], "trim_motifs() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.trim_motifs"]], "usage() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.usage"]], "usage() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.usage"]], "usage() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.usage"]], "veclen() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.veclen"]], "vectorize() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.vectorize"]], "mmtbx.cablam.fingerprints": [[280, "module-mmtbx.cablam.fingerprints"]], "mmtbx.cablam.fingerprints.antiparallel_beta": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta"]], "mmtbx.cablam.fingerprints.antiparallel_beta_bridge": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta_bridge"]], "mmtbx.cablam.fingerprints.how_to": [[280, "module-mmtbx.cablam.fingerprints.how_to"]], "mmtbx.cablam.fingerprints.parallel_beta": [[280, "module-mmtbx.cablam.fingerprints.parallel_beta"]], "mmtbx.cablam.fingerprints.regular_helix_definitions": [[280, "module-mmtbx.cablam.fingerprints.regular_helix_definitions"]], "empty (class in mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.empty"]], "find_data_dir() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.find_data_dir"]], "generate_chemical_components_codes() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.generate_chemical_components_codes"]], "get_alternative_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_alternative_name"]], "get_atom_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_names"]], "get_atom_type_symbol() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_type_symbol"]], "get_bond_pairs() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_bond_pairs"]], "get_cif_dictionary() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_dictionary"]], "get_cif_filename() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_filename"]], "get_field_simple() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_field_simple"]], "get_func() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_func"]], "get_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_group"]], "get_header() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_header"]], "get_hydrogen_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_hydrogen_names"]], "get_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_name"]], "get_restraints_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_restraints_group"]], "get_smiles() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_smiles"]], "get_type() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_type"]], "get_typed_field() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_typed_field"]], "is_code() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_code"]], "is_residue_specified() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_residue_specified"]], "mmtbx.chemical_components": [[281, "module-mmtbx.chemical_components"]], "mmtbx.chemical_components.cif_parser": [[281, "module-mmtbx.chemical_components.cif_parser"]], "run() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.run"]], "run2() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.run2"]], "smart_split_cif_line() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.smart_split_cif_line"]], "args (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.args"]], "check_files() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.check_files"]], "cif_file_names (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_file_names"]], "cif_objects (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_objects"]], "create_model_manager() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.create_model_manager"]], "crystal_symmetry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.crystal_symmetry"]], "f_obs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.f_obs"]], "fmodel (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.fmodel"]], "generate_master_phil_with_inputs() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generate_master_phil_with_inputs"]], "generic_simple_input_phil() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generic_simple_input_phil"]], "geometry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.geometry"]], "hl_coeffs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.hl_coeffs"]], "intensity_flag (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.intensity_flag"]], "load_and_validate_unmerged_data() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.load_and_validate_unmerged_data"]], "load_model_and_data (class in mmtbx.command_line)": [[282, "mmtbx.command_line.load_model_and_data"]], "log (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.log"]], "master_phil (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.master_phil"]], "miller_arrays (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.miller_arrays"]], "mmtbx.command_line": [[282, "module-mmtbx.command_line"]], "params (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.params"]], "pdb_file_names (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_file_names"]], "pdb_hierarchy (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_hierarchy"]], "pdb_inp (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_inp"]], "processed_pdb_file (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.processed_pdb_file"]], "r_free_flags (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.r_free_flags"]], "raw_data (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_data"]], "raw_flags (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_flags"]], "save_data_mtz() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.save_data_mtz"]], "sequence (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.sequence"]], "show_symmetry_error() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.show_symmetry_error"]], "start_log_file() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.start_log_file"]], "test_flag_value (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.test_flag_value"]], "unknown_residues_error_message (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unknown_residues_error_message"]], "unknown_residues_flag (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unknown_residues_flag"]], "unmerged_i_obs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unmerged_i_obs"]], "validate_input_params() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.validate_input_params"]], "working_phil (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.working_phil"]], "xray_structure (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.xray_structure"]], "bond_angle_registry (class in mmtbx.conformation_dependent_library.bond_angle_registry)": [[283, "mmtbx.conformation_dependent_library.bond_angle_registry.bond_angle_registry"]], "convert_dict_to_excel() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_excel"]], "convert_dict_to_gnuplot() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_gnuplot"]], "convert_dict_to_kin2dcont() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_kin2Dcont"]], "convert_dict_to_scilab() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_scilab"]], "custom_cdl_dict (class in mmtbx.conformation_dependent_library.cdl_database)": [[283, "mmtbx.conformation_dependent_library.cdl_database.custom_cdl_dict"]], "generate_dna_rna_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_dna_rna_fragments"]], "generate_protein_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_fragments"]], "generate_protein_threes() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_threes"]], "generate_protein_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_tuples"]], "generate_residue_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_residue_tuples"]], "get_db_result() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_db_result"]], "get_grid_values() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_grid_values"]], "get_index() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_index"]], "get_managers() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_managers"]], "get_min_max_table() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_min_max_table"]], "get_rdl_database() (in module mmtbx.conformation_dependent_library.rdl_database)": [[283, "mmtbx.conformation_dependent_library.rdl_database.get_rdl_database"]], "get_restraint_values() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.get_restraint_values"]], "interpolate_2d() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_2d"]], "interpolate_at_point() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_at_point"]], "mmtbx.conformation_dependent_library": [[283, "module-mmtbx.conformation_dependent_library"]], "mmtbx.conformation_dependent_library.altloc_weighting": [[283, "module-mmtbx.conformation_dependent_library.altloc_weighting"]], "mmtbx.conformation_dependent_library.bond_angle_registry": [[283, "module-mmtbx.conformation_dependent_library.bond_angle_registry"]], "mmtbx.conformation_dependent_library.cdl_database": [[283, "module-mmtbx.conformation_dependent_library.cdl_database"]], "mmtbx.conformation_dependent_library.rdl_database": [[283, "module-mmtbx.conformation_dependent_library.rdl_database"]], "mmtbx.conformation_dependent_library.tst_cdl": [[283, "module-mmtbx.conformation_dependent_library.tst_cdl"]], "mmtbx.conformation_dependent_library.utils": [[283, "module-mmtbx.conformation_dependent_library.utils"]], "print_grid() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.print_grid"]], "restraints_show() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.restraints_show"]], "round_to_ten() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.round_to_ten"]], "run() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.run"]], "run() (in module mmtbx.conformation_dependent_library.altloc_weighting)": [[283, "mmtbx.conformation_dependent_library.altloc_weighting.run"]], "run() (in module mmtbx.conformation_dependent_library.cdl_database)": [[283, "mmtbx.conformation_dependent_library.cdl_database.run"]], "run() (in module mmtbx.conformation_dependent_library.rdl_database)": [[283, "mmtbx.conformation_dependent_library.rdl_database.run"]], "run() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.run"]], "run_apply() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.run_apply"]], "test_average() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_average"]], "test_cdl_lookup() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cdl_lookup"]], "test_cis_trans_peptide() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cis_trans_peptide"]], "test_phi_psi_key() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_phi_psi_key"]], "test_res_type() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_res_type"]], "test_threes_methods() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_threes_methods"]], "update_restraints() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.update_restraints"]], "update_restraints() (in module mmtbx.conformation_dependent_library.altloc_weighting)": [[283, "mmtbx.conformation_dependent_library.altloc_weighting.update_restraints"]], "adp_refinement() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.adp_refinement"]], "build_den_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_proxies"]], "build_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_restraints"]], "bulk_solvent_and_scale() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.bulk_solvent_and_scale"]], "check_den_pair_consistency() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.check_den_pair_consistency"]], "count_atoms_per_chain() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.count_atoms_per_chain"]], "den_restraints (class in mmtbx.den)": [[284, "mmtbx.den.den_restraints"]], "distance_squared() (in module mmtbx.den)": [[284, "mmtbx.den.distance_squared"]], "dump_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.dump_den_network"]], "exercise() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.exercise"]], "find_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.find_atom_pairs"]], "get_current_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_current_eq_distances"]], "get_den_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_den_atom_pairs"]], "get_n_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_n_proxies"]], "get_optimization_grid() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_optimization_grid"]], "get_selection_strings() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_selection_strings"]], "import_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.import_eq_distances"]], "load_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.load_den_network"]], "manager (class in mmtbx.den.refinement)": [[284, "mmtbx.den.refinement.manager"]], "minimize() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.minimize"]], "mmtbx.den": [[284, "module-mmtbx.den"]], "mmtbx.den.plot_weights": [[284, "module-mmtbx.den.plot_weights"]], "mmtbx.den.refinement": [[284, "module-mmtbx.den.refinement"]], "output_kinemage() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.output_kinemage"]], "plot_weights_pyplot() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.plot_weights_pyplot"]], "proxy_select() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.proxy_select"]], "remove_non_matching_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.remove_non_matching_pairs"]], "select_random_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.select_random_den_restraints"]], "show_den_opt_summary_cartesian() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.show_den_opt_summary_cartesian"]], "show_den_opt_summary_torsion() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.show_den_opt_summary_torsion"]], "show_den_summary() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.show_den_summary"]], "target_and_gradients() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.target_and_gradients"]], "try_den_weight_cartesian() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.try_den_weight_cartesian"]], "try_den_weight_torsion() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.try_den_weight_torsion"]], "update_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.update_eq_distances"]], "active_indices (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.active_indices"]], "add_cycle() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.add_cycle"]], "anisotropic_correction() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.anisotropic_correction"]], "calculate_solvent_mask() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.calculate_solvent_mask"]], "compute_map() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_map"]], "compute_map_coefficients() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_map_coefficients"]], "compute_phase_source() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_phase_source"]], "d_min (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.d_min"]], "density_modification (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.density_modification"]], "density_truncation() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.density_truncation"]], "dm_stats (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.dm_stats"]], "extract_loggraph() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.extract_loggraph"]], "f_obs_active (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.f_obs_active"]], "format_summary() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.format_summary"]], "get_cycle_stats() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_cycle_stats"]], "get_fom_for_plot() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_fom_for_plot"]], "get_stats() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.get_stats"]], "histogram() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.histogram"]], "hl_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.hl_coeffs_in_original_setting"]], "local_standard_deviation_map (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.local_standard_deviation_map"]], "map_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.map_coeffs_in_original_setting"]], "mask() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.mask"]], "matthews_analysis() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.matthews_analysis"]], "miller_array_in_original_setting() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.miller_array_in_original_setting"]], "mmtbx.density_modification": [[285, "module-mmtbx.density_modification"]], "ncs_averaging() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.ncs_averaging"]], "next_cycle() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.next_cycle"]], "radius (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.radius"]], "rms() (in module mmtbx.density_modification)": [[285, "mmtbx.density_modification.rms"]], "show_cycle_summary() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.show_cycle_summary"]], "solvent_adjust() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_adjust"]], "solvent_flattening() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flattening"]], "solvent_flipping() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flipping"]], "start_and_end_fom() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.start_and_end_fom"]], "alternate_conformations_as_multiple_models() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.alternate_conformations_as_multiple_models"]], "altloc (mmtbx.disorder.analyze_model.atom_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.altloc"]], "append_residue_group() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.append_residue_group"]], "atom_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy"]], "atom_groups() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.atom_groups"]], "atoms() (mmtbx.disorder.analyze_model.atom_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.atoms"]], "atoms_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy"]], "backrub_angle (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.backrub_angle"]], "backrub_residue (class in mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.backrub_residue"]], "carbonyl_oxygen_angle() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.carbonyl_oxygen_angle"]], "circ_len() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_len"]], "circ_mean() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_mean"]], "circ_stddev() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_stddev"]], "detect_sequence_disorder() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.detect_sequence_disorder"]], "disordered_segment (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.disordered_segment"]], "evaluate_backrub_pair_impl() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.evaluate_backrub_pair_impl"]], "extract_b() (mmtbx.disorder.analyze_model.atoms_proxy method)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy.extract_b"]], "extract_backrub_residue_groups() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.extract_backrub_residue_groups"]], "extract_occ() (mmtbx.disorder.analyze_model.atoms_proxy method)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy.extract_occ"]], "extract_validation_results() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.extract_validation_results"]], "find_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_backrubs"]], "find_ensemble_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_ensemble_backrubs"]], "find_peptide_flips() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.find_peptide_flips"]], "get_all_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_all_conformer_distances"]], "get_calphas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_calphas"]], "get_cbetas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_cbetas"]], "get_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_conformer_distances"]], "get_nconfs() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.get_nconfs"]], "get_previous_conformer() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_previous_conformer"]], "i_mod (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.i_mod"]], "icode (mmtbx.disorder.analyze_model.residue_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.icode"]], "id_str (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.id_str"]], "id_str() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.id_str"]], "is_joined_at_calpha() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.is_joined_at_calpha"]], "is_part_of_segment() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.is_part_of_segment"]], "j_mod (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.j_mod"]], "max_distance_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.max_distance_between_conformers"]], "max_distance_between_conformers() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_distance_between_conformers"]], "max_rmsd_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.max_rmsd_between_conformers"]], "max_rmsd_between_conformers() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_rmsd_between_conformers"]], "minimum_atom_group_occupancy() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.minimum_atom_group_occupancy"]], "mmtbx.disorder": [[286, "module-mmtbx.disorder"]], "mmtbx.disorder.analyze_model": [[286, "module-mmtbx.disorder.analyze_model"]], "mmtbx.disorder.backbone": [[286, "module-mmtbx.disorder.backbone"]], "n_cbeta_outliers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_cbeta_outliers"]], "n_confs() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_confs"]], "n_confs_max() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_confs_max"]], "n_outliers_of_type() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_outliers_of_type"]], "n_partial_splits() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_partial_splits"]], "n_residues() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_residues"]], "n_rotamer_changes() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_rotamer_changes"]], "only_amide_hydrogen_split() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.only_amide_hydrogen_split"]], "process_pdb_hierarchy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy"]], "process_residue_groups (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.process_residue_groups"]], "residue_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy"]], "resname (mmtbx.disorder.analyze_model.atom_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.resname"]], "resseq (mmtbx.disorder.analyze_model.residue_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.resseq"]], "rmsd (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.rmsd"]], "segments (mmtbx.disorder.analyze_model.process_pdb_hierarchy property)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.segments"]], "set_ensemble_b_factors_to_xyz_displacement() (in module mmtbx.disorder)": [[286, "mmtbx.disorder.set_ensemble_b_factors_to_xyz_displacement"]], "show() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.show"]], "show() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.show"]], "show() (mmtbx.disorder.analyze_model.process_residue_groups method)": [[286, "mmtbx.disorder.analyze_model.process_residue_groups.show"]], "show() (mmtbx.disorder.backbone.backrub_residue method)": [[286, "mmtbx.disorder.backbone.backrub_residue.show"]], "xyz (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.xyz"]], "accelerations() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.accelerations"]], "accelerations() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.accelerations"]], "cartesian_dynamics (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics"]], "center_of_mass_info() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.center_of_mass_info"]], "center_of_mass_info() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.center_of_mass_info"]], "compute_functional_and_gradients() (mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization method)": [[287, "mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization method)": [[287, "mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization.compute_functional_and_gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints.gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple.gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space.gradients"]], "gradients_calculator() (mmtbx.dynamics.simulated_annealing.run method)": [[287, "mmtbx.dynamics.simulated_annealing.run.gradients_calculator"]], "gradients_calculator_geometry_restraints (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints"]], "gradients_calculator_real_space_simple (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple"]], "gradients_calculator_reciprocal_space (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space"]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization"]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization"]], "interleaved_minimization() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.interleaved_minimization"]], "kinetic_energy_and_temperature (class in mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_and_temperature"]], "kinetic_energy_as_temperature() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_as_temperature"]], "manager() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.manager"]], "master_params() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.master_params"]], "mmtbx.dynamics": [[287, "module-mmtbx.dynamics"]], "mmtbx.dynamics.cartesian_dynamics": [[287, "module-mmtbx.dynamics.cartesian_dynamics"]], "mmtbx.dynamics.constants": [[287, "module-mmtbx.dynamics.constants"]], "mmtbx.dynamics.ensemble_cd": [[287, "module-mmtbx.dynamics.ensemble_cd"]], "mmtbx.dynamics.simulated_annealing": [[287, "module-mmtbx.dynamics.simulated_annealing"]], "print_detailed_dynamics_stats() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.print_detailed_dynamics_stats"]], "print_dynamics_stat() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.print_dynamics_stat"]], "random_velocities() (in module mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.random_velocities"]], "random_velocities() (in module mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.random_velocities"]], "run (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.run"]], "run (class in mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.run"]], "run_interleaved_minimization() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.run_interleaved_minimization"]], "set_velocities() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.set_velocities"]], "set_velocities() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.set_velocities"]], "show() (mmtbx.dynamics.simulated_annealing.run method)": [[287, "mmtbx.dynamics.simulated_annealing.run.show"]], "stop_global_motion() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.stop_global_motion"]], "stop_global_motion() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.stop_global_motion"]], "store_temperatures() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.store_temperatures"]], "temperature_as_kinetic_energy() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.temperature_as_kinetic_energy"]], "velocity_rescaling() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.velocity_rescaling"]], "velocity_rescaling() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.velocity_rescaling"]], "verlet_leapfrog_integration() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.verlet_leapfrog_integration"]], "verlet_leapfrog_integration() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.verlet_leapfrog_integration"]], "xray_grads() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.xray_grads"]], "mmtbx.f_model": [[288, "module-mmtbx.f_model"]], "mmtbx.f_model_info": [[288, "module-mmtbx.f_model_info"]], "asucontent (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ASUContent"]], "accessiblesurfaceareas (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas"]], "accessiblesurfaceresult (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceResult"]], "aggregator (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Aggregator"]], "alternate (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Alternate"]], "atom (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Atom"]], "atomdescriptor (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.AtomDescriptor"]], "case (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.Case"]], "clashcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCalculation"]], "clashcollection (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCollection"]], "clashcountcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCountCalculation"]], "clashpoint (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashPoint"]], "clashingpair (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashingPair"]], "compositecheckerbuilder (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.CompositeCheckerBuilder"]], "compound (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Compound"]], "description (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Description"]], "distancecalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.DistanceCalculation"]], "elementaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ElementAccumulator"]], "empty() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Empty"]], "greedymatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.GreedyMatch"]], "indexer (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Indexer"]], "inserter (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Inserter"]], "mcgregormatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.McGregorMatch"]], "model (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.Model"]], "molecule (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Molecule"]], "rascalmatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.RascalMatch"]], "reducingaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ReducingAccumulator"]], "separatecheckerbuilder (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder"]], "spheremodel (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModel"]], "spheremodelgroup (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModelGroup"]], "symmetryequivalent (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent"]], "accept() (mmtbx.geometry.altloc.description method)": [[289, "mmtbx.geometry.altloc.Description.accept"]], "add() (mmtbx.geometry.altloc.indexer method)": [[289, "mmtbx.geometry.altloc.Indexer.add"]], "add() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.add"]], "add() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.add"]], "add_atom() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_atom"]], "add_atoms_in() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.add_atoms_in"]], "add_bond() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_bond"]], "altid_for() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.altid_for"]], "altloc_averaged_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.altloc_averaged_calculation"]], "altloc_strategy_from_atom() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.altloc_strategy_from_atom"]], "append_neighbours() (mmtbx.geometry.asa.separatecheckerbuilder static method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.append_neighbours"]], "areas (mmtbx.geometry.asa.accessiblesurfaceareas property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas.areas"]], "asu_mapping_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.asu_mapping_for"]], "atom (mmtbx.geometry.clash.atomdescriptor property)": [[289, "mmtbx.geometry.clash.AtomDescriptor.atom"]], "atom_for (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atom_for"]], "atom_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.atom_group"]], "atom_pair() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.atom_pair"]], "atoms (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atoms"]], "atoms (mmtbx.geometry.topology.molecule property)": [[289, "mmtbx.geometry.topology.Molecule.atoms"]], "atoms() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.atoms"]], "bonds (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.bonds"]], "calculate() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.calculate"]], "calculate() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.calculate"]], "calculate_base_for_coordinates() (in module mmtbx.geometry.shared_types)": [[289, "mmtbx.geometry.shared_types.calculate_base_for_coordinates"]], "calculate_contents() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.calculate_contents"]], "chain (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.chain"]], "clashing_with() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.clashing_with"]], "composite_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.composite_distance_predicate"]], "composite_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.composite_predicate"]], "connected_segment_from() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segment_from"]], "connected_segments() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segments"]], "containment_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.containment_predicate"]], "coordinate_adaptor() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.coordinate_adaptor"]], "coordinate_of() (mmtbx.geometry.indexing.structure_indexer static method)": [[289, "mmtbx.geometry.indexing.structure_indexer.coordinate_of"]], "count() (mmtbx.geometry.clash.clashpoint method)": [[289, "mmtbx.geometry.clash.ClashPoint.count"]], "count() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.count"]], "count() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.count"]], "create() (mmtbx.geometry.clash.case class method)": [[289, "mmtbx.geometry.clash.Case.create"]], "create() (mmtbx.geometry.topology.compound class method)": [[289, "mmtbx.geometry.topology.Compound.create"]], "create_and_populate_indexer() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_and_populate_indexer"]], "create_description() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_description"]], "data_of() (mmtbx.geometry.indexing.structure_indexer static method)": [[289, "mmtbx.geometry.indexing.structure_indexer.data_of"]], "descriptor_for (mmtbx.geometry.topology.molecule property)": [[289, "mmtbx.geometry.topology.Molecule.descriptor_for"]], "descriptor_for() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.descriptor_for"]], "descriptors (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.descriptors"]], "descriptors() (mmtbx.geometry.clash.spheremodel method)": [[289, "mmtbx.geometry.clash.SphereModel.descriptors"]], "direct() (in module mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.direct"]], "distances_from() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.distances_from"]], "element_of() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.element_of"]], "elements() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.elements"]], "entities (mmtbx.geometry.altloc.aggregator property)": [[289, "mmtbx.geometry.altloc.Aggregator.entities"]], "exclude() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclude"]], "exclude_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.exclude_predicate"]], "exclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclusion"]], "filter() (in module mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.filter"]], "from_structure() (mmtbx.geometry.topology.compound class method)": [[289, "mmtbx.geometry.topology.Compound.from_structure"]], "frozenset() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.frozenset"]], "get_hash_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_hash_indexer_for"]], "get_linear_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_linear_indexer_for"]], "get_optimal_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_optimal_indexer_for"]], "get_voxelizer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_voxelizer_for"]], "group() (mmtbx.geometry.clash.spheremodelgroup method)": [[289, "mmtbx.geometry.clash.SphereModelGroup.group"]], "hash() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.hash"]], "hash_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.hash_indexer_for"]], "identity() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.identity"]], "identity_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.identity_predicate"]], "identity_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.identity_predicate"]], "include() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.include"]], "include_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.include_predicate"]], "inclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.inclusion"]], "interaction_counts_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_counts_with"]], "interaction_ranges_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_ranges_with"]], "interactions_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interactions_with"]], "is_self_clash() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.is_self_clash"]], "length() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.length"]], "length() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.length"]], "length() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.length"]], "linear_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.linear_indexer_for"]], "mmtbx.geometry": [[289, "module-mmtbx.geometry"]], "mmtbx.geometry.altloc": [[289, "module-mmtbx.geometry.altloc"]], "mmtbx.geometry.asa": [[289, "module-mmtbx.geometry.asa"]], "mmtbx.geometry.clash": [[289, "module-mmtbx.geometry.clash"]], "mmtbx.geometry.indexing": [[289, "module-mmtbx.geometry.indexing"]], "mmtbx.geometry.shared_types": [[289, "module-mmtbx.geometry.shared_types"]], "mmtbx.geometry.sphere_surface_sampling": [[289, "module-mmtbx.geometry.sphere_surface_sampling"]], "mmtbx.geometry.topology": [[289, "module-mmtbx.geometry.topology"]], "molecule (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.molecule"]], "overlap_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.overlap_predicate"]], "overlap_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.overlap_predicate"]], "pairs() (mmtbx.geometry.clash.clashcollection method)": [[289, "mmtbx.geometry.clash.ClashCollection.pairs"]], "pairs() (mmtbx.geometry.clash.clashpoint method)": [[289, "mmtbx.geometry.clash.ClashPoint.pairs"]], "points (mmtbx.geometry.asa.accessiblesurfaceareas property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas.points"]], "process_altloc() (mmtbx.geometry.altloc.aggregator method)": [[289, "mmtbx.geometry.altloc.Aggregator.process_altloc"]], "process_altloc() (mmtbx.geometry.altloc.inserter method)": [[289, "mmtbx.geometry.altloc.Inserter.process_altloc"]], "process_altloc() (mmtbx.geometry.asa.separatecheckerbuilder method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.process_altloc"]], "process_regular() (mmtbx.geometry.altloc.aggregator method)": [[289, "mmtbx.geometry.altloc.Aggregator.process_regular"]], "process_regular() (mmtbx.geometry.altloc.inserter method)": [[289, "mmtbx.geometry.altloc.Inserter.process_regular"]], "process_regular() (mmtbx.geometry.asa.separatecheckerbuilder method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.process_regular"]], "radius_adaptor() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.radius_adaptor"]], "radius_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.radius_for"]], "remapped() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.remapped"]], "remapped() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.remapped"]], "remapped() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.remapped"]], "residue_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.residue_group"]], "root (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.root"]], "simple_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.simple_distance_predicate"]], "simple_surface_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.simple_surface_calculation"]], "size() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.size"]], "sphere_model_group_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.sphere_model_group_for"]], "structure_indexer (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.structure_indexer"]], "subset() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.subset"]], "surface (mmtbx.geometry.asa.accessiblesurfaceresult property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceResult.surface"]], "to_xray_structure() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.to_xray_structure"]], "voxelizer() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.voxelizer"]], "add_coordinate_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.add_coordinate_restraints"]], "append_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley8k_proxies"]], "append_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley_proxies"]], "append_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_oldfield_proxies"]], "append_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_phi_psi_2_proxies"]], "exclude_outliers_from_reference_restraints_selection() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.exclude_outliers_from_reference_restraints_selection"]], "extract_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.extract_proxies"]], "generate_torsion_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.generate_torsion_restraints"]], "get_c_beta_torsion_proxies() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_c_beta_torsion_proxies"]], "get_cb_target_angle_pair() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_cb_target_angle_pair"]], "get_n_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley8k_proxies"]], "get_n_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley_proxies"]], "get_n_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_oldfield_proxies"]], "get_n_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_phi_psi_2_proxies"]], "get_n_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_proxies"]], "get_selection_to_sites_map() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.get_selection_to_sites_map"]], "is_proxy_present() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.is_proxy_present"]], "is_schrodinger_installed() (in module mmtbx.geometry_restraints.external)": [[290, "mmtbx.geometry_restraints.external.is_schrodinger_installed"]], "load_emsley8k_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_emsley8k_tables"]], "load_phi_psi_2_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_phi_psi_2_tables"]], "load_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_tables"]], "mmtbx.geometry_restraints": [[290, "module-mmtbx.geometry_restraints"]], "mmtbx.geometry_restraints.c_beta": [[290, "module-mmtbx.geometry_restraints.c_beta"]], "mmtbx.geometry_restraints.external": [[290, "module-mmtbx.geometry_restraints.external"]], "mmtbx.geometry_restraints.ramachandran": [[290, "module-mmtbx.geometry_restraints.ramachandran"]], "mmtbx.geometry_restraints.reference": [[290, "module-mmtbx.geometry_restraints.reference"]], "proxy_select() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.proxy_select"]], "ramachandran_manager (class in mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager"]], "ramachandran_plot_data (class in mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data"]], "select_good() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.select_good"]], "show_sorted() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.show_sorted"]], "split_array() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.split_array"]], "target_and_gradients() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.target_and_gradients"]], "update_phi_psi_targets() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.update_phi_psi_targets"]], "update_phi_psi_targets_on_init() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.update_phi_psi_targets_on_init"]], "add_arg_like_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_arg_like_h"]], "add_ca_ha1_and_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_and_ha2"]], "add_ca_ha1_or_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_or_ha2"]], "add_hhh() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_hhh"]], "add_ring_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ring_h"]], "all_master_params() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.all_master_params"]], "assert_water_is_consistent() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.assert_water_is_consistent"]], "atom_as_str() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_as_str"]], "atom_scat() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_scat"]], "build_dod_and_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_dod_and_od"]], "build_water_hydrogens_from_map() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map"]], "build_water_hydrogens_from_map2() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map2"]], "choose_h_for_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.choose_h_for_water"]], "count_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.count_rotatable"]], "distances_to_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.distances_to_peaks"]], "extract_hoh_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.extract_hoh_peaks"]], "find_hydrogen_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.find_hydrogen_peaks"]], "fit_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.fit_rotatable"]], "fit_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.fit_water"]], "get_pdb_oxygen() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.get_pdb_oxygen"]], "h_peak (class in mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.h_peak"]], "insert_atom_into_model() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.insert_atom_into_model"]], "len_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.len_peaks"]], "make_peak_dict() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.make_peak_dict"]], "map_peak_filter() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.map_peak_filter"]], "match_dod() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_dod"]], "match_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_od"]], "mmtbx.hydrogens": [[291, "module-mmtbx.hydrogens"]], "mmtbx.hydrogens.build_hydrogens": [[291, "module-mmtbx.hydrogens.build_hydrogens"]], "mmtbx.hydrogens.find": [[291, "module-mmtbx.hydrogens.find"]], "obs_map() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.obs_map"]], "one_water_correlation() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.one_water_correlation"]], "print_atom() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_atom"]], "print_scat() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_scat"]], "print_scats() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_scats"]], "regularize_model() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.regularize_model"]], "remove_zero_occupancy() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.remove_zero_occupancy"]], "rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.rotatable"]], "run() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.run"]], "run() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.run"]], "run_fit_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.run_fit_rotatable"]], "scatterers_info() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.scatterers_info"]], "select_one_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.select_one_water"]], "shortcut() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.shortcut"]], "water_and_peaks (class in mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_and_peaks"]], "water_bond_angle() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_bond_angle"]], "water_map_correlations() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_map_correlations"]], "write_atoms() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.write_atoms"]], "add_lone_pairs_for_peptyde_o() (in module mmtbx.ias)": [[292, "mmtbx.ias.add_lone_pairs_for_peptyde_o"]], "all_bonds() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.all_bonds"]], "atom (class in mmtbx.ias)": [[292, "mmtbx.ias.atom"]], "bond_density (class in mmtbx.ias)": [[292, "mmtbx.ias.bond_density"]], "check_at_bond_vector() (in module mmtbx.ias)": [[292, "mmtbx.ias.check_at_bond_vector"]], "deep_copy() (mmtbx.ias.ias method)": [[292, "mmtbx.ias.ias.deep_copy"]], "extract_ias (class in mmtbx.ias)": [[292, "mmtbx.ias.extract_ias"]], "find_peak() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.find_peak"]], "find_peak_at_bond (class in mmtbx.ias)": [[292, "mmtbx.ias.find_peak_at_bond"]], "get_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.get_ias_selection"]], "ias (class in mmtbx.ias)": [[292, "mmtbx.ias.ias"]], "ias_counters (class in mmtbx.ias)": [[292, "mmtbx.ias.ias_counters"]], "ias_position_at_lone_pairs() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_position_at_lone_pairs"]], "ias_site_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_site_position"]], "iass_as_xray_structure() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.iass_as_xray_structure"]], "manager (class in mmtbx.ias)": [[292, "mmtbx.ias.manager"]], "mmtbx.ias": [[292, "module-mmtbx.ias"]], "set_ias_name_and_predicted_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_ias_name_and_predicted_position"]], "set_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.set_ias_selection"]], "set_peaks() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_peaks"]], "set_status() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_status"]], "set_status() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.set_status"]], "setup_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.setup_ias_selection"]], "show() (mmtbx.ias.ias_counters method)": [[292, "mmtbx.ias.ias_counters.show"]], "write_pdb_file() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.write_pdb_file"]], "atom_type_flags (class in mmtbx.ions)": [[293, "mmtbx.ions.atom_type_flags"]], "bad_coord_atom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_atom"]], "bad_coord_residue (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_residue"]], "bad_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_geom"]], "bad_halide (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_halide"]], "bad_valence (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_valence"]], "bad_vectors (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_vectors"]], "calculate_valence() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valence"]], "calculate_valences() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valences"]], "charge_as_int() (mmtbx.ions.metal_parameters method)": [[293, "mmtbx.ions.metal_parameters.charge_as_int"]], "check_supported() (in module mmtbx.ions)": [[293, "mmtbx.ions.check_supported"]], "close_contact (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.close_contact"]], "coord_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.coord_geom"]], "flag_names_and_labels (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.flag_names_and_labels"]], "get_charge() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charge"]], "get_charges() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charges"]], "get_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_element"]], "get_flag_captions() (mmtbx.ions.atom_type_flags method)": [[293, "mmtbx.ions.atom_type_flags.get_flag_captions"]], "get_metal_parameters() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_metal_parameters"]], "get_valence_params() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_valence_params"]], "high_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_anom"]], "high_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_b_iso"]], "high_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fdp"]], "high_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fofc"]], "high_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_occ"]], "high_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_two_fofc"]], "is_supported_donor() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_donor"]], "is_supported_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_element"]], "like_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.like_coord"]], "low_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_anom"]], "low_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_b_iso"]], "low_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fdp"]], "low_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fofc"]], "low_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_occ"]], "low_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_two_fofc"]], "metal_parameters (class in mmtbx.ions)": [[293, "mmtbx.ions.metal_parameters"]], "missing_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.missing_geom"]], "mmtbx.ions": [[293, "module-mmtbx.ions"]], "name (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.name"]], "parameter_server (class in mmtbx.ions)": [[293, "mmtbx.ions.parameter_server"]], "params (mmtbx.ions.parameter_server attribute)": [[293, "id0"], [293, "mmtbx.ions.parameter_server.params"]], "scattering_type() (mmtbx.ions.metal_parameters method)": [[293, "mmtbx.ions.metal_parameters.scattering_type"]], "show() (mmtbx.ions.atom_type_flags method)": [[293, "mmtbx.ions.atom_type_flags.show"]], "too_few_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_few_coord"]], "too_few_non_waters (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_few_non_waters"]], "too_many_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_many_coord"]], "very_bad_valence (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.very_bad_valence"]], "clean_up_ions() (in module mmtbx.ions.build)": [[294, "mmtbx.ions.build.clean_up_ions"]], "find_and_build_ions() (in module mmtbx.ions.build)": [[294, "mmtbx.ions.build.find_and_build_ions"]], "mmtbx.ions.build": [[294, "module-mmtbx.ions.build"]], "chemicalenvironment (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.ChemicalEnvironment"]], "scatteringenvironment (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.ScatteringEnvironment"]], "altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.altloc"]], "anom_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id6"], [295, "mmtbx.ions.environment.ScatteringEnvironment.anom_density"]], "atom (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id0"], [295, "mmtbx.ions.environment.ChemicalEnvironment.atom"]], "atom (mmtbx.ions.environment.atom_contact attribute)": [[295, "id15"], [295, "mmtbx.ions.environment.atom_contact.atom"]], "atom_contact (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.atom_contact"]], "atom_i_seq() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_i_seq"]], "atom_id_no_altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_id_no_altloc"]], "atom_name() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_name"]], "b_iso (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id7"], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_iso"]], "b_mean_hoh (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id8"], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_mean_hoh"]], "charge (mmtbx.ions.environment.atom_contact attribute)": [[295, "id16"], [295, "mmtbx.ions.environment.atom_contact.charge"]], "chemistry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id1"], [295, "mmtbx.ions.environment.ChemicalEnvironment.chemistry"]], "contacts (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id2"], [295, "mmtbx.ions.environment.ChemicalEnvironment.contacts"]], "contacts_no_alts (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id3"], [295, "mmtbx.ions.environment.ChemicalEnvironment.contacts_no_alts"]], "d_min (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id9"], [295, "mmtbx.ions.environment.ScatteringEnvironment.d_min"]], "distance() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance"]], "distance_from() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance_from"]], "element (mmtbx.ions.environment.atom_contact attribute)": [[295, "id17"], [295, "mmtbx.ions.environment.atom_contact.element"]], "find_nearby_atoms() (in module mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.find_nearby_atoms"]], "fo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id10"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fo_density"]], "fofc_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofc_density"]], "fofo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofo_density"]], "fp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id11"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fp"]], "fpp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id12"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fpp"]], "geometry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id4"], [295, "mmtbx.ions.environment.ChemicalEnvironment.geometry"]], "get_valence() (mmtbx.ions.environment.chemicalenvironment method)": [[295, "mmtbx.ions.environment.ChemicalEnvironment.get_valence"]], "id_str() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.id_str"]], "is_carboxy_terminus (mmtbx.ions.environment.atom_contact attribute)": [[295, "mmtbx.ions.environment.atom_contact.is_carboxy_terminus"]], "mmtbx.ions.environment": [[295, "module-mmtbx.ions.environment"]], "occ (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id13"], [295, "mmtbx.ions.environment.ScatteringEnvironment.occ"]], "occ (mmtbx.ions.environment.atom_contact property)": [[295, "mmtbx.ions.environment.atom_contact.occ"]], "pai (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id14"], [295, "mmtbx.ions.environment.ScatteringEnvironment.pai"]], "resname() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.resname"]], "rt_mx (mmtbx.ions.environment.atom_contact attribute)": [[295, "id18"], [295, "mmtbx.ions.environment.atom_contact.rt_mx"]], "site_cart (mmtbx.ions.environment.atom_contact attribute)": [[295, "id19"], [295, "mmtbx.ions.environment.atom_contact.site_cart"]], "vector (mmtbx.ions.environment.atom_contact attribute)": [[295, "id20"], [295, "mmtbx.ions.environment.atom_contact.vector"]], "wavelengeth (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.wavelengeth"]], "wavelength (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.wavelength"]], "find_coordination_geometry() (in module mmtbx.ions.geometry)": [[296, "mmtbx.ions.geometry.find_coordination_geometry"]], "mmtbx.ions.geometry": [[296, "module-mmtbx.ions.geometry"]], "is_favorable_halide_environment() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_favorable_halide_environment"]], "is_negatively_charged_oxygen() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_negatively_charged_oxygen"]], "mmtbx.ions.halides": [[297, "module-mmtbx.ions.halides"]], "anom_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.ANOM_PEAK"]], "atomproperties (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.AtomProperties"]], "bad_coord_atom (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_ATOM"]], "bad_coord_residue (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_RESIDUE"]], "bad_fpp (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_FPP"]], "bad_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_GEOMETRY"]], "bad_halide (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_HALIDE"]], "bad_valences (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VALENCES"]], "bad_vectors (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VECTORS"]], "close_contact (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.CLOSE_CONTACT"]], "coording_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.COORDING_GEOMETRY"]], "fofc_hole (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_HOLE"]], "fofc_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_PEAK"]], "high_2fofc (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_2FOFC"]], "high_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_B"]], "high_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_OCC"]], "like_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LIKE_COORD"]], "low_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_B"]], "low_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_OCC"]], "no_2fofc_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_2FOFC_PEAK"]], "no_anom_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_ANOM_PEAK"]], "no_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_GEOMETRY"]], "too_few_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_FEW_COORD"]], "too_few_non_waters (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_FEW_NON_WATERS"]], "too_many_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_MANY_COORD"]], "very_bad_valences (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.VERY_BAD_VALENCES"]], "altloc (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.altloc"]], "analyze_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_substructure"]], "analyze_water() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_water"]], "analyze_waters() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_waters"]], "atom_selection (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.atom_selection"]], "atom_weight() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.atom_weight"]], "b_iso (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.b_iso"]], "chain_id (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.chain_id"]], "check_fpp_ratio() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_fpp_ratio"]], "check_ion_environment() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_ion_environment"]], "chem_env (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.chem_env"]], "create_manager() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.create_manager"]], "element (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.element"]], "error_strs (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.error_strs"]], "find_anomalous_scatterers() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.find_anomalous_scatterers"]], "find_nearby_atoms() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.find_nearby_atoms"]], "get_atom_type() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.get_atom_type"]], "get_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_b_iso"]], "get_fp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fp"]], "get_fpp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fpp"]], "get_initial_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_initial_b_iso"]], "get_map() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map"]], "get_map_gaussian_fit() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_gaussian_fit"]], "get_map_sphere_variance() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_sphere_variance"]], "get_strict_valence_flag() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_strict_valence_flag"]], "guess_b_iso_real() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_b_iso_real"]], "guess_molecular_weight() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_molecular_weight"]], "has_compatible_ligands() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.has_compatible_ligands"]], "icode (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.icode"]], "identity() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.identity"]], "ion_master_phil() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_master_phil"]], "ion_result (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_result"]], "is_compatible_anomalous_scattering() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_anomalous_scattering"]], "is_compatible_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_site"]], "is_correctly_identified() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_correctly_identified"]], "looks_like_halide_ion() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.looks_like_halide_ion"]], "looks_like_nucleotide_phosphate_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.looks_like_nucleotide_phosphate_site"]], "manager (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.manager"]], "map_stats() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.map_stats"]], "mmtbx.ions.identify": [[298, "module-mmtbx.ions.identify"]], "model_id (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.model_id"]], "name (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.name"]], "number_of_atoms_within_radius() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_atoms_within_radius"]], "number_of_backbone_oxygens() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_backbone_oxygens"]], "number_of_favored_ligand_residues() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_favored_ligand_residues"]], "occupancy (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.occupancy"]], "outlier (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.outlier"]], "principal_axes_of_inertia() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.principal_axes_of_inertia"]], "refine_anomalous_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.refine_anomalous_substructure"]], "resname (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.resname"]], "resseq (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.resseq"]], "scatter_env (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.scatter_env"]], "score (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.score"]], "segid (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.segid"]], "show() (mmtbx.ions.identify.ion_result method)": [[298, "mmtbx.ions.identify.ion_result.show"]], "show_brief() (mmtbx.ions.identify.ion_result method)": [[298, "mmtbx.ions.identify.ion_result.show_brief"]], "show_current_scattering_statistics() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.show_current_scattering_statistics"]], "show_ion_results() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.show_ion_results"]], "show_properties() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.show_properties"]], "show_summary() (mmtbx.ions.identify.water_result method)": [[298, "mmtbx.ions.identify.water_result.show_summary"]], "symop (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.symop"]], "update_maps() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.update_maps"]], "update_structure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.update_structure"]], "validate_ion() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.validate_ion"]], "validate_ions() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.validate_ions"]], "water_result (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.water_result"]], "water_selection() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.water_selection"]], "xyz (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.xyz"]], "analyze_water() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_water"]], "analyze_waters() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_waters"]], "atom_info_str (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id0"], [299, "mmtbx.ions.svm.svm_prediction.atom_info_str"]], "atom_types (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id1"], [299, "mmtbx.ions.svm.svm_prediction.atom_types"]], "final_choice (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id2"], [299, "mmtbx.ions.svm.svm_prediction.final_choice"]], "i_seq (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id3"], [299, "mmtbx.ions.svm.svm_prediction.i_seq"]], "ion_anomalous_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_anomalous_vector"]], "ion_class() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_class"]], "ion_electron_density_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_electron_density_vector"]], "ion_geometry_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_geometry_vector"]], "ion_model_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_model_vector"]], "ion_nearby_atoms_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_nearby_atoms_vector"]], "ion_valence_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_valence_vector"]], "ion_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_vector"]], "manager (class in mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.manager"]], "map_stats (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id4"], [299, "mmtbx.ions.svm.svm_prediction.map_stats"]], "mmtbx.ions.svm": [[299, "module-mmtbx.ions.svm"]], "pdb_id_str (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id5"], [299, "mmtbx.ions.svm.svm_prediction.pdb_id_str"]], "predict_ion() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.predict_ion"]], "scores (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id6"], [299, "mmtbx.ions.svm.svm_prediction.scores"]], "show() (mmtbx.ions.svm.svm_prediction method)": [[299, "mmtbx.ions.svm.svm_prediction.show"]], "show_brief() (mmtbx.ions.svm.svm_prediction method)": [[299, "mmtbx.ions.svm.svm_prediction.show_brief"]], "svm_prediction (class in mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.svm_prediction"]], "dump_sites() (in module mmtbx.ions.svm.dump_sites)": [[300, "mmtbx.ions.svm.dump_sites.dump_sites"]], "mmtbx.ions.svm.dump_sites": [[300, "module-mmtbx.ions.svm.dump_sites"]], "filter_svm_outputs() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.filter_svm_outputs"]], "iterate_sites() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.iterate_sites"]], "mmtbx.ions.svm.utils": [[301, "module-mmtbx.ions.svm.utils"]], "scale_to() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.scale_to"]], "anonymize_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.anonymize_ions"]], "collect_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.collect_ions"]], "compare_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.compare_ions"]], "count_coordinating_residues() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.count_coordinating_residues"]], "fit_gaussian() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.fit_gaussian"]], "mmtbx.ions.utils": [[302, "module-mmtbx.ions.utils"]], "sort_atoms_permutation() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.sort_atoms_permutation"]], "add_fan() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_fan"]], "add_spring() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_spring"]], "angle_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.angle_outlier_as_kinemage"]], "bond_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.bond_outlier_as_kinemage"]], "build_name_hash() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.build_name_hash"]], "cbeta_dev() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.cbeta_dev"]], "chiral_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.chiral_outlier_as_kinemage"]], "export_molprobity_result_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.export_molprobity_result_as_kinemage"]], "get_altid_controls() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_altid_controls"]], "get_angle_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_angle_outliers"]], "get_bond_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_bond_outliers"]], "get_chain_color() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_chain_color"]], "get_default_header() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_default_header"]], "get_footer() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_footer"]], "get_ions() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_ions"]], "get_kin_lots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_kin_lots"]], "get_master_phil() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_master_phil"]], "get_residue_bonds() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_residue_bonds"]], "kin_vec() (in module mmtbx.kinemage)": [[303, "mmtbx.kinemage.kin_vec"]], "make_multikin() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_multikin"]], "make_probe_dots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_probe_dots"]], "midpoint() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.midpoint"]], "mmtbx.kinemage": [[303, "module-mmtbx.kinemage"]], "mmtbx.kinemage.validation": [[303, "module-mmtbx.kinemage.validation"]], "pperp_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.pperp_outliers"]], "rama_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.rama_outliers"]], "rotamer_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.rotamer_outliers"]], "run() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.run"]], "usage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.usage"]], "condition_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_"]], "condition_name() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_name"]], "condition_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_number_"]], "get_condition() (mmtbx.ligands.xtal_screens.server method)": [[304, "mmtbx.ligands.xtal_screens.server.get_condition"]], "ligands() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands"]], "ligands_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands_"]], "mmtbx.ligands": [[304, "module-mmtbx.ligands"]], "mmtbx.ligands.xtal_screens": [[304, "module-mmtbx.ligands.xtal_screens"]], "ph() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.pH"]], "ph_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.pH_"]], "screen_name_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.screen_name_"]], "screen_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.screen_number_"]], "server (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.server"]], "solution (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.solution"]], "tube_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.tube_number_"]], "well_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.well_number_"]], "add_box() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.add_box"]], "amplitudes() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.amplitudes"]], "apply_new_sites_to_hierarchies() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_hierarchies"]], "apply_new_sites_to_xray_structure() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_xray_structure"]], "as_p1_map() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.as_p1_map"]], "asu_map_from_fmodel() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.asu_map_from_fmodel"]], "atom_iselection() (mmtbx.maps.write_xplor_map_file method)": [[305, "mmtbx.maps.write_xplor_map_file.atom_iselection"]], "b_factor_sharpening_by_map_kurtosis_maximization() (in module mmtbx.maps)": [[305, "mmtbx.maps.b_factor_sharpening_by_map_kurtosis_maximization"]], "box_around_selection() (mmtbx.maps.write_xplor_map_file method)": [[305, "mmtbx.maps.write_xplor_map_file.box_around_selection"]], "box_iterator() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.box_iterator"]], "boxes (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.boxes"]], "cast_map_coeff_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.cast_map_coeff_params"]], "ccp4_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.ccp4_map"]], "combine_maps() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.combine_maps"]], "combine_with() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.combine_with"]], "common_frame_of_reference (class in mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.common_frame_of_reference"]], "compute_f_calc() (in module mmtbx.maps)": [[305, "mmtbx.maps.compute_f_calc"]], "compute_fo_minus_fo_map (class in mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map"]], "compute_map_and_combine() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.compute_map_and_combine"]], "compute_map_coefficients (class in mmtbx.maps)": [[305, "mmtbx.maps.compute_map_coefficients"]], "compute_original_map() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.compute_original_map"]], "compute_xplor_maps() (in module mmtbx.maps)": [[305, "mmtbx.maps.compute_xplor_maps"]], "convert_to_non_anomalous() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.convert_to_non_anomalous"]], "counter (class in mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.counter"]], "create_fmodel() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.create_fmodel"]], "create_map_from_pdb_and_mtz() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.create_map_from_pdb_and_mtz"]], "create_omit_regions() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.create_omit_regions"]], "decode_resolve_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.decode_resolve_map_coeffs"]], "exercise() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.exercise"]], "extract_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.extract_map_coeffs"]], "extract_phenix_refine_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.extract_phenix_refine_map_coeffs"]], "fast_maps_from_hkl_file (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file"]], "finish_job() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.finish_job"]], "fo_minus_fo_master_params() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.fo_minus_fo_master_params"]], "format_map_coeffs_for_resolve() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.format_map_coeffs_for_resolve"]], "frac_max (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.frac_max"]], "frac_min (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.frac_min"]], "generate_p1_box() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.generate_p1_box"]], "generate_water_omit_map (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.generate_water_omit_map"]], "get_anomalous_map() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_anomalous_map"]], "get_default_map_coefficients_phil() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_default_map_coefficients_phil"]], "get_inverse_matrix() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.get_inverse_matrix"]], "get_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.get_map"]], "get_map() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.get_map"]], "get_map_coeff_labels() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeff_labels"]], "get_map_coeffs_for_build() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeffs_for_build"]], "get_maps_from_fmodel() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_maps_from_fmodel"]], "get_maps_from_fmodel() (mmtbx.maps.utils.fast_maps_from_hkl_file method)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file.get_maps_from_fmodel"]], "get_p1_map_unscaled() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.get_p1_map_unscaled"]], "good_atoms_selection() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.good_atoms_selection"]], "grid_max() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.grid_max"]], "inner_loop() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.inner_loop"]], "inverse_transform_hierarchy() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.inverse_transform_hierarchy"]], "join_selections() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.join_selections"]], "kick_fmodel() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_fmodel"]], "kick_map_coeffs() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_map_coeffs"]], "launcher (class in mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.launcher"]], "low_volume_density_elimination() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.low_volume_density_elimination"]], "map_and_map_coeff_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_and_map_coeff_master_params"]], "map_coefficients() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.map_coefficients"]], "map_coefficients_from_fmodel() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_coefficients_from_fmodel"]], "map_coeffs_from_map() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.map_coeffs_from_map"]], "map_coeffs_from_mtz_file() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.map_coeffs_from_mtz_file"]], "map_coeffs_list (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.map_coeffs_list"]], "map_coeffs_mtz_label_manager (class in mmtbx.maps)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager"]], "maps_including_io_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.maps_including_IO_master_params"]], "mask_grid() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.mask_grid"]], "mmtbx.maps": [[305, "module-mmtbx.maps"]], "mmtbx.maps.composite_omit_map": [[305, "module-mmtbx.maps.composite_omit_map"]], "mmtbx.maps.fem": [[305, "module-mmtbx.maps.fem"]], "mmtbx.maps.fobs_minus_fobs_map": [[305, "module-mmtbx.maps.fobs_minus_fobs_map"]], "mmtbx.maps.kick": [[305, "module-mmtbx.maps.kick"]], "mmtbx.maps.superpose": [[305, "module-mmtbx.maps.superpose"]], "mmtbx.maps.utils": [[305, "module-mmtbx.maps.utils"]], "n_atoms (mmtbx.maps.composite_omit_map.omit_box property)": [[305, "mmtbx.maps.composite_omit_map.omit_box.n_atoms"]], "n_atoms (mmtbx.maps.composite_omit_map.omit_regions property)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.n_atoms"]], "n_boxes (mmtbx.maps.composite_omit_map.omit_regions property)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.n_boxes"]], "noise_filtered_map_coefficients() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.noise_filtered_map_coefficients"]], "omit_box (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_box"]], "omit_box() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.omit_box"]], "omit_region_results (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results"]], "omit_regions (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_regions"]], "outer_loop() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.outer_loop"]], "phases() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.phases"]], "prepare_f_obs_and_flags() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.prepare_f_obs_and_flags"]], "r_free (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.r_free"]], "r_work (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.r_work"]], "random_weight_averaged_map_coefficients() (mmtbx.maps.kick.weighted_average method)": [[305, "mmtbx.maps.kick.weighted_average.random_weight_averaged_map_coefficients"]], "randomize_completeness() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_completeness"]], "randomize_completeness2() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_completeness2"]], "randomize_struture_factors() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_struture_factors"]], "remove_common_isotropic_adp() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.remove_common_isotropic_adp"]], "resolve_filter_map() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.resolve_filter_map"]], "result_as_sf() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.result_as_sf"]], "run (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.run"]], "run (class in mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.run"]], "run (class in mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.run"]], "run() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.run"]], "run() (mmtbx.maps.fobs_minus_fobs_map.launcher method)": [[305, "mmtbx.maps.fobs_minus_fobs_map.launcher.run"]], "run() (mmtbx.maps.superpose.transform_maps method)": [[305, "mmtbx.maps.superpose.transform_maps.run"]], "run() (mmtbx.maps.utils.fast_maps_from_hkl_file method)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file.run"]], "selection (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.selection"]], "selection (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.selection"]], "serial (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.serial"]], "serial (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.serial"]], "serial (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.serial"]], "show() (mmtbx.maps.composite_omit_map.omit_box method)": [[305, "mmtbx.maps.composite_omit_map.omit_box.show"]], "show() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.show"]], "show() (mmtbx.maps.fem.counter method)": [[305, "mmtbx.maps.fem.counter.show"]], "to_asu_map() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.to_asu_map"]], "transform_map_by_lsq_fit() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.transform_map_by_lsq_fit"]], "transform_maps (class in mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.transform_maps"]], "truncate_with_roots() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.truncate_with_roots"]], "validate_params() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.validate_params"]], "weighted_average (class in mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.weighted_average"]], "write_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_map_coeffs"]], "write_map_coeffs() (mmtbx.maps.utils.generate_water_omit_map method)": [[305, "mmtbx.maps.utils.generate_water_omit_map.write_map_coeffs"]], "write_map_file() (mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map method)": [[305, "mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map.write_map_file"]], "write_mc() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.write_mc"]], "write_mtz_file() (mmtbx.maps.compute_map_coefficients method)": [[305, "mmtbx.maps.compute_map_coefficients.write_mtz_file"]], "write_output_files() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.write_output_files"]], "write_pdb_file() (mmtbx.maps.utils.generate_water_omit_map method)": [[305, "mmtbx.maps.utils.generate_water_omit_map.write_pdb_file"]], "write_xplor_map() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_xplor_map"]], "write_xplor_map_file (class in mmtbx.maps)": [[305, "mmtbx.maps.write_xplor_map_file"]], "write_xplor_map_file() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_xplor_map_file"]], "zero_below_threshold() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.zero_below_threshold"]], "asu_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.asu_mask"]], "bulk_solvent (class in mmtbx.masks)": [[306, "mmtbx.masks.bulk_solvent"]], "bulk_solvent_mask() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.bulk_solvent_mask"]], "compute_f_mask() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.compute_f_mask"]], "deep_copy() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.deep_copy"]], "manager (class in mmtbx.masks)": [[306, "mmtbx.masks.manager"]], "mask_as_xplor_map() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.mask_as_xplor_map"]], "mask_data_whole_uc() (mmtbx.masks.asu_mask method)": [[306, "mmtbx.masks.asu_mask.mask_data_whole_uc"]], "mask_from_xray_structure (class in mmtbx.masks)": [[306, "mmtbx.masks.mask_from_xray_structure"]], "mmtbx.masks": [[306, "module-mmtbx.masks"]], "select() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.select"]], "shell_f_masks() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks"]], "shell_f_masks_twin() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks_twin"]], "show_summary() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.show_summary"]], "smooth_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.smooth_mask"]], "structure_factors() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.structure_factors"]], "subtract_non_uniform_solvent_region_in_place() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.subtract_non_uniform_solvent_region_in_place"]], "alpha_beta (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta"]], "alpha_beta() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta"]], "alpha_beta_calc (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc"]], "alpha_beta_est_manager (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager"]], "alpha_beta_for_each_reflection() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta_for_each_reflection"]], "distribution_as_array() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_array"]], "distribution_as_xplor_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_xplor_file"]], "f_ordered_solvent() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.f_ordered_solvent"]], "fcalc_from_distribution() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.fcalc_from_distribution"]], "figures_of_merit_() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.figures_of_merit_"]], "fo_fc_alpha_over_eps_beta() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fo_fc_alpha_over_eps_beta"]], "fom() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fom"]], "form_factor() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.form_factor"]], "form_factor() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.form_factor"]], "map_of_coeff_scaled() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.map_of_coeff_scaled"]], "max_number_of_shells() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.max_number_of_shells"]], "mmtbx.max_lik": [[307, "module-mmtbx.max_lik"]], "mmtbx.max_lik.max_like_non_uniform": [[307, "module-mmtbx.max_lik.max_like_non_uniform"]], "mmtbx.max_lik.maxlik": [[307, "module-mmtbx.max_lik.maxlik"]], "ordered_solvent_distribution (class in mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution"]], "phase_error() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.phase_error"]], "print_all_reflections_in_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.print_all_reflections_in_file"]], "sigma_miss() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.sigma_miss"]], "smooth() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.smooth"]], "monomerlibraryservererror": [[308, "mmtbx.monomer_library.server.MonomerLibraryServerError"]], "residuelinkclass (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass"]], "active_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.active_atoms"]], "ad_hoc_single_atom_residue (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ad_hoc_single_atom_residue"]], "add_angle_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_angle_proxies"]], "add_angle_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_angle_proxies"]], "add_bond_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_bond_proxies"]], "add_bond_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_bond_proxies"]], "add_chirality_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_chirality_proxies"]], "add_chirality_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_chirality_proxies"]], "add_dihedral_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_dihedral_proxies"]], "add_dihedral_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_dihedral_proxies"]], "add_parallelity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_parallelity_proxies"]], "add_parallelity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_parallelity_proxies"]], "add_planarity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_planarity_proxies"]], "add_planarity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_planarity_proxies"]], "adjust_class() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.adjust_class"]], "all_associated_i_seqs() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.all_associated_i_seqs"]], "all_atoms_are_in_main_conf() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.all_atoms_are_in_main_conf"]], "angle_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.angle_counters"]], "angle_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.angle_list"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.apply_change_in_place"]], "apply_chem_mod_list() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.apply_chem_mod_list"]], "apply_glyco_link_using_proxies_and_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.apply_glyco_link_using_proxies_and_atoms"]], "apply_mod() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.apply_mod"]], "apply_mod() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.apply_mod"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_atom.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.as_chem_comp"]], "as_cif() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.as_cif"]], "as_cif_block() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.as_cif_block"]], "as_cif_loop() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.as_cif_loop"]], "as_geometry_restraints_motif() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.as_geometry_restraints_motif"]], "as_geometry_restraints_motif_manipulation() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.as_geometry_restraints_motif_manipulation"]], "as_geometry_restraints_motif_manipulation() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.as_geometry_restraints_motif_manipulation"]], "assign() (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate method)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.assign"]], "assign_charge() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_charge"]], "assign_directly() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_directly"]], "assign_from_monomer_mapping() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_from_monomer_mapping"]], "atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_by_id"]], "atom_dict() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_dict"]], "atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond.atom_ids"]], "atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tor.atom_ids"]], "atom_ids() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_ids"]], "atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_list"]], "atom_name_interpretation (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_name_interpretation"]], "atom_names_given (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_given"]], "atom_names_mappings (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_mappings"]], "atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.atom_selection"]], "bond_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.bond_counters"]], "bond_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.bond_list"]], "build_all_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies"]], "build_angle_start_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_angle_start_by_tor_id"]], "build_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_chain_proxies"]], "build_conformation_dependent_angle_proxies() (in module mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.build_conformation_dependent_angle_proxies"]], "build_i_q_packed_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_i_q_packed_by_tor_id"]], "build_rotamer_tor_atom_ids_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_rotamer_tor_atom_ids_by_tor_id"]], "chainid (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chainid"]], "change_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.change_atom_in_place"]], "check_all_classes() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.check_all_classes"]], "check_comp() (in module mmtbx.monomer_library.cif_triage)": [[308, "mmtbx.monomer_library.cif_triage.check_comp"]], "check_for_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_for_acid"]], "check_for_peptide_links() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.check_for_peptide_links"]], "check_valence() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence"]], "check_valence_and_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence_and_acid"]], "chem_comp (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp"]], "chem_comp (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chem_comp"]], "chem_comp_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_angle"]], "chem_comp_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_atom"]], "chem_comp_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond"]], "chem_comp_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_chir"]], "chem_comp_deriv (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_deriv"]], "chem_comp_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_plane_atom"]], "chem_comp_rotamer_info (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_rotamer_info"]], "chem_comp_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym"]], "chem_comp_synonym_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym_atom"]], "chem_comp_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tor"]], "chem_comp_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tree"]], "chem_link (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link"]], "chem_link_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_angle"]], "chem_link_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_bond"]], "chem_link_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_chir"]], "chem_link_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_plane"]], "chem_link_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_tor"]], "chem_mod (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod"]], "chem_mod_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle"]], "chem_mod_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_atom"]], "chem_mod_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond"]], "chem_mod_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir"]], "chem_mod_ids (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chem_mod_ids"]], "chem_mod_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom"]], "chem_mod_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor"]], "chem_mod_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree"]], "chem_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_plane"]], "chir_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chir_list"]], "chirality_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chirality_counters"]], "cif_keywords() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.cif_keywords"]], "cif_object (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.cif_object"]], "cif_output_holder (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.cif_output_holder"]], "clash_guard() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.clash_guard"]], "classification (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.classification"]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.classification"]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.classification"]], "comp_comp_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id"]], "conf_altloc (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.conf_altloc"]], "conf_altloc (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.conf_altloc"]], "conformation_dependent_restraints (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints"]], "conformer_i_seq (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq"]], "construct_geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.construct_geometry_restraints_manager"]], "convert() (mmtbx.monomer_library.pdb_interpretation.conformer_i_seq method)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq.convert"]], "convert_all() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_all"]], "convert_all() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_all"]], "convert_ccp4_tor_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_ccp4_tor_list"]], "convert_comp_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_comp_list"]], "convert_comp_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_list"]], "convert_comp_synonym_atom_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_synonym_atom_list"]], "convert_comp_synonym_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_synonym_list"]], "convert_deriv_list_dict() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_deriv_list_dict"]], "convert_lib_atom() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_atom"]], "convert_lib_synonym() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_synonym"]], "convert_lib_vdw() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_vdw"]], "convert_link_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_link_list"]], "convert_link_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_link_list"]], "convert_list_block() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_list_block"]], "convert_mod_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_mod_list"]], "convert_mod_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_mod_list"]], "correct_hydrogen_geometries() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.correct_hydrogen_geometries"]], "counters (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.counters"]], "create_disulfides() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_disulfides"]], "create_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_link"]], "delete_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.delete_atom_in_place"]], "delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.delta"]], "dihedral_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.dihedral_counters"]], "discard_conflicting_pdb_element_column() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.discard_conflicting_pdb_element_column"]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.discard_tables"]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.discard_tables"]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.duplicate_atoms"]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.duplicate_atoms"]], "empty (class in mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.empty"]], "ener_lib (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.ener_lib"]], "ener_lib_as_nonbonded_params() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ener_lib_as_nonbonded_params"]], "energy_lib_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_atom"]], "energy_lib_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_synonym"]], "energy_lib_vdw (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_vdw"]], "epsilon (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.epsilon"]], "esd_as_weight() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.esd_as_weight"]], "evaluate (class in mmtbx.monomer_library.rna_sugar_pucker_analysis)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate"]], "evaluate_registry_process_result() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.evaluate_registry_process_result"]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.expected_atoms"]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.expected_atoms"]], "extract_bonds_to_omit() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.extract_bonds_to_omit"]], "extract_secondary_structure() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.extract_secondary_structure"]], "extract_xray_structure() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.extract_xray_structure"]], "fatal_problems_message() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.fatal_problems_message"]], "fatal_problems_report() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.fatal_problems_report"]], "find_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.find_mon_lib_file"]], "flush_log() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.flush_log"]], "format_exception_message() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.format_exception_message"]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.generate_atoms_from_atom_groups"]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.generate_atoms_from_atom_groups"]], "generate_loop_data() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.generate_loop_data"]], "generic_metal_run() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.generic_metal_run"]], "geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.geometry_restraints_manager"]], "geometry_restraints_proxy_registries (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries"]], "geostd_list_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.geostd_list_cif"]], "get_c1_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_C1_carbon"]], "get_alpha_beta() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_alpha_beta"]], "get_angle() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_angle"]], "get_angle() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_angle"]], "get_angles_from_included_bonds() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_angles_from_included_bonds"]], "get_anomeric_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_carbon"]], "get_anomeric_hydrogen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_hydrogen"]], "get_any_linking_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_any_linking_carbon"]], "get_bad_hydrogen_i_seqs() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.get_bad_hydrogen_i_seqs"]], "get_basepair_target_distance() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_basepair_target_distance"]], "get_bond() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_bond"]], "get_bond() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_bond"]], "get_bond() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_bond"]], "get_bonded() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded"]], "get_bonded_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded_from_atom_groups"]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_bonds_and_angles"]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_bonds_and_angles"]], "get_chir_volume_ideal() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_chir_volume_ideal"]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_volume_ideal"]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_volume_ideal"]], "get_chiral_i_seqs() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_chiral_i_seqs"]], "get_chiral_sign() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_chiral_sign"]], "get_chiral_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_chiral_volume"]], "get_classes() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_classes"]], "get_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_classification"]], "get_code() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_code"]], "get_comp_comp_id_and_atom_name_interpretation() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_and_atom_name_interpretation"]], "get_comp_comp_id_direct() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_direct"]], "get_comp_comp_id_mod() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_mod"]], "get_default_bondlength() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_default_bondlength"]], "get_distance2() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_distance2"]], "get_distance2() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_distance2"]], "get_glyco_link_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_glyco_link_atoms"]], "get_hand() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_hand"]], "get_isomer() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_isomer"]], "get_lib_link() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link"]], "get_lib_link_peptide() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link_peptide"]], "get_link_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon"]], "get_link_carbon_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon_on_distance"]], "get_link_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen"]], "get_link_oxygen_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen_on_distance"]], "get_link_phi_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_phi_carbon"]], "get_planes() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_planes"]], "get_planes() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_planes"]], "get_planes() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.get_planes"]], "get_restraints_loading_flags() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_restraints_loading_flags"]], "get_ring_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_carbon"]], "get_ring_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen"]], "get_ring_oxygen_substitute() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen_substitute"]], "get_rows() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.get_rows"]], "get_unknown_atoms() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.get_unknown_atoms"]], "get_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_volume"]], "glyco_link_class (class in mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class"]], "group_planes() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.group_planes"]], "hydrogen_deuterium_aliases() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.hydrogen_deuterium_aliases"]], "i_atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.i_atom_by_id"]], "i_conformer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.i_conformer"]], "id_dict (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.id_dict"]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.ignored_atoms"]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.ignored_atoms"]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.incomplete_info"]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.incomplete_info"]], "initialize_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.initialize_tables"]], "involves_broken_bonds() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.involves_broken_bonds"]], "involves_special_positions() (mmtbx.monomer_library.pdb_interpretation.special_position_dict method)": [[308, "mmtbx.monomer_library.pdb_interpretation.special_position_dict.involves_special_positions"]], "is_2p (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p"]], "is_2p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_delta"]], "is_2p_o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_o3p_distance_c1p_outbound_line"]], "is_2p_p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_p_distance_c1p_outbound_line"]], "is_3p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_3p_delta"]], "is_atom_group_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_group_pair_linked"]], "is_atom_metal_coordinated() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_metal_coordinated"]], "is_atom_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked"]], "is_atom_pair_linked_tuple() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked_tuple"]], "is_correct() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.is_correct"]], "is_delta_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_delta_outlier"]], "is_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_dna"]], "is_epsilon_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_epsilon_outlier"]], "is_first_conformer_in_chain (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_first_conformer_in_chain"]], "is_glyco_amino_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_amino_bond"]], "is_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_bond"]], "is_match() (mmtbx.monomer_library.pdb_interpretation.link_match_one method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one.is_match"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.is_matching_mod_for"]], "is_n_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_n_glyco_bond"]], "is_o_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_o_glyco_bond"]], "is_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_peptide"]], "is_proper_match() (mmtbx.monomer_library.pdb_interpretation.link_match method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match.is_proper_match"]], "is_rna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna"]], "is_rna2p (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna2p"]], "is_rna_dna (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna_dna"]], "is_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna_dna"]], "is_same_model_as_before() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.is_same_model_as_before"]], "is_standard_glyco_link() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.is_standard_glyco_link"]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_terminus"]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_terminus"]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_unusual"]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_unusual"]], "is_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_water"]], "iselection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.iselection"]], "iselection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.iselection"]], "iter_until_loop() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.iter_until_loop"]], "labels() (mmtbx.monomer_library.pdb_interpretation.source_info_server method)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server.labels"]], "lib_link (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.lib_link"]], "link_link_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.link_link_id"]], "link_match (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match"]], "link_match_one (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one"]], "linking_mixins (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.linking_mixins"]], "load_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.load_mon_lib_file"]], "lookup() (mmtbx.monomer_library.conformation_dependent_restraints.pgd_server method)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server.lookup"]], "looped_data (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.looped_data"]], "looped_ids() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.looped_ids"]], "merge_and_overwrite_cifs() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.merge_and_overwrite_cifs"]], "missing_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.missing_hydrogen_atoms"]], "missing_non_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.missing_non_hydrogen_atoms"]], "mmtbx.monomer_library": [[308, "module-mmtbx.monomer_library"]], "mmtbx.monomer_library.bondlength_defaults": [[308, "module-mmtbx.monomer_library.bondlength_defaults"]], "mmtbx.monomer_library.cif_triage": [[308, "module-mmtbx.monomer_library.cif_triage"]], "mmtbx.monomer_library.cif_types": [[308, "module-mmtbx.monomer_library.cif_types"]], "mmtbx.monomer_library.conformation_dependent_restraints": [[308, "module-mmtbx.monomer_library.conformation_dependent_restraints"]], "mmtbx.monomer_library.conv_v2_v3": [[308, "module-mmtbx.monomer_library.conv_v2_v3"]], "mmtbx.monomer_library.correct_hydrogen_geometries": [[308, "module-mmtbx.monomer_library.correct_hydrogen_geometries"]], "mmtbx.monomer_library.glyco_chiral_values": [[308, "module-mmtbx.monomer_library.glyco_chiral_values"]], "mmtbx.monomer_library.glyco_utils": [[308, "module-mmtbx.monomer_library.glyco_utils"]], "mmtbx.monomer_library.hydrogen_restrictions": [[308, "module-mmtbx.monomer_library.hydrogen_restrictions"]], "mmtbx.monomer_library.idealized_aa": [[308, "module-mmtbx.monomer_library.idealized_aa"]], "mmtbx.monomer_library.linking_mixins": [[308, "module-mmtbx.monomer_library.linking_mixins"]], "mmtbx.monomer_library.linking_setup": [[308, "module-mmtbx.monomer_library.linking_setup"]], "mmtbx.monomer_library.linking_utils": [[308, "module-mmtbx.monomer_library.linking_utils"]], "mmtbx.monomer_library.pdb_interpretation": [[308, "module-mmtbx.monomer_library.pdb_interpretation"]], "mmtbx.monomer_library.rna_sugar_pucker_analysis": [[308, "module-mmtbx.monomer_library.rna_sugar_pucker_analysis"]], "mmtbx.monomer_library.rotamer_utils": [[308, "module-mmtbx.monomer_library.rotamer_utils"]], "mmtbx.monomer_library.server": [[308, "module-mmtbx.monomer_library.server"]], "mod_mod_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id"]], "mon_lib_cif_loader (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_cif_loader"]], "mon_lib_ener_lib_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_ener_lib_cif"]], "mon_lib_list_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_list_cif"]], "mon_lib_names (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.mon_lib_names"]], "mon_lib_srv (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.mon_lib_srv"]], "monomer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.monomer"]], "monomer_atom_dict (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.monomer_atom_dict"]], "monomer_mapping (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping"]], "monomer_mapping_summary (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary"]], "n_expected_atoms() (mmtbx.monomer_library.pdb_interpretation.source_info_server method)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server.n_expected_atoms"]], "n_unknown_type_symbols() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.n_unknown_type_symbols"]], "new_if_defined() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.new_if_defined"]], "next() (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator.next"]], "next() (mmtbx.monomer_library.server.trivial_html_tag_filter method)": [[308, "mmtbx.monomer_library.server.trivial_html_tag_filter.next"]], "non_hydrogen_atoms() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.non_hydrogen_atoms"]], "nonbonded_energy_type_registry (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.nonbonded_energy_type_registry"]], "normalize_atom_ids_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalize_atom_ids_in_place"]], "normalized_angle_list() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_angle_list"]], "normalized_bond_list() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.normalized_bond_list"]], "normalized_bond_list() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_bond_list"]], "normalized_rna_dna (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_rna_dna"]], "o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.o3p_distance_c1p_outbound_line"]], "o3p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.o3p_perp_xyz"]], "p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.p_distance_c1p_outbound_line"]], "p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.p_perp_xyz"]], "parallelity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.parallelity_counters"]], "pdb_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_atoms"]], "pdb_residue (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_residue"]], "pdb_residue_id_str (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_residue_id_str"]], "pgd_server (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server"]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection"]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.phil_atom_selection"]], "phil_atom_selection_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection_multiple"]], "phil_atom_selections_as_i_seqs() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs"]], "phil_atom_selections_as_i_seqs_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs_multiple"]], "planarity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.planarity_counters"]], "plane_atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.plane_atom_list"]], "possible_cyclic_peptide() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.possible_cyclic_peptide"]], "print_apply() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.print_apply"]], "print_dict() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.print_dict"]], "print_filtered_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.print_filtered_cif"]], "process (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.process"]], "process_apply_cif_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_apply_cif_link"]], "process_apply_cif_modification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_apply_cif_modification"]], "process_atom_groups_for_linking_single_link() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.process_atom_groups_for_linking_single_link"]], "process_cif() (mmtbx.monomer_library.server.process_cif_mixin method)": [[308, "mmtbx.monomer_library.server.process_cif_mixin.process_cif"]], "process_cif_mixin (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.process_cif_mixin"]], "process_cif_object() (mmtbx.monomer_library.server.process_cif_mixin method)": [[308, "mmtbx.monomer_library.server.process_cif_mixin.process_cif_object"]], "process_custom_links() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_links"]], "process_custom_nonbonded_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_nonbonded_exclusions"]], "process_custom_nonbonded_symmetry_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_nonbonded_symmetry_exclusions"]], "process_geometry_restraints_edits() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits"]], "process_geometry_restraints_edits_angle() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_angle"]], "process_geometry_restraints_edits_bond() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_bond"]], "process_geometry_restraints_edits_dihedral() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_dihedral"]], "process_geometry_restraints_edits_parallelity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_parallelity"]], "process_geometry_restraints_edits_planarity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_planarity"]], "process_geometry_restraints_remove() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_remove"]], "process_geometry_restraints_scale() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_scale"]], "process_geostd_rna_dna() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.process_geostd_rna_dna"]], "process_hydrogen_bonds() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_hydrogen_bonds"]], "process_nonbonded_for_links() (mmtbx.monomer_library.linking_mixins.linking_mixins method)": [[308, "mmtbx.monomer_library.linking_mixins.linking_mixins.process_nonbonded_for_links"]], "read_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.read_cif"]], "remove_link() (mmtbx.monomer_library.linking_mixins.residuelinkclass method)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass.remove_link"]], "rename_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_angle"]], "rename_atom() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_atom"]], "rename_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_bond"]], "rename_chir() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_chir"]], "rename_generic() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_generic"]], "rename_link_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_angle"]], "rename_link_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_bond"]], "rename_link_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_tor"]], "rename_plan() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_plan"]], "rename_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tor"]], "rename_tree() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tree"]], "report() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.report"]], "report() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report"]], "report_unknown_message() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report_unknown_message"]], "reset() (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator.reset"]], "residue_altloc() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_altloc"]], "residue_dict() (in module mmtbx.monomer_library.idealized_aa)": [[308, "mmtbx.monomer_library.idealized_aa.residue_dict"]], "residue_id_str() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.residue_id_str"]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_name"]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.residue_name"]], "resolve_unexpected() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.resolve_unexpected"]], "rotamer_info() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_info"]], "rotamer_info_master_phil() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_info_master_phil"]], "rotamer_info_phil_str_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_info_phil_str_list"]], "rotamer_iterator (class in mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator"]], "rotamer_iterator() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_iterator"]], "rotamer_iterator() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.rotamer_iterator"]], "run() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.run"]], "run() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.run"]], "run() (in module mmtbx.monomer_library.hydrogen_restrictions)": [[308, "mmtbx.monomer_library.hydrogen_restrictions.run"]], "run() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.run"]], "scattering_type_registry (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.scattering_type_registry"]], "search_for_ncs() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.search_for_ncs"]], "sel_backbone() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_backbone"]], "sel_backbone() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_backbone"]], "sel_backbone_or_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_backbone_or_sidechain"]], "sel_backbone_or_sidechain() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_backbone_or_sidechain"]], "sel_classification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_classification"]], "sel_classification() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_classification"]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_phosphate"]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_phosphate"]], "sel_residues_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_residues_within"]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_ribose"]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_ribose"]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_sidechain"]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_sidechain"]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_within"]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_within"]], "selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.selection"]], "selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.selection"]], "selection_manager (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager"]], "server (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.server"]], "set_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.set_classification"]], "show() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.show"]], "show() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show"]], "show() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.show"]], "show_loop() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.show_loop"]], "show_loop_data() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show_loop_data"]], "show_loop_header() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show_loop_header"]], "show_residue_groups() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.show_residue_groups"]], "site_symmetry_table() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.site_symmetry_table"]], "sites_cart_exact() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sites_cart_exact"]], "skip_if_non_linking() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.skip_if_non_linking"]], "source_info (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.source_info"]], "source_info_server (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server"]], "special_position_dict (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.special_position_dict"]], "sulfur_class() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.sulfur_class"]], "summary() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.summary"]], "summary() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.summary"]], "tardy_model() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.tardy_model"]], "test_for_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_peptide"]], "test_for_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_rna_dna"]], "test_for_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_water"]], "tor_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.tor_list"]], "trans_field() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.trans_field"]], "trivial_html_tag_filter (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.trivial_html_tag_filter"]], "type_symbol_registry_base (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base"]], "unexpected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.unexpected_atoms"]], "unexpected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.unexpected_atoms"]], "update() (mmtbx.monomer_library.pdb_interpretation.cif_output_holder method)": [[308, "mmtbx.monomer_library.pdb_interpretation.cif_output_holder.update"]], "update_internals_due_to_coordinates_change() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.update_internals_due_to_coordinates_change"]], "update_restraints() (mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints method)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints.update_restraints"]], "update_skip_if_longer() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.update_skip_if_longer"]], "validate_geometry_edits_params() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.validate_geometry_edits_params"]], "xray_structure() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.xray_structure"]], "chains_info (class in mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.Chains_info"]], "abs() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.abs"]], "add_cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_cc"]], "add_cc_list() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_cc_list"]], "add_chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_chain_residue_id"]], "add_identity_op() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_identity_op"]], "add_identity_op() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_identity_op"]], "add_note() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_note"]], "add_operator() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.add_operator"]], "add_residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_residues_in_common_list"]], "add_rmsd_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_rmsd_list"]], "add_source_info() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_source_info"]], "adjust_magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.adjust_magnification"]], "adjust_magnification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.adjust_magnification"]], "apply_cob_to_vector() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.apply_cob_to_vector"]], "apply_ligand_ncs (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs"]], "apply_ncs_to_sites() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.apply_ncs_to_sites"]], "apply_transforms() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.apply_transforms"]], "as_ncs_spec_string() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.as_ncs_spec_string"]], "cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.cc"]], "centers() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.centers"]], "chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.chain_residue_id"]], "change_of_basis() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.change_of_basis"]], "combine_ligands_and_hierarchy() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.combine_ligands_and_hierarchy"]], "compute_transform_grad() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.compute_transform_grad"]], "coordinate_offset() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.coordinate_offset"]], "copy_rot_trans() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_rot_trans"]], "copy_vector_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_vector_list"]], "crystal_symmetry_to_ncs() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.crystal_symmetry_to_ncs"]], "deep_copy() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.deep_copy"]], "deep_copy() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy"]], "deep_copy_ops_to_keep() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy_ops_to_keep"]], "deep_copy_order() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy_order"]], "delete_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.delete_inv"]], "display_all() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.display_all"]], "display_summary() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.display_summary"]], "distance_from_center() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.distance_from_center"]], "euler_frac_to_rot_trans() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.euler_frac_to_rot_trans"]], "extend_helix_operators() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.extend_helix_operators"]], "extend_helix_operators() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.extend_helix_operators"]], "extract_ligand_residues() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.extract_ligand_residues"]], "extract_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.extract_point_group_symmetry"]], "find_ncs_in_hierarchy() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.find_ncs_in_hierarchy"]], "flip_atoms_in_ncs_groups() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.flip_atoms_in_ncs_groups"]], "format_all_for_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_biomt"]], "format_all_for_group_specification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_group_specification"]], "format_all_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_phenix_refine"]], "format_all_for_resolve() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_resolve"]], "format_for_biomt() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_biomt"]], "format_for_phenix_refine() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_phenix_refine"]], "format_for_resolve() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_resolve"]], "format_group_specification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_group_specification"]], "format_phil_for_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_ncs"]], "format_phil_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_phenix_refine"]], "generate_ncs_ops() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.generate_ncs_ops"]], "get_1_char_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_char_after_key"]], "get_1_value_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_value_after_key"]], "get_3_values_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_3_values_after_key"]], "get_bool_selection_to_keep() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_bool_selection_to_keep"]], "get_c_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_c_symmetry"]], "get_chain_xyz() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chain_xyz"]], "get_chains_info() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chains_info"]], "get_copy_master_selections_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_copy_master_selections_from_match_dict"]], "get_d_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_d_symmetry"]], "get_final_maps_and_cc (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.get_final_maps_and_cc"]], "get_forwards_reverse_helix() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_forwards_reverse_helix"]], "get_helical_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_helical_symmetry"]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_helix_parameters"]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_parameters"]], "get_helix_theta() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_theta"]], "get_helix_z_translation() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_z_translation"]], "get_info_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_info_from_match_dict"]], "get_inverses() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_inverses"]], "get_list_of_best_ncs_copy_map_correlation() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_list_of_best_ncs_copy_map_correlation"]], "get_match_rmsd() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_match_rmsd"]], "get_matching_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_matching_atoms"]], "get_ncs_from_text() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_ncs_from_text"]], "get_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_ncs_name"]], "get_new_fcalc_map() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_new_fcalc_map"]], "get_new_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_new_group"]], "get_order_dict() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_order_dict"]], "get_preliminary_ncs_groups() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_preliminary_ncs_groups"]], "get_refine_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_refine_selection"]], "get_res_range_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_res_range_after_key"]], "get_rot_y() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_y"]], "get_rot_z() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_z"]], "get_sites_cc() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_sites_cc"]], "get_theta_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_theta_along_z"]], "get_trans_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_trans_along_z"]], "get_weight() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_weight"]], "group_operators (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.group_operators"]], "helix_rt_forwards() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_forwards"]], "helix_rt_reverse() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_reverse"]], "identity_op_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.identity_op_id"]], "identity_op_id_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.identity_op_id_in_first_group"]], "import_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.import_ncs_group"]], "init_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_ncs_group"]], "init_oper() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_oper"]], "invert_matrices() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.invert_matrices"]], "invert_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.invert_matrices"]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_helical_along_z"]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_helical_along_z"]], "is_identity() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_identity"]], "is_in_range() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_in_range"]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_point_group_symmetry"]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_point_group_symmetry"]], "is_same_transform() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_same_transform"]], "is_similar_ncs_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_similar_ncs_group"]], "is_similar_ncs_object() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_similar_ncs_object"]], "magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.magnification"]], "make_flips_if_necessary_torsion() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.make_flips_if_necessary_torsion"]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.map_inside_unit_cell"]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.map_inside_unit_cell"]], "max_operators() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.max_operators"]], "mmtbx.ncs": [[309, "module-mmtbx.ncs"]], "mmtbx.ncs.ligands": [[309, "module-mmtbx.ncs.ligands"]], "mmtbx.ncs.ncs": [[309, "module-mmtbx.ncs.ncs"]], "mmtbx.ncs.ncs_search": [[309, "module-mmtbx.ncs.ncs_search"]], "mmtbx.ncs.ncs_utils": [[309, "module-mmtbx.ncs.ncs_utils"]], "mmtbx_res_alignment() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.mmtbx_res_alignment"]], "my_get_rot_trans() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.my_get_rot_trans"]], "my_selection() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.my_selection"]], "n_ligands (mmtbx.ncs.ligands.apply_ligand_ncs property)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.n_ligands"]], "n_ncs_oper() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.n_ncs_oper"]], "ncs (class in mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs"]], "ncs_domain_pdb() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.ncs_domain_pdb"]], "ncs_from_import() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_import"]], "ncs_from_pdb_input_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_pdb_input_BIOMT"]], "ncs_group (class in mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs_group"]], "ncs_grouping_and_group_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.ncs_grouping_and_group_dict"]], "ncs_groups() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_groups"]], "ncs_oper_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_oper_in_first_group"]], "ncs_read() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_read"]], "note() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.note"]], "offset_inside_cell() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.offset_inside_cell"]], "offset_inside_zero_one() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.offset_inside_zero_one"]], "oper_adds_offset() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.oper_adds_offset"]], "overall_cc() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_cc"]], "overall_note() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_note"]], "overall_rmsd() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_rmsd"]], "print_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.print_list"]], "read_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.read_ncs"]], "remove_clashing_atoms() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.remove_clashing_atoms"]], "remove_extra() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_extra"]], "remove_far_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.remove_far_atoms"]], "remove_items_from_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.remove_items_from_selection"]], "remove_ncs_not_consistent_with_space_group_number() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_ncs_not_consistent_with_space_group_number"]], "remove_quotes_from_chain_id() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_quotes_from_chain_id"]], "remove_single_quotes() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_single_quotes"]], "resid_str() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.resid_str"]], "residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.residues_in_common_list"]], "rmsd_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rmsd_list"]], "rota_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rota_matrices"]], "rota_matrices_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rota_matrices_inv"]], "rotate_about_y() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_about_y"]], "rotate_about_z() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_about_z"]], "rotate_matrices() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_matrices"]], "rotate_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rotate_matrices"]], "rotation_to_angles() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.rotation_to_angles"]], "rotations_translations_forward_euler() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rotations_translations_forward_euler"]], "round() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.round"]], "sample_operators (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.sample_operators"]], "save_existing_group_info() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_existing_group_info"]], "save_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_ncs_group"]], "save_oper() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_oper"]], "search_ncs_relations() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.search_ncs_relations"]], "select_first_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_group"]], "select_first_ncs_operator() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_operator"]], "selected_positions() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.selected_positions"]], "set_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_ncs_name"]], "set_shift_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_shift_cart"]], "set_unit_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_unit_ncs"]], "setup_maps() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.setup_maps"]], "shake_transformations() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.shake_transformations"]], "shift_back_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.shift_back_cart"]], "shift_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.shift_cart"]], "shortcut_1() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.shortcut_1"]], "show_summary() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.show_summary"]], "show_summary() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.show_summary"]], "sort_by_z_translation() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.sort_by_z_translation"]], "sort_by_z_translation() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.sort_by_z_translation"]], "source_of_ncs_info() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.source_of_ncs_info"]], "translations_orth() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.translations_orth"]], "translations_orth_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.translations_orth_inv"]], "value() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.value"]], "write_maps() (mmtbx.ncs.ligands.apply_ligand_ncs method)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.write_maps"]], "write_maps() (mmtbx.ncs.ligands.get_final_maps_and_cc method)": [[309, "mmtbx.ncs.ligands.get_final_maps_and_cc.write_maps"]], "write_pdb() (mmtbx.ncs.ligands.apply_ligand_ncs method)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.write_pdb"]], "xyz_distance() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.xyz_distance"]], "get_results() (mmtbx.pdbtools.modify method)": [[310, "mmtbx.pdbtools.modify.get_results"]], "master_params() (in module mmtbx.pdbtools)": [[310, "mmtbx.pdbtools.master_params"]], "mmtbx.pdbtools": [[310, "module-mmtbx.pdbtools"]], "modify (class in mmtbx.pdbtools)": [[310, "mmtbx.pdbtools.modify"]], "apply_default_filter() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.apply_default_filter"]], "blue_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.blue_color_model"]], "color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.color_model"]], "convert_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.convert_histogram_data"]], "convert_to_histogram() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.convert_to_histogram"]], "draw() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw"]], "draw_box() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_box"]], "draw_dashed_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_dashed_line"]], "draw_labels() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_labels"]], "draw_solid_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_solid_line"]], "filter_and_convert() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.filter_and_convert"]], "format_value() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.format_value"]], "get_absolute_label_position() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_absolute_label_position"]], "get_basic_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_basic_histogram_data"]], "get_bin_color() (mmtbx.polygon.output.blue_color_model method)": [[311, "mmtbx.polygon.output.blue_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.grayscale_color_model method)": [[311, "mmtbx.polygon.output.grayscale_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.rainbow_color_model method)": [[311, "mmtbx.polygon.output.rainbow_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.red_color_model method)": [[311, "mmtbx.polygon.output.red_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.rmb_color_model method)": [[311, "mmtbx.polygon.output.rmb_color_model.get_bin_color"]], "get_color_key() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.get_color_key"]], "get_histogram_colors() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_histogram_colors"]], "get_line_segments() (mmtbx.polygon.output.polygon_layout method)": [[311, "mmtbx.polygon.output.polygon_layout.get_line_segments"]], "get_polygon_intersection() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_polygon_intersection"]], "get_statistics_percentiles() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.get_statistics_percentiles"]], "get_stats_and_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_stats_and_histogram_data"]], "grayscale_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.grayscale_color_model"]], "histogram_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.histogram_layout"]], "hsv2rgb() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.hsv2rgb"]], "load_db() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.load_db"]], "mmtbx.polygon": [[311, "module-mmtbx.polygon"]], "mmtbx.polygon.output": [[311, "module-mmtbx.polygon.output"]], "original_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.original_color_model"]], "polygon() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.polygon"]], "polygon_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.polygon_layout"]], "rainbow_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.rainbow_color_model"]], "ratio_cutoffs (mmtbx.polygon.output.renderer attribute)": [[311, "mmtbx.polygon.output.renderer.ratio_cutoffs"]], "red_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.red_color_model"]], "renderer (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.renderer"]], "resize() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.resize"]], "rmb_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.rmb_color_model"]], "select_dict() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.select_dict"]], "set_color_model() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.set_color_model"]], "set_colors() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.set_colors"]], "show_histogram() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.show_histogram"]], "around_atom (class in mmtbx.real_space)": [[312, "mmtbx.real_space.around_atom"]], "data() (mmtbx.real_space.around_atom method)": [[312, "mmtbx.real_space.around_atom.data"]], "data() (mmtbx.real_space.sampled_model_density method)": [[312, "mmtbx.real_space.sampled_model_density.data"]], "distances() (mmtbx.real_space.around_atom method)": [[312, "mmtbx.real_space.around_atom.distances"]], "mmtbx.real_space": [[312, "module-mmtbx.real_space"]], "sampled_model_density (class in mmtbx.real_space)": [[312, "mmtbx.real_space.sampled_model_density"]], "write_as_xplor_map() (mmtbx.real_space.sampled_model_density method)": [[312, "mmtbx.real_space.sampled_model_density.write_as_xplor_map"]], "action() (in module mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.action"]], "add() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.add"]], "add() (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator.add"]], "add_occupancy_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.add_occupancy_selection"]], "add_rotamer_restraints() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.add_rotamer_restraints"]], "annealing_callback (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.annealing_callback"]], "apply_shifts() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.apply_shifts"]], "apply_shifts() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.apply_shifts"]], "apply_transformation() (in module mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.apply_transformation"]], "apply_transformation() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.apply_transformation"]], "apply_transformation_() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.apply_transformation_"]], "as_ave (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.as_ave"]], "assemble_constraint_groups_3d() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.assemble_constraint_groups_3d"]], "average_sites_cart() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.average_sites_cart"]], "bs_ave (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.bs_ave"]], "ca() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.ca"]], "call_back() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.call_back"]], "callback_after_step() (mmtbx.refinement.geometry_minimization.lbfgs method)": [[313, "mmtbx.refinement.geometry_minimization.lbfgs.callback_after_step"]], "callback_after_step() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.callback_after_step"]], "check_all() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.check_all"]], "collect() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.collect"]], "collect() (mmtbx.refinement.monitors method)": [[313, "mmtbx.refinement.monitors.collect"]], "collect() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.collect"]], "compute_functional_and_gradients() (mmtbx.refinement.anomalous_scatterer_groups.minimizer method)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.compute_functional_and_gradients"]], "compute_target() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.compute_target"]], "coordinate_shifts (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts"]], "count_occupancies() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.count_occupancies"]], "crystal_symmetry() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.crystal_symmetry"]], "d_e_pot_d_sites() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.d_e_pot_d_sites"]], "d_target_d_f_calc_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.d_target_d_f_calc_work"]], "d_target_d_f_model_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.d_target_d_f_model_work"]], "d_target_d_site_cart() (mmtbx.refinement.targets.target_result_mixin method)": [[313, "mmtbx.refinement.targets.target_result_mixin.d_target_d_site_cart"]], "data_target_and_grads() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space.data_target_and_grads"]], "data_target_and_grads() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.data_target_and_grads"]], "deep_copy() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.deep_copy"]], "dump_statistics() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.dump_statistics"]], "e_pot() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.e_pot"]], "evaluate_after_end() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.evaluate_after_end"]], "evaluate_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model"]], "evaluate_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.evaluate_model"]], "expand (class in mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand"]], "expand_angle_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_angle_proxies"]], "expand_bond_params_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_bond_params_table"]], "expand_dihedral_or_chirality_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_dihedral_or_chirality_proxies"]], "expand_model_or_conformer_indices() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_model_or_conformer_indices"]], "expand_nonbonded_types() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_nonbonded_types"]], "expand_pair_sym_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_pair_sym_table"]], "expand_planarity_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_planarity_proxies"]], "expand_site_symmetry_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_site_symmetry_table"]], "extract_partial_occupancy_selections() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.extract_partial_occupancy_selections"]], "finalize() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.finalize"]], "find_anomalous_scatterer_groups() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.find_anomalous_scatterer_groups"]], "finite_difference_test() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.finite_difference_test"]], "finite_difference_test() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.finite_difference_test"]], "format_stats_for_phenix_gui() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.format_stats_for_phenix_gui"]], "get_best_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.get_best_model"]], "get_restraints_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_restraints_tg"]], "get_shifts() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.get_shifts"]], "get_single_atom_selection_string() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.get_single_atom_selection_string"]], "get_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_tg"]], "gradients_wrt_atomic_parameters() (mmtbx.refinement.targets.target_result_mixin method)": [[313, "mmtbx.refinement.targets.target_result_mixin.gradients_wrt_atomic_parameters"]], "gradients_wrt_par() (mmtbx.refinement.group.target_and_grads method)": [[313, "mmtbx.refinement.group.target_and_grads.gradients_wrt_par"]], "gradients_wrt_r() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_r"]], "gradients_wrt_t() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_t"]], "grads_asu_to_one_ncs() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_asu_to_one_ncs"]], "grads_one_ncs_to_asu() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_one_ncs_to_asu"]], "group_minimizer (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.group_minimizer"]], "inflate() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.inflate"]], "is_bool() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_bool"]], "is_size_t() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_size_t"]], "lbfgs (class in mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.lbfgs"]], "lbfgs (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.lbfgs"]], "lbfgs (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs"]], "list_3d_as_bool_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.list_3d_as_bool_selection"]], "ls_ff_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_ff_weights"]], "ls_sigma_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_sigma_weights"]], "macro_cycle_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.macro_cycle_header"]], "make_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_header"]], "make_sub_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_sub_header"]], "manager (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.manager"]], "manager (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.manager"]], "manager (class in mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.manager"]], "manager (class in mmtbx.refinement.refinement_flags)": [[313, "mmtbx.refinement.refinement_flags.manager"]], "manager (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.manager"]], "min_max_mean() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.min_max_mean"]], "minimize() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.minimize"]], "minimize_wrapper_for_ramachandran() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.minimize_wrapper_for_ramachandran"]], "minimizer (class in mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer"]], "minimizer (class in mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.minimizer"]], "mmtbx.refinement": [[313, "module-mmtbx.refinement"]], "mmtbx.refinement.adp_refinement": [[313, "module-mmtbx.refinement.adp_refinement"]], "mmtbx.refinement.anomalous_scatterer_groups": [[313, "module-mmtbx.refinement.anomalous_scatterer_groups"]], "mmtbx.refinement.geometry_minimization": [[313, "module-mmtbx.refinement.geometry_minimization"]], "mmtbx.refinement.group": [[313, "module-mmtbx.refinement.group"]], "mmtbx.refinement.inspect_tardy_trajectory": [[313, "module-mmtbx.refinement.inspect_tardy_trajectory"]], "mmtbx.refinement.minimization": [[313, "module-mmtbx.refinement.minimization"]], "mmtbx.refinement.minimization_ncs_constraints": [[313, "module-mmtbx.refinement.minimization_ncs_constraints"]], "mmtbx.refinement.occupancies": [[313, "module-mmtbx.refinement.occupancies"]], "mmtbx.refinement.orca": [[313, "module-mmtbx.refinement.orca"]], "mmtbx.refinement.print_statistics": [[313, "module-mmtbx.refinement.print_statistics"]], "mmtbx.refinement.refinement_flags": [[313, "module-mmtbx.refinement.refinement_flags"]], "mmtbx.refinement.rigid_body": [[313, "module-mmtbx.refinement.rigid_body"]], "mmtbx.refinement.select_best_starting_model": [[313, "module-mmtbx.refinement.select_best_starting_model"]], "mmtbx.refinement.tardy": [[313, "module-mmtbx.refinement.tardy"]], "mmtbx.refinement.targets": [[313, "module-mmtbx.refinement.targets"]], "mmtbx.refinement.weights_params": [[313, "module-mmtbx.refinement.weights_params"]], "monitor (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.monitor"]], "monitors (class in mmtbx.refinement)": [[313, "mmtbx.refinement.monitors"]], "neutron_flag (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.neutron_flag"]], "neutron_line() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.neutron_line"]], "occupancy_regroupping() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.occupancy_regroupping"]], "occupancy_selections() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.occupancy_selections"]], "pack() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.pack"]], "pack() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.pack"]], "pack() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.pack"]], "pack_gradients() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.pack_gradients"]], "pack_unpack() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.pack_unpack"]], "phaser_sad_target_functor (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor"]], "potential_object (class in mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.potential_object"]], "prepare_for_minimization() (mmtbx.refinement.targets.phaser_sad_target_functor method)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor.prepare_for_minimization"]], "prepare_for_minimization() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.prepare_for_minimization"]], "r_free (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_free"]], "r_free() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.r_free"]], "r_free_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_free_start"]], "r_frees (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.r_frees"]], "r_work (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_work"]], "r_work() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.r_work"]], "r_work_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_work_start"]], "r_works (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.r_works"]], "refinable_params_one_ncs_to_asu() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.refinable_params_one_ncs_to_asu"]], "refine_adp (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.refine_adp"]], "refine_anomalous_substructure() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.refine_anomalous_substructure"]], "refinement_monitor (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor"]], "requires_experimental_phases() (mmtbx.refinement.targets.target_attributes method)": [[313, "mmtbx.refinement.targets.target_attributes.requires_experimental_phases"]], "restraints_target_and_grads() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.restraints_target_and_grads"]], "rigid_body_minimizer (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer"]], "rigid_body_shift_accumulator (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator"]], "rigid_groups_from_pdb_chains() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_groups_from_pdb_chains"]], "rmsd_calculation() (mmtbx.refinement.orca.expand method)": [[313, "mmtbx.refinement.orca.expand.rmsd_calculation"]], "rmsd_calculator() (mmtbx.refinement.orca.expand method)": [[313, "mmtbx.refinement.orca.expand.rmsd_calculator"]], "rotation() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.rotation"]], "run() (in module mmtbx.refinement.inspect_tardy_trajectory)": [[313, "mmtbx.refinement.inspect_tardy_trajectory.run"]], "run() (in module mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.run"]], "run2 (class in mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.run2"]], "run_constrained (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.run_constrained"]], "run_lbfgs() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.run_lbfgs"]], "save_best_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.save_best_model"]], "save_pdb_file() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.save_pdb_file"]], "save_updated_data() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.save_updated_data"]], "score() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.score"]], "select() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.select"]], "select() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select"]], "select_detached() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select_detached"]], "select_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.select_model"]], "set_refinable_parameters() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.set_refinable_parameters"]], "show() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.show"]], "show() (mmtbx.refinement.adp_refinement.weight_result method)": [[313, "mmtbx.refinement.adp_refinement.weight_result.show"]], "show() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.show"]], "show() (mmtbx.refinement.group.manager method)": [[313, "mmtbx.refinement.group.manager.show"]], "show() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.show"]], "show() (mmtbx.refinement.occupancies.manager method)": [[313, "mmtbx.refinement.occupancies.manager.show"]], "show() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.show"]], "show() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.show"]], "show() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.show"]], "show() (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator.show"]], "show() (mmtbx.refinement.select_best_starting_model.evaluate_model method)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.show"]], "show() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.show"]], "show_current_r_factors_summary() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.show_current_r_factors_summary"]], "show_helper() (mmtbx.refinement.occupancies.manager method)": [[313, "mmtbx.refinement.occupancies.manager.show_helper"]], "show_process_info() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_process_info"]], "show_rigid_body_rotations_and_translations() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_rigid_body_rotations_and_translations"]], "show_times() (in module mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.show_times"]], "show_times() (in module mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.show_times"]], "show_times() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_times"]], "space_group_info() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.space_group_info"]], "sphere_similarity_restraints (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.sphere_similarity_restraints"]], "split_resolution_range() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.split_resolution_range"]], "stats_table (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.stats_table"]], "steps (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.steps"]], "strip_model() (in module mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.strip_model"]], "success() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.success"]], "szs() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.szs"]], "target() (mmtbx.refinement.group.target_and_grads method)": [[313, "mmtbx.refinement.group.target_and_grads.target"]], "target() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.target"]], "target_and_gradients() (mmtbx.refinement.group.sphere_similarity_restraints method)": [[313, "mmtbx.refinement.group.sphere_similarity_restraints.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.target_and_gradients"]], "target_and_grads (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.target_and_grads"]], "target_and_grads (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.target_and_grads"]], "target_attributes (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_attributes"]], "target_function_and_grads_geometry_minimization (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization"]], "target_function_and_grads_real_space (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space"]], "target_function_and_grads_reciprocal_space (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space"]], "target_function_is_invariant_under_allowed_origin_shifts() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.target_function_is_invariant_under_allowed_origin_shifts"]], "target_functor (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_functor"]], "target_memory() (mmtbx.refinement.targets.phaser_sad_target_functor method)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor.target_memory"]], "target_per_reflection() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_per_reflection"]], "target_result (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_result"]], "target_result_mixin (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_result_mixin"]], "target_test() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_test"]], "target_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_work"]], "trajectory_output (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.trajectory_output"]], "translation() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.translation"]], "try_weight() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.try_weight"]], "ucf() (in module mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.ucf"]], "unpack() (mmtbx.refinement.anomalous_scatterer_groups.minimizer method)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer.unpack"]], "unpack_x() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.unpack_x"]], "unpack_x() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.unpack_x"]], "unpack_x() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.unpack_x"]], "update_cdl_restraints() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.update_cdl_restraints"]], "update_xray_structure() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.update_xray_structure"]], "updaterdl() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.updaterdl"]], "validate() (mmtbx.refinement.targets.target_attributes method)": [[313, "mmtbx.refinement.targets.target_attributes.validate"]], "weight_result (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.weight_result"]], "xray_line() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.xray_line"]], "xray_structure (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.xray_structure"]], "bin_generator_equal_range() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_range"]], "bin_generator_equal_size() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_size"]], "bivariate_histogram() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bivariate_histogram"]], "closest_to_mean() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.closest_to_mean"]], "dist2() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.dist2"]], "ensemble_mean_geometry_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_mean_geometry_stats"]], "ensemble_mean_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.ensemble_mean_hierarchy"]], "ensemble_reduction() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_reduction"]], "ensemble_rmsf_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_rmsf_stats"]], "get_centroid_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_centroid_hierarchy"]], "get_rmsf_b_factor_per_residue_per_atom() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_rmsf_B_factor_per_residue_per_atom"]], "get_selected_hierarchys() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, 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method)": [[315, "mmtbx.refinement.real_space.structure_monitor.assert_pdb_hierarchy_xray_structure_sync"]], "backrub_move() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.backrub_move"]], "box_refinement_manager (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager"]], "check_sites_match() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.check_sites_match"]], "cluster (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.cluster"]], "common_map_values() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.common_map_values"]], "compute_functional_and_gradients() (mmtbx.refinement.real_space.rigid_body.refine method)": [[315, "mmtbx.refinement.real_space.rigid_body.refine.compute_functional_and_gradients"]], "compute_map() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.compute_map"]], "compute_target() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.compute_target"]], "compute_target() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.compute_target"]], "compute_target() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.compute_target"]], "count_outliers() (mmtbx.refinement.real_space.fit_residues.run method)": [[315, "mmtbx.refinement.real_space.fit_residues.run.count_outliers"]], "d_e_pot_d_sites() (mmtbx.refinement.real_space.rigid_body.refine method)": [[315, "mmtbx.refinement.real_space.rigid_body.refine.d_e_pot_d_sites"]], "diff_map (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map"]], "easy (class in mmtbx.refinement.real_space.individual_sites)": [[315, 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mmtbx.refinement.real_space.fit_residues)": [[315, "mmtbx.refinement.real_space.fit_residues.fix_outliers"]], "flatten() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.flatten"]], "flatten() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.flatten"]], "format_info_string() (mmtbx.refinement.real_space.residue_monitor method)": [[315, "mmtbx.refinement.real_space.residue_monitor.format_info_string"]], "generate_angles_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.generate_angles_nested"]], "get_nonbonded_bumpers() (mmtbx.refinement.real_space.fit_residues.run method)": [[315, "mmtbx.refinement.real_space.fit_residues.run.get_nonbonded_bumpers"]], "get_radii() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radii"]], "get_radius() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radius"]], "get_rotamer_iterator() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.get_rotamer_iterator"]], "get_rotamer_iterator() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_rotamer_iterator"]], "get_target_value() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_target_value"]], "get_vector_flat() (mmtbx.refinement.real_space.cluster method)": [[315, "mmtbx.refinement.real_space.cluster.get_vector_flat"]], "grid_sample_around_c_n_axis() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.grid_sample_around_c_n_axis"]], "initialize() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.initialize"]], "initialize() (mmtbx.refinement.real_space.structure_monitor method)": [[315, 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(class in mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.refine_mz"]], "refinery (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery"]], "reset() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.reset"]], "reset() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.reset"]], "reset() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.reset"]], "residue_monitor (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.residue_monitor"]], "rmsds() (mmtbx.refinement.real_space.individual_sites.refinery method)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery.rmsds"]], "rmsds() (mmtbx.refinement.real_space.individual_sites.simple method)": [[315, "mmtbx.refinement.real_space.individual_sites.simple.rmsds"]], "rsr_model (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.rsr_model"]], "run (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.run"]], "run (class in mmtbx.refinement.real_space.fit_residues)": [[315, "mmtbx.refinement.real_space.fit_residues.run"]], "run (class in mmtbx.refinement.real_space.weight)": [[315, "mmtbx.refinement.real_space.weight.run"]], "run() (in module mmtbx.refinement.real_space.fit_water)": [[315, "mmtbx.refinement.real_space.fit_water.run"]], "run_with_minimization (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization"]], "score (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score"]], "score2 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score2"]], "score3 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score3"]], "score4 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score4"]], "sel_all() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_all"]], "sel_outliers() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers"]], "sel_outliers_and_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_and_poormap"]], "sel_outliers_or_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_or_poormap"]], "sel_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_poormap"]], "selection_around_to_negate() (in module mmtbx.refinement.real_space)": [[315, 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"mmtbx.refinement.real_space.weight.run.show"]], "show_residues() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.show_residues"]], "side_chain_fit_evaluator (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator"]], "simple (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.simple"]], "sites_cart() (mmtbx.refinement.real_space.individual_sites.diff_map method)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map.sites_cart"]], "sites_cart() (mmtbx.refinement.real_space.individual_sites.simple method)": [[315, "mmtbx.refinement.real_space.individual_sites.simple.sites_cart"]], "structure_monitor (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.structure_monitor"]], "torsion_search() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.torsion_search"]], "torsion_search_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.torsion_search_nested"]], "tune_up (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.tune_up"]], "update() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.update"]], "update() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.update"]], "update() (mmtbx.refinement.real_space.score2 method)": [[315, "mmtbx.refinement.real_space.score2.update"]], "update() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.update"]], "update() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.update"]], "update() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.update"]], "update_statistics() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.update_statistics"]], "update_target_map() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager.update_target_map"]], "update_xray_structure() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager.update_xray_structure"]], "ndimtable (class in mmtbx.rotamer.n_dim_table)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable"]], "namedrot (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.NamedRot"]], "propertyfile (class in mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.PropertyFile"]], "ramachandraneval (class in mmtbx.rotamer.ramachandran_eval)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval"]], "rotamereval (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval"]], "rotamerid (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID"]], "sidechainangles (class in mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles"]], "aatables (mmtbx.rotamer.rotamer_eval.rotamereval attribute)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.aaTables"]], "anglesforaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForAA"]], "anglesforrot (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForRot"]], "atomsforangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsForAngle"]], "atomsmovewithangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsMoveWithAngle"]], "bin2index() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index"]], "bin2index_limit() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index_limit"]], "centerof() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.centerOf"]], "check_table_name() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.check_table_name"]], "chi_angles() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.chi_angles"]], "chisperaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.chisPerAA"]], "clampinclusive() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.clampInclusive"]], "collect_residue_torsion_angles() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.collect_residue_torsion_angles"]], "collect_sidechain_chi_angles() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.collect_sidechain_chi_angles"]], "contains() (mmtbx.rotamer.rotamer_eval.namedrot method)": [[316, "mmtbx.rotamer.rotamer_eval.NamedRot.contains"]], "createfromtext() (mmtbx.rotamer.n_dim_table.ndimtable static method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.createFromText"]], "draw_plot() (mmtbx.rotamer.graphics.rotarama_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin.draw_plot"]], "draw_ramachandran_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_ramachandran_plot"]], "draw_rotamer_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_rotamer_plot"]], "eval_residue_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_residue_completeness"]], "eval_sidechain_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_sidechain_completeness"]], "evaluate() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate"]], "evaluate() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate"]], "evaluate_residue() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue"]], "evaluate_residue_2() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue_2"]], "evaluate_sites() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate_sites"]], "exercise() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.exercise"]], "extent (mmtbx.rotamer.graphics.ramachandran_plot_mixin attribute)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin.extent"]], "extent (mmtbx.rotamer.graphics.rotarama_plot_mixin attribute)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin.extent"]], "extract_chi_atoms() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.extract_chi_atoms"]], "find_rotarama_data_dir() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.find_rotarama_data_dir"]], "find_source_dir() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.find_source_dir"]], "find_source_dir() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.find_source_dir"]], "format_ramachandran_plot_title() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.format_ramachandran_plot_title"]], "frequencies_from_rotamer (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.frequencies_from_rotamer"]], "get_atom_dict() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.get_atom_dict"]], "get_omega_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_omega_atoms"]], "get_phi_psi_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_phi_psi_atoms"]], "get_phi_psi_indices() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_phi_psi_indices"]], "get_residue_ramachandran_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_ramachandran_data"]], "get_residue_rotamer_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_rotamer_data"]], "get_rotamer_angles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_angles"]], "get_rotamer_expectation_frequencies() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_expectation_frequencies"]], "get_rotamers() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamers"]], "identify() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.identify"]], "improper_cnab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_cnab_from_atoms"]], "improper_ncab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_ncab_from_atoms"]], "is_cis_peptide() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.is_cis_peptide"]], "iterator() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.iterator"]], "makeatomdict() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.makeAtomDict"]], "measureangle() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureAngle"]], "measurechiangles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureChiAngles"]], "mmtbx.rotamer": [[316, "module-mmtbx.rotamer"]], "mmtbx.rotamer.graphics": [[316, "module-mmtbx.rotamer.graphics"]], "mmtbx.rotamer.n_dim_table": [[316, "module-mmtbx.rotamer.n_dim_table"]], "mmtbx.rotamer.ramachandran_eval": [[316, "module-mmtbx.rotamer.ramachandran_eval"]], "mmtbx.rotamer.rotamer_eval": [[316, "module-mmtbx.rotamer.rotamer_eval"]], "mmtbx.rotamer.sidechain_angles": [[316, "module-mmtbx.rotamer.sidechain_angles"]], "mon_lib_query() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.mon_lib_query"]], "names (mmtbx.rotamer.rotamer_eval.rotamerid attribute)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.names"]], "nearest_rotamer_sites_cart() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.nearest_rotamer_sites_cart"]], "omega_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.omega_from_atoms"]], "open_rotarama_dlite() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.open_rotarama_dlite"]], "phi_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_atoms"]], "phi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_sites"]], "phi_psi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_psi_from_sites"]], "process() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.process"]], "process() (mmtbx.rotamer.sidechain_angles.propertyfile method)": [[316, "mmtbx.rotamer.sidechain_angles.PropertyFile.process"]], "psi_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.psi_from_atoms"]], "psi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.psi_from_sites"]], "ramachandran_plot (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot"]], "ramachandran_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin"]], "resatomstochi (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.resAtomsToChi"]], "rotamer_plot (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotamer_plot"]], "rotamer_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotamer_plot_mixin"]], "rotamersforaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.rotamersForAA"]], "rotarama_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin"]], "setvalueat() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.setValueAt"]], "set_labels() (mmtbx.rotamer.graphics.ramachandran_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin.set_labels"]], "set_labels() (mmtbx.rotamer.graphics.rotamer_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotamer_plot_mixin.set_labels"]], "valueat() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.valueAt"]], "whereis() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.whereIs"]], "wrap_chis() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.wrap_chis"]], "wrap_sym() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.wrap_sym"]], "wrapbin() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.wrapbin"]], "mmtbx.rsr": [[317, "module-mmtbx.rsr"]], "absence_type() (mmtbx.scaling.absences.conditions_for_operator method)": [[318, "mmtbx.scaling.absences.conditions_for_operator.absence_type"]], "absences (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.absences"]], "absences_list (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.absences_list"]], "acentric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_e_sq_minus_one_library"]], "acentric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_f_ratio_library"]], "acentric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_i_ratio_library"]], "add_wavelength_info() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.add_wavelength_info"]], "alpha_beta() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.alpha_beta"]], "alpha_beta() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.alpha_beta"]], "analyse() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.analyse"]], "analyze_absences (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.analyze_absences"]], "analyze_aniso_correction() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.analyze_aniso_correction"]], "analyze_intensity_statistics() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.analyze_intensity_statistics"]], "analyze_measurability (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_measurability"]], "analyze_resolution_limits (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits"]], "aniso_b_min (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_min"]], "aniso_b_ratio (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_ratio"]], "aniso_range_of_b (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_range_of_b"]], "aniso_ratio_p_value() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.aniso_ratio_p_value"]], "anisotropic_correction() (in module mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.anisotropic_correction"]], "ano_scaling (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.ano_scaling"]], "anomalous (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.anomalous"]], "apply_scale_to_original_data() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.apply_scale_to_original_data"]], "average_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver.average_all"]], "axis_type (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.axis_type"]], "basic_analyses (class in mmtbx.scaling.basic_analyses)": [[318, "mmtbx.scaling.basic_analyses.basic_analyses"]], "basic_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.basic_wilson_outliers"]], "beamstop_shadow_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.beamstop_shadow_outliers"]], "britton_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.britton_frac"]], "britton_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.britton_test"]], "calc_correlation() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.calc_correlation"]], "cc_one_half_outer (mmtbx.scaling.xtriage.merging_statistics property)": [[318, "mmtbx.scaling.xtriage.merging_statistics.cc_one_half_outer"]], "centric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_e_sq_minus_one_library"]], "centric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_f_ratio_library"]], "centric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_i_ratio_library"]], "change_symmetry() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.change_symmetry"]], "check() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check"]], "check_condition() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_condition"]], "check_conditions() (mmtbx.scaling.absences.analyze_absences method)": [[318, "mmtbx.scaling.absences.analyze_absences.check_conditions"]], "check_for_pathological_input_data() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.check_for_pathological_input_data"]], "check_mask() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_mask"]], "closest_rational() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.closest_rational"]], "cns_fa_driver (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver"]], "combined_scaling (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling"]], "comparator() (mmtbx.scaling.absences.sgi_iterator method)": [[318, "mmtbx.scaling.absences.sgi_iterator.comparator"]], "completeness_enforcement (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.completeness_enforcement"]], "component (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.component"]], "compute_coefs() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_coefs"]], "compute_coefs() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_coefs"]], "compute_determinant() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_determinant"]], "compute_determinant() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_determinant"]], "compute_fa_values() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_fa_values"]], "compute_fa_values() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_fa_values"]], "compute_functional() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_functional"]], "compute_functional_and_gradients() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.compute_functional_and_gradients"]], "compute_gradient() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient"]], "compute_gradient_fd() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient_fd"]], "compute_maha_l() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.compute_maha_l"]], "compute_ratios() (mmtbx.scaling.twin_analyses.wilson_moments method)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.compute_ratios"]], "condition() (mmtbx.scaling.absences.conditions_for_operator method)": [[318, "mmtbx.scaling.absences.conditions_for_operator.condition"]], "conditions_for_operator (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.conditions_for_operator"]], "correlation_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses"]], "curve() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.curve"]], "data_analysis (class in mmtbx.scaling)": [[318, "mmtbx.scaling.data_analysis"]], "data_as_flex_arrays() (mmtbx.scaling.relative_wilson.summary method)": [[318, "mmtbx.scaling.relative_wilson.summary.data_as_flex_arrays"]], "data_strength_and_completeness (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness"]], "data_summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.data_summary"]], "default_2wmad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_2wmad"]], "default_3wmad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_3wmad"]], "default_rip() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_rip"]], "default_sad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_sad"]], "default_sir() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_sir"]], "default_siras() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_siras"]], "delta (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.delta"]], "delta_f_prime_f_double_prime_ratio (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.delta_f_prime_f_double_prime_ratio"]], "delta_generator (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.delta_generator"]], "delta_le_page (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_le_page"]], "delta_le_page() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_le_page"]], "delta_lebedev (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_lebedev"]], "delta_lebedev() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_lebedev"]], "delta_santoro (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_santoro"]], "delta_santoro() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_santoro"]], "density_calculator (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.density_calculator"]], "detect_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers"]], "detect_outliers_rms() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_rms"]], "detect_outliers_sigma() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_sigma"]], "detect_outliers_solve() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_solve"]], "detect_pseudo_translations (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations"]], "eobs_and_ecalc_miller_array_normalizers() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.eobs_and_ecalc_miller_array_normalizers"]], "estimate_d_min() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.estimate_d_min"]], "exercise() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.exercise"]], "exercise() (in module mmtbx.scaling.thorough_outlier_test)": [[318, "mmtbx.scaling.thorough_outlier_test.exercise"]], "expected_intensity (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.expected_intensity"]], "extreme_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.extreme_wilson_outliers"]], "f_double_prime_ratio (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio"]], "find_maximum() (mmtbx.scaling.twin_analyses.correlation_analyses method)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses.find_maximum"]], "finish_job() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.finish_job"]], "flush() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.flush"]], "fom() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.fom"]], "fom() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.fom"]], "format_it() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.format_it"]], "fraction_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.fraction_outliers"]], "functional() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.functional"]], "gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein.gamma"]], "gamma_nucleic (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_nucleic"]], "gamma_protein (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein"]], "get_alpha() (mmtbx.scaling.twin_analyses.britton_test method)": [[318, "mmtbx.scaling.twin_analyses.britton_test.get_alpha"]], "get_completeness() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_completeness"]], "get_data_file() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_data_file"]], "get_log_p_solc() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.get_log_p_solc"]], "get_merging_statistics() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_merging_statistics"]], "get_r_value_total() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.get_r_value_total"]], "get_relative_wilson() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_relative_wilson"]], "get_twin_laws() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.get_twin_laws"]], "get_z_scores() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.get_z_scores"]], "gradients() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.gradients"]], "guesstimate() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.guesstimate"]], "guesstimate_mod_hkl() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.guesstimate_mod_hkl"]], "gui_output (mmtbx.scaling.loggraph_output attribute)": [[318, "mmtbx.scaling.loggraph_output.gui_output"]], "gui_output (mmtbx.scaling.xtriage_output attribute)": [[318, "mmtbx.scaling.xtriage_output.gui_output"]], "h (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.h"]], "h_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.h_frac"]], "h_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.h_test"]], "halton_x() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.halton_x"]], "has_abnormal_intensity_statistics() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_abnormal_intensity_statistics"]], "has_higher_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_higher_symmetry"]], "has_pseudo_translational_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_pseudo_translational_symmetry"]], "has_twinning() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_twinning"]], "hessian() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian"]], "hessian_transform() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian_transform"]], "high_resolution_for_twin_tests() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.high_resolution_for_twin_tests"]], "i_over_sigma_outer_shell (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.i_over_sigma_outer_shell"]], "i_over_sigma_outer_shell() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.i_over_sigma_outer_shell"]], "i_sigi_completeness_stats (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.i_sigi_completeness_stats"]], "ice_ring_checker (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.ice_ring_checker"]], "is_centric() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.is_centric"]], "is_elliptically_truncated() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.is_elliptically_truncated"]], "is_twinned() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.is_twinned"]], "iso_b_wilson (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.iso_b_wilson"]], "kernel_normalisation (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.kernel_normalisation"]], "l_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.l_test"]], "l_test_mean_l (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l"]], "l_test_mean_l_squared (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l_squared"]], "launcher (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.launcher"]], "likelihood() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.likelihood"]], "list() (mmtbx.scaling.absences.sgi_iterator method)": [[318, "mmtbx.scaling.absences.sgi_iterator.list"]], "local_lsq_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_lsq_scaling"]], "local_moment_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_moment_scaling"]], "local_nikonov_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_nikonov_scaling"]], "local_scaling_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver"]], "log_binned_completeness (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.log_binned_completeness"]], "log_p() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.log_p"]], "loggraph_output (class in mmtbx.scaling)": [[318, "mmtbx.scaling.loggraph_output"]], "low_d_cut (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.low_d_cut"]], "ls_rel_scale_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.ls_rel_scale_driver"]], "macromolecule_fraction() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.macromolecule_fraction"]], "make_big_header() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.make_big_header"]], "make_log_beam_stop() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_beam_stop"]], "make_log_model() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_model"]], "make_log_wilson() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_wilson"]], "make_pg_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_pg_r_table"]], "make_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_r_table"]], "make_sym_op_table() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.make_sym_op_table"]], "massage_data (class in mmtbx.scaling.massage_twin_detwin_data)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data"]], "matthews_n_copies() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.matthews_n_copies"]], "matthews_rupp (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.matthews_rupp"]], "max_d_min_delta() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.max_d_min_delta"]], "max_estimated_twin_fraction (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.max_estimated_twin_fraction"]], "max_twin_fraction() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.max_twin_fraction"]], "merge_data_and_guess_space_groups() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.merge_data_and_guess_space_groups"]], "merging_statistics (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.merging_statistics"]], "ml_aniso_absolute_scaling (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling"]], "ml_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.ml_frac"]], "ml_iso_absolute_scaling (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling"]], "ml_murray_rust (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust"]], "ml_murray_rust_with_ncs (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs"]], "mmtbx.scaling": [[318, "module-mmtbx.scaling"]], "mmtbx.scaling.absence_likelihood": [[318, "module-mmtbx.scaling.absence_likelihood"]], "mmtbx.scaling.absences": [[318, "module-mmtbx.scaling.absences"]], "mmtbx.scaling.absolute_scaling": [[318, "module-mmtbx.scaling.absolute_scaling"]], "mmtbx.scaling.basic_analyses": [[318, "module-mmtbx.scaling.basic_analyses"]], "mmtbx.scaling.data_statistics": [[318, "module-mmtbx.scaling.data_statistics"]], "mmtbx.scaling.fa_estimation": [[318, "module-mmtbx.scaling.fa_estimation"]], "mmtbx.scaling.fest": [[318, "module-mmtbx.scaling.fest"]], "mmtbx.scaling.make_param": [[318, "module-mmtbx.scaling.make_param"]], "mmtbx.scaling.massage_twin_detwin_data": [[318, "module-mmtbx.scaling.massage_twin_detwin_data"]], "mmtbx.scaling.matthews": [[318, "module-mmtbx.scaling.matthews"]], "mmtbx.scaling.outlier_plots": [[318, "module-mmtbx.scaling.outlier_plots"]], "mmtbx.scaling.outlier_rejection": [[318, "module-mmtbx.scaling.outlier_rejection"]], "mmtbx.scaling.pair_analyses": [[318, "module-mmtbx.scaling.pair_analyses"]], "mmtbx.scaling.pre_scale": [[318, "module-mmtbx.scaling.pre_scale"]], "mmtbx.scaling.random_omit": [[318, "module-mmtbx.scaling.random_omit"]], "mmtbx.scaling.relative_scaling": [[318, "module-mmtbx.scaling.relative_scaling"]], "mmtbx.scaling.relative_wilson": [[318, "module-mmtbx.scaling.relative_wilson"]], "mmtbx.scaling.remove_outliers": [[318, "module-mmtbx.scaling.remove_outliers"]], "mmtbx.scaling.rip_scale": [[318, "module-mmtbx.scaling.rip_scale"]], "mmtbx.scaling.sad_scale": [[318, "module-mmtbx.scaling.sad_scale"]], "mmtbx.scaling.sigmaa_estimation": [[318, "module-mmtbx.scaling.sigmaa_estimation"]], "mmtbx.scaling.sir_scale": [[318, "module-mmtbx.scaling.sir_scale"]], "mmtbx.scaling.siras_scale": [[318, "module-mmtbx.scaling.siras_scale"]], "mmtbx.scaling.ta_alpha_beta_calc": [[318, "module-mmtbx.scaling.ta_alpha_beta_calc"]], "mmtbx.scaling.thorough_outlier_test": [[318, "module-mmtbx.scaling.thorough_outlier_test"]], "mmtbx.scaling.twin_analyses": [[318, "module-mmtbx.scaling.twin_analyses"]], "mmtbx.scaling.twmad_scale": [[318, "module-mmtbx.scaling.twmad_scale"]], "mmtbx.scaling.xtriage": [[318, "module-mmtbx.scaling.xtriage"]], "model_based_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.model_based_outliers"]], "modify_weights() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.modify_weights"]], "mum_dad (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.mum_dad"]], "mum_dad (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.mum_dad"]], "n_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.n_outliers"]], "n_outliers() (mmtbx.scaling.relative_wilson.summary method)": [[318, "mmtbx.scaling.relative_wilson.summary.n_outliers"]], "n_problems (mmtbx.scaling.xtriage.summary property)": [[318, "mmtbx.scaling.xtriage.summary.n_problems"]], "n_z_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.n_z_test"]], "naive_fa_estimation (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.naive_fa_estimation"]], "new_format (mmtbx.scaling.xtriage.xtriage_analyses attribute)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.new_format"]], "new_format (mmtbx.scaling.xtriage.xtriage_summary attribute)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.new_format"]], "newline() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.newline"]], "newline() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.newline"]], "newline() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.newline"]], "normalise_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver.normalise_all"]], "nucleic() (mmtbx.scaling.matthews.component class method)": [[318, "mmtbx.scaling.matthews.component.nucleic"]], "number_of_wilson_outliers (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.number_of_wilson_outliers"]], "number_table() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.number_table"]], "obliquity (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.obliquity"]], "operator (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.operator"]], "original_intensities_flag() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.original_intensities_flag"]], "out (mmtbx.scaling.printed_output attribute)": [[318, "mmtbx.scaling.printed_output.out"]], "outlier_manager (class in mmtbx.scaling.outlier_rejection)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager"]], "outlier_rejection (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection"]], "overall_i_sig_i (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.overall_i_sig_i"]], "p_solc_calc() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.p_solc_calc"]], "p_solc_calc() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.p_solc_calc"]], "p_value() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.p_value"]], "p_vm_calculator (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.p_vm_calculator"]], "pack() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.pack"]], "pack() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.pack"]], "patterson_verdict (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.patterson_verdict"]], "patterson_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.patterson_verdict"]], "perform_least_squares_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_least_squares_scaling"]], "perform_local_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_local_scaling"]], "perform_outlier_rejection() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_outlier_rejection"]], "phase_errors() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.phase_errors"]], "phase_errors() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.phase_errors"]], "phil_lego (class in mmtbx.scaling.make_param)": [[318, "mmtbx.scaling.make_param.phil_lego"]], "plotit() (in module mmtbx.scaling.outlier_plots)": [[318, "mmtbx.scaling.outlier_plots.plotit"]], "possible_outliers (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.possible_outliers"]], "pre_scaler (class in mmtbx.scaling.pre_scale)": [[318, "mmtbx.scaling.pre_scale.pre_scaler"]], "print_banner() (in module mmtbx.scaling.fest)": [[318, "mmtbx.scaling.fest.print_banner"]], "print_banner() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.print_banner"]], "print_help() (in module mmtbx.scaling.remove_outliers)": [[318, "mmtbx.scaling.remove_outliers.print_help"]], "print_help() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.print_help"]], "printed_output (class in mmtbx.scaling)": [[318, 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"mmtbx.scaling.random_omit.random_omit_data"]], "refinery (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.refinery"]], "reindexing (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.reindexing"]], "relative_wilson (class in mmtbx.scaling.relative_wilson)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson"]], "remove_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.remove_outliers"]], "remove_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.remove_outliers"]], "resolution_cut() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.resolution_cut"]], "resolution_dependent_r_values() (mmtbx.scaling.twin_analyses.r_values method)": [[318, "mmtbx.scaling.twin_analyses.r_values.resolution_dependent_r_values"]], "resolution_limit_of_anomalous_signal() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.resolution_limit_of_anomalous_signal"]], "return_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data.return_data"]], "return_point_groups() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.return_point_groups"]], "run() (in module mmtbx.scaling.fest)": [[318, "mmtbx.scaling.fest.run"]], "run() (in module mmtbx.scaling.make_param)": [[318, "mmtbx.scaling.make_param.run"]], "run() (in module mmtbx.scaling.outlier_plots)": [[318, "mmtbx.scaling.outlier_plots.run"]], "run() (in module mmtbx.scaling.remove_outliers)": [[318, "mmtbx.scaling.remove_outliers.run"]], "run() (in module mmtbx.scaling.rip_scale)": [[318, "mmtbx.scaling.rip_scale.run"]], "run() (in module mmtbx.scaling.sad_scale)": [[318, 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"score_isigi() (mmtbx.scaling.absences.analyze_absences method)": [[318, "mmtbx.scaling.absences.analyze_absences.score_isigi"]], "select_and_transform() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.select_and_transform"]], "set_sigma_ratio() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.set_sigma_ratio"]], "set_sigma_ratio() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.set_sigma_ratio"]], "sgi_iterator (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.sgi_iterator"]], "show() (mmtbx.scaling.absences.absences_list method)": [[318, "mmtbx.scaling.absences.absences_list.show"]], "show() (mmtbx.scaling.data_analysis method)": [[318, "mmtbx.scaling.data_analysis.show"]], "show() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.show"]], "show() (mmtbx.scaling.relative_scaling.ls_rel_scale_driver method)": [[318, "mmtbx.scaling.relative_scaling.ls_rel_scale_driver.show"]], "show() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.show"]], "show() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.show"]], "show() (mmtbx.scaling.xtriage_analysis method)": [[318, "mmtbx.scaling.xtriage_analysis.show"]], "show() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show"]], "show_big_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_big_header"]], "show_big_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_big_header"]], "show_big_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_big_header"]], "show_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_header"]], "show_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_header"]], "show_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_header"]], "show_lines() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_lines"]], "show_lines() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_lines"]], "show_lines() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_lines"]], "show_paragraph_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_paragraph_header"]], "show_paragraph_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_paragraph_header"]], "show_paragraph_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_paragraph_header"]], "show_plot() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_plot"]], "show_plot() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_plot"]], "show_plot() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_plot"]], "show_plots_row() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_plots_row"]], "show_plots_row() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_plots_row"]], "show_plots_row() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_plots_row"]], "show_preformatted_text() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_preformatted_text"]], "show_preformatted_text() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_preformatted_text"]], "show_preformatted_text() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_preformatted_text"]], "show_short() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.show_short"]], "show_short() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.show_short"]], "show_sub_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_sub_header"]], "show_sub_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_sub_header"]], "show_sub_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_sub_header"]], "show_summary() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.show_summary"]], "show_table() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_table"]], "show_table() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_table"]], "show_table() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_table"]], "show_text() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_text"]], "show_text() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_text"]], "show_text() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_text"]], "show_text_columns() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_text_columns"]], "show_text_columns() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_text_columns"]], "show_text_columns() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_text_columns"]], "show_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.show_verdict"]], "show_worrisome_shells() (mmtbx.scaling.data_statistics.wilson_scaling method)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling.show_worrisome_shells"]], "sigma_gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein.sigma_gamma"]], "sigmaa() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.sigmaa"]], "sigmaa() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.sigmaa"]], "sigmaa_estimator (class in mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator"]], "sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator_kernel_width_d_star_cubed"]], "sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_estimator_kernel_width_d_star_cubed"]], "sigmaa_model_error() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.sigmaa_model_error"]], "sigmaa_model_error() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.sigmaa_model_error"]], "sigmaa_point_estimator (class in mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator"]], "sigmaa_point_estimator (class in mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator"]], "singh_ramasheshan_fa_estimate (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate"]], "singh_ramasheshan_fa_estimate (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate"]], "solc() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.solc"]], "solvent_fraction() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.solvent_fraction"]], "std() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.std"]], "strain_tensor() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.strain_tensor"]], "string_it() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.string_it"]], "suggest_likely_candidates() (mmtbx.scaling.absences.protein_space_group_choices method)": [[318, "mmtbx.scaling.absences.protein_space_group_choices.suggest_likely_candidates"]], "suggest_new_space_groups() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.suggest_new_space_groups"]], "summarize_issues() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.anomalous method)": [[318, "mmtbx.scaling.data_statistics.anomalous.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.ice_ring_checker method)": [[318, "mmtbx.scaling.data_statistics.ice_ring_checker.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.wilson_scaling method)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.data_summary method)": [[318, "mmtbx.scaling.xtriage.data_summary.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.merging_statistics method)": [[318, "mmtbx.scaling.xtriage.merging_statistics.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage_analysis method)": [[318, "mmtbx.scaling.xtriage_analysis.summarize_issues"]], "summary (class in mmtbx.scaling.relative_wilson)": [[318, "mmtbx.scaling.relative_wilson.summary"]], "summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.summary"]], "summary() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.summary"]], "symmetry_issues (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues"]], "t (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.t"]], "ta_alpha_beta_calc (class in mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc"]], "table (mmtbx.scaling.twin_analyses.britton_test property)": [[318, "mmtbx.scaling.twin_analyses.britton_test.table"]], "table (mmtbx.scaling.twin_analyses.h_test property)": [[318, "mmtbx.scaling.twin_analyses.h_test.table"]], "table (mmtbx.scaling.twin_analyses.l_test property)": [[318, "mmtbx.scaling.twin_analyses.l_test.table"]], "table (mmtbx.scaling.twin_analyses.ml_murray_rust property)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust.table"]], "table (mmtbx.scaling.twin_analyses.n_z_test property)": [[318, "mmtbx.scaling.twin_analyses.n_z_test.table"]], "target() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.target"]], "tau (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.tau"]], "test() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.test"]], "test() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.test"]], "twin_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses"]], "twin_analyses_brief() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses_brief"]], "twin_law (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law"]], "twin_law_dependent_twin_tests (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests"]], "twin_law_quality (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality"]], "twin_laws (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_laws"]], "twin_results_interpretation (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation"]], "twin_type (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.twin_type"]], "twmad_fa_driver (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.twmad_fa_driver"]], "type (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.type"]], "u (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.u"]], "unpack() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.unpack"]], "unpack() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.unpack"]], "validate_params() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.validate_params"]], "vm() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.vm"]], "vm() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.vm"]], "vm_prop_table() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.vm_prop_table"]], "warn() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.warn"]], "warn() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.warn"]], "warn() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.warn"]], "weighted_cc() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.weighted_cc"]], "wilson_moments (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments"]], "wilson_normalised_intensities (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.wilson_normalised_intensities"]], "wilson_scaling (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling"]], "write() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.write"]], "write() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.write"]], "write() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.write"]], "write_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data.write_data"]], "write_datasets() (mmtbx.scaling.random_omit.random_omit_data method)": [[318, "mmtbx.scaling.random_omit.random_omit_data.write_datasets"]], "xtriage_analyses (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses"]], "xtriage_analysis (class in mmtbx.scaling)": [[318, "mmtbx.scaling.xtriage_analysis"]], "xtriage_output (class in mmtbx.scaling)": [[318, "mmtbx.scaling.xtriage_output"]], "xtriage_summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.xtriage_summary"]], "apply_phil_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.apply_phil_str"]], "as_pdb_records() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_pdb_records"]], "as_phil_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.as_phil_str"]], "as_restraint_group_phil() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_restraint_group_phil"]], "as_restraint_groups() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_restraint_groups"]], "base_pair_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selection"]], "base_pair_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selections"]], "beta_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selection"]], "beta_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selections"]], "build_selections() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.build_selections"]], "calculate_structure_content() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.calculate_structure_content"]], "contiguous_ss_selections() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.contiguous_ss_selections"]], "create_all_new_restraints() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_all_new_restraints"]], "create_helix_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_helix_hydrogen_bond_proxies"]], "create_protein_hbond_proxies() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_protein_hbond_proxies"]], "create_sheet_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_sheet_hydrogen_bond_proxies"]], "find_approximate_helices() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_approximate_helices"]], "find_automatically() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_automatically"]], "find_base_pairs() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_base_pairs"]], "find_helices_simple (class in mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple"]], "find_sec_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_sec_str"]], "get_default_ss_params() (mmtbx.secondary_structure.manager static method)": [[319, "mmtbx.secondary_structure.manager.get_default_ss_params"]], "get_helix_types() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_helix_types"]], "get_ksdssp_exe_path() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.get_ksdssp_exe_path"]], "get_residue_name_from_selection() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.get_residue_name_from_selection"]], "get_simple_bonds() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_simple_bonds"]], "helix_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selection"]], "helix_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selections"]], "hydrogen_bond_from_selection_pair() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.hydrogen_bond_from_selection_pair"]], "initialize() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.initialize"]], "is_approximately_helical() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.is_approximately_helical"]], "manager (class in mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.manager"]], "mmtbx.secondary_structure": [[319, "module-mmtbx.secondary_structure"]], "mmtbx.secondary_structure.proteins": [[319, "module-mmtbx.secondary_structure.proteins"]], "mmtbx.secondary_structure.utils": [[319, "module-mmtbx.secondary_structure.utils"]], "process_break() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.process_break"]], "push_back() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.push_back"]], "records_for_pdb_file() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.records_for_pdb_file"]], "run() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.run"]], "run_ksdssp() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.run_ksdssp"]], "run_ksdssp_direct() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.run_ksdssp_direct"]], "sec_str_from_phil() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.sec_str_from_phil"]], "show() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.show"]], "show_summary() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.show_summary"]], "mmtbx.secondary_structure.build": [[320, "module-mmtbx.secondary_structure.build"]], "add() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.add"]], "add_new_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.add_new_solvent"]], "compare_peaks_with_positions() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.compare_peaks_with_positions"]], "find_peaks() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.find_peaks"]], "is_water_last() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.is_water_last"]], "manager (class in mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager"]], "manager (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.manager"]], "maps (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.maps"]], "master_params() (in module mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.master_params"]], "master_params() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.master_params"]], "mmtbx.solvent": [[321, "module-mmtbx.solvent"]], "mmtbx.solvent.ensemble_ordered_solvent": [[321, "module-mmtbx.solvent.ensemble_ordered_solvent"]], "mmtbx.solvent.ordered_solvent": [[321, "module-mmtbx.solvent.ordered_solvent"]], "move_solvent_to_the_end_of_atom_list() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.move_solvent_to_the_end_of_atom_list"]], "msg_accumulator (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator"]], "randomize_new_velocities() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.randomize_new_velocities"]], "randomize_velocity() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.randomize_velocity"]], "refine_adp() (mmtbx.solvent.ordered_solvent.manager method)": [[321, "mmtbx.solvent.ordered_solvent.manager.refine_adp"]], "refine_occupancies() (mmtbx.solvent.ordered_solvent.manager method)": [[321, "mmtbx.solvent.ordered_solvent.manager.refine_occupancies"]], "remove_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.remove_solvent"]], "reset_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.reset_solvent"]], "score_atom() (mmtbx.solvent.ordered_solvent.maps method)": [[321, "mmtbx.solvent.ordered_solvent.maps.score_atom"]], "set_prefix() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.set_prefix"]], "show() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.show"]], "show() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.show"]], "as_cif_block() (mmtbx.tls.tools.tls_groups method)": [[322, "mmtbx.tls.tools.tls_groups.as_cif_block"]], "check_u_cart() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.check_u_cart"]], "combine_tls_and_u_local() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.combine_tls_and_u_local"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_from_uaniso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uaniso_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_from_uiso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uiso_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_xray_target_minimizer method)": [[322, "mmtbx.tls.tools.tls_xray_target_minimizer.compute_functional_and_gradients"]], "ensemble_generator (class in mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.ensemble_generator"]], "extract_tls_from_pdb() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.extract_tls_from_pdb"]], "finite_differences_grads_of_xray_target_wrt_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.finite_differences_grads_of_xray_target_wrt_tls"]], "formula_49() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.formula_49"]], "generate_tlsos() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.generate_tlsos"]], "get_axes_and_atoms_i_seqs() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.get_axes_and_atoms_i_seqs"]], "get_u_cart() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.get_u_cart"]], "make_tlso_compatible_with_u_positive_definite() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.make_tlso_compatible_with_u_positive_definite"]], "mmtbx.tls": [[322, 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"mmtbx.validation.model_properties.atom_occupancy"]], "atom_selection (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.atom_selection"]], "atom_selection (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.atom_selection"]], "atom_selection (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.atom_selection"]], "atom_selection (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.atom_selection"]], "atom_selection (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.atom_selection"]], "atom_selection (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.atom_selection"]], "atom_selection (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.atom_selection"]], "atom_selection (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.atom_selection"]], "atom_selection (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.atom_selection"]], "atom_selection (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.atom_selection"]], "atom_selection (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.atom_selection"]], "atom_selection (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.atom_selection"]], "atom_selection (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.atom_selection"]], "atom_selection (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.atom_selection"]], "atom_selection (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.atom_selection"]], "atom_selection (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.atom_selection"]], "atom_selection (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.atom_selection"]], "atom_selection (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.atom_selection"]], "atom_selection (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.atom_selection"]], "atom_selection (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.atom_selection"]], "atom_selection (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.atom_selection"]], "atom_selection (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.atom_selection"]], "atom_selection (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atom_selection"]], "atom_selection (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.atom_selection"]], "atom_selection (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.atom_selection"]], "atom_selection (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.atom_selection"]], "atom_selection (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.atom_selection"]], "atom_selection_string() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.atom_selection_string"]], "atom_selection_string() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.atom_selection_string"]], "atoms (class in mmtbx.validation)": [[326, "mmtbx.validation.atoms"]], "atoms_info (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.atoms_info"]], "atoms_info (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.atoms_info"]], "atoms_info (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.atoms_info"]], "atoms_info (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.atoms_info"]], "atoms_info (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.atoms_info"]], "atoms_info (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.atoms_info"]], "atoms_info (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.atoms_info"]], "atoms_info (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.atoms_info"]], "atoms_info (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.atoms_info"]], "atoms_info (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atoms_info"]], "b_factor_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.b_factor_cutoff"]], "b_histogram (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_histogram"]], "b_iso (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.b_iso"]], "b_iso (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.b_iso"]], "b_iso (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.b_iso"]], "b_iso (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.b_iso"]], "b_iso (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.b_iso"]], "b_iso (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.b_iso"]], "b_iso (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.b_iso"]], "b_iso (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.b_iso"]], "b_iso_mean (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.b_iso_mean"]], "b_max (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_max"]], "b_mean (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_mean"]], "b_min (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_min"]], "bad_adps (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.bad_adps"]], "beta_ideal (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.beta_ideal"]], "bond (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bond"]], "bonds (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bonds"]], "bonds (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.bonds"]], "bonds (mmtbx.validation.rna_validate.rna_validation attribute)": [[326, "mmtbx.validation.rna_validate.rna_validation.bonds"]], "build_name_hash() (in module mmtbx.validation.utils)": 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(mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.chain_id"]], "chain_id (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.chain_id"]], "chain_id (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.chain_id"]], "chain_id (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.chain_id"]], "chain_id (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.chain_id"]], "chain_id (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.chain_id"]], "chain_id (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.chain_id"]], "chain_id (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, 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(mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.delta"]], "delta (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.delta"]], "delta (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.delta"]], "delta_angle (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.delta_angle"]], "delta_max (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.delta_max"]], "deviation (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.deviation"]], "deviation (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.deviation"]], "different_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, 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method)": [[326, "mmtbx.validation.graphics.rotarama_plot_mixin.draw_plot"]], "draw_ramachandran_plot() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.draw_ramachandran_plot"]], "draw_rotamer_plot() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.draw_rotamer_plot"]], "dummy_validation (class in mmtbx.validation)": [[326, "mmtbx.validation.dummy_validation"]], "element (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.element"]], "element (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.element"]], "element (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.element"]], "element (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.element"]], "element (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.element"]], "entity (class in mmtbx.validation)": [[326, "mmtbx.validation.entity"]], "epsilon_angle (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.epsilon_angle"]], "evalscore() (mmtbx.validation.ramalyze.ramalyze static method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evalScore"]], "evaluatescore() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evaluateScore"]], "evaluatescore() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.evaluateScore"]], "evaluate_residue() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_residue"]], "evaluate_residue() (mmtbx.validation.rotalyze.residue_evaluator method)": [[326, "mmtbx.validation.rotalyze.residue_evaluator.evaluate_residue"]], "evaluate_rotamer() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_rotamer"]], "evaluation (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.evaluation"]], "evaluation (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.evaluation"]], "everything (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.everything"]], "exercise() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.exercise"]], "export_ramachandran_distribution() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.export_ramachandran_distribution"]], "export_rotamer_distribution() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.export_rotamer_distribution"]], "extent (mmtbx.validation.graphics.rotarama_plot_mixin attribute)": [[326, "mmtbx.validation.graphics.rotarama_plot_mixin.extent"]], "extent (mmtbx.validation.ramalyze.ramachandran_plot_mixin attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_plot_mixin.extent"]], "extract_atoms_from_residue_group() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.extract_atoms_from_residue_group"]], "extract_coordinates() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.extract_coordinates"]], "extract_ligand_atom_group() (in module mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.extract_ligand_atom_group"]], "extract_ligand_residue() (in module mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.extract_ligand_residue"]], "extract_residue_groups() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.extract_residue_groups"]], "fast (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.fast"]], "fav_percent (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.fav_percent"]], "filter_dicts() (mmtbx.validation.clashscore.probe_clashscore_manager method)": [[326, "mmtbx.validation.clashscore.probe_clashscore_manager.filter_dicts"]], "find_atom_group() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.find_atom_group"]], "find_region_max_value() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.find_region_max_value"]], "find_residue() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.find_residue"]], "find_sequence_mismatches() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.find_sequence_mismatches"]], "fmodel (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.fmodel"]], "fmodel (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.fmodel"]], "fofc (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.fofc"]], "fofc (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.fofc"]], "fofc_max (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_max"]], "fofc_mean (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_mean"]], "fofc_min (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_min"]], "format_chi_angles() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.format_chi_angles"]], "format_old() (mmtbx.validation.cbetadev.cbeta method)": [[326, "mmtbx.validation.cbetadev.cbeta.format_old"]], "format_old() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.format_old"]], "format_old() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.format_old"]], "format_old() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.format_old"]], "format_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.format_old"]], "format_ramachandran_plot_title() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.format_ramachandran_plot_title"]], "format_score() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.format_score"]], "format_values() (mmtbx.validation.restraints.planarity method)": [[326, "mmtbx.validation.restraints.planarity.format_values"]], "format_values() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_angle method)": [[326, "mmtbx.validation.rna_validate.rna_angle.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_bond method)": [[326, "mmtbx.validation.rna_validate.rna_bond.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_pucker method)": [[326, "mmtbx.validation.rna_validate.rna_pucker.format_values"]], "formate_values() (mmtbx.validation.restraints.bond method)": [[326, "mmtbx.validation.restraints.bond.formate_values"]], "fsc (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.fsc"]], "get_alignment() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_alignment"]], "get_allowed_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_count_and_fraction"]], "get_allowed_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_goal"]], "get_altloc() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.get_altloc"]], "get_altloc_from_id_str() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_id_str"]], "get_altloc_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_three"]], "get_atoms_info() (in module mmtbx.validation)": [[326, "mmtbx.validation.get_atoms_info"]], "get_beta_ideal() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_beta_ideal"]], "get_bin() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_bin"]], "get_bonds_angles_rmsds() (mmtbx.validation.restraints.combined method)": [[326, "mmtbx.validation.restraints.combined.get_bonds_angles_rmsds"]], "get_cas_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_cas_from_three"]], "get_center() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_center"]], "get_chi1_chi2() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.get_chi1_chi2"]], "get_cis_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_cis_pro_count_and_fraction"]], "get_clashscore() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore"]], "get_clashscore_b_cutoff() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore_b_cutoff"]], "get_condensed_clashes() (mmtbx.validation.clashscore.probe_clashscore_manager method)": [[326, "mmtbx.validation.clashscore.probe_clashscore_manager.get_condensed_clashes"]], "get_contours() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_contours"]], "get_coordinates_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_range"]], "get_coordinates_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_ranges"]], "get_dihedral() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_dihedral"]], "get_expected_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_expected_count"]], "get_favored_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_count_and_fraction"]], "get_favored_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_goal"]], "get_favored_goal() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_favored_goal"]], "get_favored_peaks() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_peaks"]], "get_favored_regions() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_regions"]], "get_general_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_general_count_and_fraction"]], "get_gly_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_gly_count_and_fraction"]], "get_highlighted_residues() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_highlighted_residues"]], "get_ileval_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_ileval_count_and_fraction"]], "get_inverted_atoms() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_inverted_atoms"]], "get_master_phil() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_master_phil"]], "get_matching_atom_group() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_matching_atom_group"]], "get_mean_coordinate() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_mean_coordinate"]], "get_mean_coordinate_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_range"]], "get_mean_coordinate_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_ranges"]], "get_mean_xyz() (in module mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.get_mean_xyz"]], "get_missing_chains() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_missing_chains"]], "get_n_total_by_model() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_n_total_by_model"]], "get_n_total_by_model() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_n_total_by_model"]], "get_n_total_by_model() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_n_total_by_model"]], "get_occupancy() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_occupancy"]], "get_omega() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_omega"]], "get_omega_atoms() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_omega_atoms"]], "get_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_count"]], "get_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_percent"]], "get_outlier_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_outlier_plot_values"]], "get_outliers() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_outliers"]], "get_outliers_count_and_fraction() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_count_and_fraction"]], "get_outliers_fraction_for_model() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_fraction_for_model"]], "get_outliers_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_outliers_goal"]], "get_outliers_goal() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_outliers_goal"]], "get_outliers_goal() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_goal"]], "get_outliers_table() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_outliers_table"]], "get_phi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_phi"]], "get_phi_psi_dict() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.get_phi_psi_dict"]], "get_phi_psi_residues_count() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_phi_psi_residues_count"]], "get_plot_data() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plot_data"]], "get_plot_data() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_plot_data"]], "get_plots() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plots"]], "get_prepro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_prepro_count_and_fraction"]], "get_psi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_psi"]], "get_ranges() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_ranges"]], "get_real_space_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_real_space_plot_values"]], "get_relative_sequence_copy_number() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_relative_sequence_copy_number"]], "get_residue_key() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_residue_key"]], "get_residue_range() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_residue_range"]], "get_result_class() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_class"]], "get_result_class() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_result_class"]], "get_result_class() (mmtbx.validation.experimental.real_space method)": [[326, "mmtbx.validation.experimental.real_space.get_result_class"]], "get_result_class() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_angles method)": [[326, "mmtbx.validation.rna_validate.rna_angles.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_bonds method)": [[326, "mmtbx.validation.rna_validate.rna_bonds.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_result_class"]], "get_result_class() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_result_class"]], "get_result_class() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_result_class"]], "get_result_class() (mmtbx.validation.waters.waters method)": [[326, "mmtbx.validation.waters.waters.get_result_class"]], "get_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_count"]], "get_rna_backbone_dihedrals() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rna_backbone_dihedrals"]], "get_rna_pucker_ref() (mmtbx.validation.rna_validate.rna_pucker_ref method)": [[326, "mmtbx.validation.rna_validate.rna_pucker_ref.get_rna_pucker_ref"]], "get_rotarama_data() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rotarama_data"]], "get_segid_as_chainid() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_segid_as_chainid"]], "get_selected() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_selected"]], "get_sequence_n_copies() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies"]], "get_sequence_n_copies_from_files() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies_from_files"]], "get_sugar_xyz_mean() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_sugar_xyz_mean"]], "get_table_data() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_table_data"]], "get_trans_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_trans_pro_count_and_fraction"]], "get_weighted_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_count"]], "get_weighted_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_percent"]], "get_weighted_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_result_count"]], "group_chains_and_sequences() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.group_chains_and_sequences"]], "gui_formats (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_formats"]], "gui_formats (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_formats"]], "gui_formats (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_formats"]], "gui_formats (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_formats"]], "gui_formats (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_formats"]], "gui_formats (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_formats"]], "gui_formats (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.gui_formats"]], "gui_formats (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.gui_formats"]], "gui_formats (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.gui_formats"]], "gui_formats (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.gui_formats"]], "gui_formats (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.gui_formats"]], "gui_formats (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.gui_formats"]], "gui_list_headers (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_list_headers"]], "gui_list_headers (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_list_headers"]], "gui_list_headers (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_list_headers"]], "gui_list_headers (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_list_headers"]], "gui_list_headers (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_list_headers"]], "gui_list_headers (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.gui_list_headers"]], "gui_list_headers (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.gui_list_headers"]], "has_heavy_atoms() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.has_heavy_atoms"]], "header() (mmtbx.validation.cbetadev.cbeta static method)": [[326, "mmtbx.validation.cbetadev.cbeta.header"]], "header() (mmtbx.validation.clashscore.clash static method)": [[326, "mmtbx.validation.clashscore.clash.header"]], "header() (mmtbx.validation.entity static method)": [[326, "mmtbx.validation.entity.header"]], "header() (mmtbx.validation.experimental.residue_real_space static method)": [[326, "mmtbx.validation.experimental.residue_real_space.header"]], "header() (mmtbx.validation.ramalyze.ramachandran static method)": [[326, "mmtbx.validation.ramalyze.ramachandran.header"]], "header() (mmtbx.validation.restraints.bond static method)": [[326, "mmtbx.validation.restraints.bond.header"]], "header() (mmtbx.validation.restraints.planarity static method)": [[326, "mmtbx.validation.restraints.planarity.header"]], "header() (mmtbx.validation.restraints.restraint static method)": [[326, "mmtbx.validation.restraints.restraint.header"]], "header() (mmtbx.validation.rna_validate.rna_angle static method)": [[326, "mmtbx.validation.rna_validate.rna_angle.header"]], "header() (mmtbx.validation.rna_validate.rna_bond static method)": [[326, "mmtbx.validation.rna_validate.rna_bond.header"]], "header() (mmtbx.validation.rna_validate.rna_pucker static method)": [[326, "mmtbx.validation.rna_validate.rna_pucker.header"]], "header() (mmtbx.validation.rotalyze.rotamer static method)": [[326, "mmtbx.validation.rotalyze.rotamer.header"]], "header() (mmtbx.validation.waters.water static method)": [[326, "mmtbx.validation.waters.water.header"]], "icode (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.icode"]], "icode (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.icode"]], "icode (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.icode"]], "icode (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.icode"]], "icode (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.icode"]], "icode (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.icode"]], "icode (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.icode"]], "icode (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.icode"]], "icode (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.icode"]], "icode (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.icode"]], "icode (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.icode"]], "icode (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.icode"]], "icode (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.icode"]], "icode (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.icode"]], "icode (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.icode"]], "icode (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.icode"]], "id_str (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.id_str"]], "id_str (mmtbx.validation.ramalyze.c_alpha attribute)": [[326, "mmtbx.validation.ramalyze.c_alpha.id_str"]], "id_str() (mmtbx.validation.atom_base method)": [[326, "mmtbx.validation.atom_base.id_str"]], "id_str() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str"]], "id_str() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.id_str"]], "id_str() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.id_str"]], "id_str() (mmtbx.validation.model_properties.atom_occupancy method)": [[326, "mmtbx.validation.model_properties.atom_occupancy.id_str"]], "id_str() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.id_str"]], "id_str() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.id_str"]], "id_str() (mmtbx.validation.rna_validate.rna_angle method)": [[326, "mmtbx.validation.rna_validate.rna_angle.id_str"]], "id_str() (mmtbx.validation.rna_validate.rna_bond method)": [[326, "mmtbx.validation.rna_validate.rna_bond.id_str"]], "id_str() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.id_str"]], "id_str_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_no_atom_name"]], "id_str_old() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.id_str_old"]], "id_str_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.id_str_old"]], "id_str_src_atom_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_src_atom_no_atom_name"]], "ideal (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.ideal"]], "ideal_xyz (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.ideal_xyz"]], "idealized_calpha_angles() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.idealized_calpha_angles"]], "ignore_hd (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.ignore_hd"]], "incomplete (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.incomplete"]], "incomplete (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.incomplete"]], "increment_category_counts() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.increment_category_counts"]], "info (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.info"]], "isprepro() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.isPrePro"]], "is_bad_water() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_bad_water"]], "is_cis_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_cis_peptide"]], "is_cis_peptide() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.is_cis_peptide"]], "is_delta_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_delta_outlier"]], "is_epsilon_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_epsilon_outlier"]], "is_handedness_swap() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_handedness_swap"]], "is_heavy_atom() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_heavy_atom"]], "is_in_chain() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_in_chain"]], "is_outlier() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_outlier"]], "is_pseudochiral() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_pseudochiral"]], "is_same_residue() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue"]], "is_same_residue_group() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue_group"]], "is_similar() (mmtbx.validation.clashscore.probe_line_info method)": [[326, "mmtbx.validation.clashscore.probe_line_info.is_similar"]], "is_single_residue_object() (mmtbx.validation.atom method)": [[326, "mmtbx.validation.atom.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_single_residue_object"]], "is_trans_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_trans_peptide"]], "iter_residue_groups() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.iter_residue_groups"]], "iter_results() (mmtbx.validation.model_properties.xray_structure_statistics method)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.iter_results"]], "iter_results() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.iter_results"]], "kinemage_header (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.kinemage_header"]], "kinemage_key() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.kinemage_key"]], "label (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.label"]], "label (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.label"]], "label (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.label"]], "labels (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.labels"]], "ligand_validation (class in mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.ligand_validation"]], "ligands (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.ligands"]], "list_dict (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.list_dict"]], "local_altloc_from_atoms() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.local_altloc_from_atoms"]], "macromolecules (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.macromolecules"]], "marks (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.marks"]], "markup (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.markup"]], "markup (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.markup"]], "match_dihedral_to_name() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.match_dihedral_to_name"]], "max (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.max"]], "max (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.max"]], "max (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.max"]], "max (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.max"]], "max (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.max"]], "max (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.max"]], "max_b_factor (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.max_b_factor"]], "mean (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.mean"]], "mean (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.mean"]], "mean (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.mean"]], "mean (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.mean"]], "mean (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.mean"]], "mean (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.mean"]], "merge_dict() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.merge_dict"]], "merge_two_dicts() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.merge_two_dicts"]], "merging_and_model_statistics() (in module mmtbx.validation.experimental)": [[326, "mmtbx.validation.experimental.merging_and_model_statistics"]], "min (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.min"]], "min (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.min"]], "min (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.min"]], "min (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.min"]], "min (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.min"]], "min (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.min"]], "mmtbx.validation": [[326, "module-mmtbx.validation"]], "mmtbx.validation.analyze_peptides": [[326, "module-mmtbx.validation.analyze_peptides"]], "mmtbx.validation.cbetadev": [[326, "module-mmtbx.validation.cbetadev"]], "mmtbx.validation.clashscore": [[326, "module-mmtbx.validation.clashscore"]], "mmtbx.validation.experimental": [[326, "module-mmtbx.validation.experimental"]], "mmtbx.validation.graphics": [[326, "module-mmtbx.validation.graphics"]], "mmtbx.validation.ligands": [[326, "module-mmtbx.validation.ligands"]], "mmtbx.validation.model_properties": [[326, "module-mmtbx.validation.model_properties"]], "mmtbx.validation.ramalyze": [[326, "module-mmtbx.validation.ramalyze"]], "mmtbx.validation.restraints": [[326, "module-mmtbx.validation.restraints"]], "mmtbx.validation.rna_validate": [[326, "module-mmtbx.validation.rna_validate"]], "mmtbx.validation.rotalyze": [[326, "module-mmtbx.validation.rotalyze"]], "mmtbx.validation.sequence": [[326, "module-mmtbx.validation.sequence"]], "mmtbx.validation.utils": [[326, "module-mmtbx.validation.utils"]], "mmtbx.validation.waters": [[326, "module-mmtbx.validation.waters"]], "model (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.model"]], "model (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.model"]], "model (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.model"]], "model (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.model"]], "model (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.model"]], "model_id (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.model_id"]], "model_id (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.model_id"]], "model_id (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.model_id"]], "model_id (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.model_id"]], "model_id (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.model_id"]], "model_id (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.model_id"]], "model_id (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.model_id"]], "model_id (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.model_id"]], "model_id (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.model_id"]], "model_id (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.model_id"]], "model_id (mmtbx.validation.waters.water attribute)": [[326, 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(mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.wx_column_widths"]], "wx_column_widths (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.wx_column_widths"]], "wx_column_widths (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.wx_column_widths"]], "wx_column_widths (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.wx_column_widths"]], "wx_column_widths (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.wx_column_widths"]], "wx_column_widths (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.wx_column_widths"]], "wx_column_widths (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, 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"mmtbx.validation.atom_info.xyz"]], "xyz (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.xyz"]], "xyz (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.xyz"]], "xyz (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.xyz"]], "xyz (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.xyz"]], "xyz (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.xyz"]], "xyz (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.xyz"]], "xyz (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.xyz"]], "xyz (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.xyz"]], "xyz (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.xyz"]], "xyz (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.xyz"]], "xyz (mmtbx.validation.ramalyze.c_alpha attribute)": [[326, "mmtbx.validation.ramalyze.c_alpha.xyz"]], "xyz (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.xyz"]], "xyz (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.xyz"]], "xyz (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.xyz"]], "xyz (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.xyz"]], "xyz (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.xyz"]], "xyz (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.xyz"]], "xyz (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.xyz"]], "xyz (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.xyz"]], "xyz (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.xyz"]], "xyz (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.xyz"]], "xyz (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.xyz"]], "xyz (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.xyz"]], "xyz (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.xyz"]], "xyz (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.xyz"]], "xyz (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.xyz"]], "xyz_center (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.xyz_center"]], "z_max (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_max"]], "z_max (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_max"]], "z_max (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_max"]], "z_max (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_max"]], "z_max (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_max"]], "z_max (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_max"]], "z_mean (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_mean"]], "z_mean (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_mean"]], "z_mean (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_mean"]], "z_mean (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_mean"]], "z_mean (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_mean"]], "z_mean (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_mean"]], "z_min (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_min"]], "z_min (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_min"]], "z_min (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_min"]], "z_min (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_min"]], "z_min (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_min"]], "z_min (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_min"]], "zero_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.zero_occ"]], "zoom_info() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.zoom_info"]], "molprobityparser (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.MolProbityParser"]], "molprobitytemplate (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.MolProbityTemplate"]], "add_default_options() (mmtbx.validation.molprobity.molprobityparser method)": [[327, "mmtbx.validation.molprobity.MolProbityParser.add_default_options"]], "add_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.add_outlier"]], "adp_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.adp_stats"]], "altloc (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.altloc"]], "angle_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.angle_rmsd"]], "as_mmcif_records() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.as_mmcif_records"]], "as_multi_criterion_view() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.as_multi_criterion_view"]], "atom_selection (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.atom_selection"]], "atoms_to_observations_ratio() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.atoms_to_observations_ratio"]], "b_iso_mean() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.b_iso_mean"]], "binned_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.binned_data"]], "bond_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.bond_rmsd"]], "c_beta_deviations (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.c_beta_deviations"]], "cbeta_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.cbeta_outliers"]], "cbetadev (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.cbetadev"]], "chain_id (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.chain_id"]], "clashes (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.clashes"]], "clashscore (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.clashscore"]], "clashscore() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.clashscore"]], "crystal_symmetry (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.crystal_symmetry"]], "d_max (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.d_max"]], "d_max_min() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.d_max_min"]], "d_min (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.d_min"]], "d_min (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.d_min"]], "d_min() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.d_min"]], "data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.data"]], "data_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.data_stats"]], "display_wx_plots() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.display_wx_plots"]], "display_wx_plots() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.display_wx_plots"]], "file_name (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.file_name"]], "finalize_coords() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.finalize_coords"]], "find_missing_atoms() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.find_missing_atoms"]], "fmodel_statistics_by_resolution() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_by_resolution"]], "fmodel_statistics_graph_data() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_graph_data"]], "formats (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.formats"]], "get_altloc() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_altloc"]], "get_atoms_str() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_atoms_str"]], "get_bond_and_angle_outliers() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_bond_and_angle_outliers"]], "get_master_phil() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_master_phil"]], "get_outlier_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_outlier_plot_values"]], "get_polygon_statistics() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_polygon_statistics"]], "get_real_space_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_real_space_plot_values"]], "get_residue_group_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_residue_group_data"]], "get_results_as_pdb_json() (mmtbx.validation.molprobity.molprobitytemplate method)": [[327, "mmtbx.validation.molprobity.MolProbityTemplate.get_results_as_PDB_JSON"]], "get_statistics_for_phenix_gui() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_statistics_for_phenix_gui"]], "get_y_limits() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_y_limits"]], "header_info (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.header_info"]], "hydrogens (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.hydrogens"]], "i_seq (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.i_seq"]], "icode (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.icode"]], "is_cbeta_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_cbeta_outlier"]], "is_clash_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_clash_outlier"]], "is_geometry_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_geometry_outlier"]], "is_map_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_map_outlier"]], "is_phenix_refinement() (mmtbx.validation.molprobity.pdb_header_info method)": [[327, "mmtbx.validation.molprobity.pdb_header_info.is_phenix_refinement"]], "is_populated (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.is_populated"]], "is_ramachandran_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_ramachandran_outlier"]], "is_rotamer_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_rotamer_outlier"]], "iter_molprobity_gui_fields() (mmtbx.validation.molprobity.summary method)": [[327, "mmtbx.validation.molprobity.summary.iter_molprobity_gui_fields"]], "kinemage_file (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.kinemage_file"]], "labels (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.labels"]], "merging (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.merging"]], "missing_atoms (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.missing_atoms"]], "mmtbx.validation.molprobity": [[327, "module-mmtbx.validation.molprobity"]], "mmtbx.validation.molprobity.mp_geo": [[327, "module-mmtbx.validation.molprobity.mp_geo"]], "mmtbx.validation.molprobity.nqh_minimize": [[327, "module-mmtbx.validation.molprobity.nqh_minimize"]], "model (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model"]], "model_statistics_geometry (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_statistics_geometry"]], "model_statistics_geometry_result (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_statistics_geometry_result"]], "model_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_stats"]], "model_stats_new (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_stats_new"]], "molprobity (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity"]], "molprobity_flags() (in module mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity_flags"]], "molprobity_score() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.molprobity_score"]], "molprobity_version_number (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.molprobity_version_number"]], "mpscore (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.mpscore"]], "multi_criterion_view (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.multi_criterion_view"]], "n_confs (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.n_confs"]], "n_tls_groups (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.n_tls_groups"]], "neutron_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.neutron_stats"]], "nqh_flips (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.nqh_flips"]], "occupancy (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.occupancy"]], "omegalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.omegalyze"]], "outlier (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outlier"]], "outliers (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outliers"]], "parse_user_mods() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.parse_user_mods"]], "pdb_header_info (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.pdb_header_info"]], "pdb_hierarchy (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.pdb_hierarchy"]], "polygon_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.polygon_stats"]], "process_outliers() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.process_outliers"]], "program (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.program"]], "r_free (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.r_free"]], "r_free (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.r_free"]], "r_free() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.r_free"]], "r_work (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.r_work"]], "r_work (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.r_work"]], "r_work() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.r_work"]], "rama_allowed() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_allowed"]], "rama_favored (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rama_favored"]], "rama_favored() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_favored"]], "rama_outliers (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rama_outliers"]], "rama_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_outliers"]], "ramalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.ramalyze"]], "real_space (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.real_space"]], "refinement_program (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.refinement_program"]], "residue_multi_criterion (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion"]], "residues (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.residues"]], "resname (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.resname"]], "resseq (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.resseq"]], "restraints (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.restraints"]], "rms_angles (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.rms_angles"]], "rms_angles() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rms_angles"]], "rms_bonds (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.rms_bonds"]], "rms_bonds() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rms_bonds"]], "rna (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.rna"]], "rota_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rota_outliers"]], "rotalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.rotalyze"]], "rotamer_outliers (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rotamer_outliers"]], "run() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.run"]], "run() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.run"]], "run_molprobity_program() (in module mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.run_molprobity_program"]], "score (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.score"]], "segid (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.segid"]], "sequence (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.sequence"]], "show() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.show"]], "show() (mmtbx.validation.molprobity.pdb_header_info method)": [[327, "mmtbx.validation.molprobity.pdb_header_info.show"]], "show() (mmtbx.validation.molprobity.summary method)": [[327, "mmtbx.validation.molprobity.summary.show"]], "show_summary() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.show_summary"]], "space_group() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.space_group"]], "space_group_info() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.space_group_info"]], "summarize() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.summarize"]], "summary (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.summary"]], "twin_law() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.twin_law"]], "unit_cell() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.unit_cell"]], "waters (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.waters"]], "wilson_b (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.wilson_b"]], "write_coot_script() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.write_coot_script"]], "xtriage (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.xtriage"]], "xyz (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.xyz"]], "add_nodes_to_query_if_needed_in_place() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.add_nodes_to_query_if_needed_in_place"]], "alt_atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.alt_atom_id"]], "atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.atom_id"]], "atoms (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.atoms"]], "ccp4_partial_charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ccp4_partial_charge"]], "ccp4_type_energy (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ccp4_type_energy"]], "charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.charge"]], "chem_comp_atom (class in mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom"]], "chemical_id_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.chemical_id_search"]], "combine_split_structure() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.combine_split_structure"]], "comp_id (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.comp_id"]], "count_non_hydrogen_atoms() (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.count_non_hydrogen_atoms"]], "descriptor (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.descriptor"]], "fetch_pdb_data() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.fetch_pdb_data"]], "filter_pdb_file (class in mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.filter_pdb_file"]], "find_data_arrays() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.find_data_arrays"]], "get_cif_float() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_float"]], "get_cif_int() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_int"]], "get_cif_number() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_number"]], "get_high_resolution_and_residue_count_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_and_residue_count_for_structures"]], "get_high_resolution_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_for_structures"]], "get_ligand_info_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_ligand_info_for_structures"]], "get_program() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.get_program"]], "get_r_work_rfree_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_r_work_rfree_for_structures"]], "mmtbx.wwpdb": [[328, "module-mmtbx.wwpdb"]], "mmtbx.wwpdb.rcsb_web_services": [[328, "module-mmtbx.wwpdb.rcsb_web_services"]], "mmtbx.wwpdb.standard_geometry_cif": [[328, "module-mmtbx.wwpdb.standard_geometry_cif"]], "mmtbx.wwpdb.utils": [[328, "module-mmtbx.wwpdb.utils"]], "pdbx_align (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_align"]], "pdbx_aromatic_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_aromatic_flag"]], "pdbx_leaving_atom_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_leaving_atom_flag"]], "pdbx_model_cartn_x_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_x_ideal"]], "pdbx_model_cartn_y_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_y_ideal"]], "pdbx_model_cartn_z_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_z_ideal"]], "pdbx_ordinal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_ordinal"]], "pdbx_stereo_config (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_stereo_config"]], "polymeric_type_filter() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.polymeric_type_filter"]], "post_query() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_query"]], "post_report_query_with_pdb_list() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_report_query_with_pdb_list"]], "process_chem_comp_atom_buffer (class in mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer"]], "process_chem_comps() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comps"]], "ref_radii_asa_probe (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ref_radii_asa_probe"]], "resolution_filter() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.resolution_filter"]], "sequence_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.sequence_search"]], "site_ideal() (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.site_ideal"]], "type_symbol (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.type_symbol"]], "accessor() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.accessor"]], "accessor() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.accessor"]], "accessor() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.accessor"]], "accessor() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.accessor"]], "accessor() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.accessor"]], "accessor() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.accessor"]], "accessor() (scitbx.array_family.flex.py_object method)": [[331, "scitbx.array_family.flex.py_object.accessor"]], "accessor() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.accessor"]], "accessor() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.accessor"]], "accessor() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.accessor"]], "accessor() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.accessor"]], "accessor() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.accessor"]], "accessor() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.accessor"]], "add_selected() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.add_selected"]], "all() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all"]], "all() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all"]], "all() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all"]], "all() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all"]], "all() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.all"]], "all() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all"]], "all() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all"]], "all() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all"]], "all() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all"]], "all() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.all"]], "all() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.all"]], "all() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.all"]], "all() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.all"]], "all_approx_equal() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal"]], "all_approx_equal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal"]], "all_approx_equal_relatively() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal_relatively"]], "all_approx_equal_relatively() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal_relatively"]], "all_eq() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all_eq"]], "all_eq() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_eq"]], "all_eq() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_eq"]], "all_eq() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_eq"]], "all_eq() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_eq"]], "all_eq() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_eq"]], "all_eq() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_eq"]], "all_eq() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_eq"]], "all_ge() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_ge"]], "all_ge() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_ge"]], "all_ge() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_ge"]], "all_ge() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_ge"]], "all_ge() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_ge"]], "all_gt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_gt"]], "all_gt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_gt"]], "all_gt() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_gt"]], "all_gt() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_gt"]], "all_gt() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_gt"]], "all_le() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_le"]], "all_le() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_le"]], "all_le() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_le"]], "all_le() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_le"]], "all_le() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_le"]], "all_lt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_lt"]], "all_lt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_lt"]], "all_lt() (scitbx.array_family.flex.int method)": [[331, 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(scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_ne"]], "all_size (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.all_size"]], "angle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.angle"]], "angle() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.angle"]], "append() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.append"]], "append() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.append"]], "append() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.append"]], "append() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.append"]], "append() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.append"]], "append() 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(scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.origin"]], "origin() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.origin"]], "origin() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.origin"]], "origin() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.origin"]], "part_names() (scitbx.array_family.flex.complex_double static method)": [[331, "scitbx.array_family.flex.complex_double.part_names"]], "part_names() (scitbx.array_family.flex.vec3_double static method)": [[331, "scitbx.array_family.flex.vec3_double.part_names"]], "parts() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.parts"]], "parts() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.parts"]], "parts() (scitbx.array_family.flex.vec3_double method)": 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method)": [[331, "scitbx.array_family.flex.bool.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.sym_mat3_double method)": [[331, 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method)": [[334, "scitbx.matrix.rec.norm_sq"]], "normalize() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.normalize"]], "ortho() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.ortho"]], "outer_product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.outer_product"]], "product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.product"]], "quaternion_inverse() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.quaternion_inverse"]], "r3_rotation_matrix_as_unit_quaternion() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.r3_rotation_matrix_as_unit_quaternion"]], "r3_rotation_matrix_as_x_y_z_angles() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.r3_rotation_matrix_as_x_y_z_angles"]], "rec (class in scitbx.matrix)": [[334, "scitbx.matrix.rec"]], "resolve_partitions() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.resolve_partitions"]], "rotate() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.rotate"]], "rotate_2d() 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"scitbx.matrix.rec.trace"]], "transpose() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.transpose"]], "transpose_multiply() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.transpose_multiply"]], "unit_quaternion_as_axis_and_angle() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.unit_quaternion_as_axis_and_angle"]], "unit_quaternion_as_r3_rotation_matrix() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.unit_quaternion_as_r3_rotation_matrix"]], "unit_quaternion_product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.unit_quaternion_product"]], "vector_to_001_rotation() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.vector_to_001_rotation"]], "load_cxi_phil() (in module xfel.phil_preferences)": [[337, "xfel.phil_preferences.load_cxi_phil"]], "xfel": [[337, "module-xfel"]], "xfel.phil_preferences": [[337, "module-xfel.phil_preferences"]], "xfel.cftbx": [[338, "module-xfel.cftbx"]], "add_tiles_to_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.add_tiles_to_cbf"]], "cbf_file_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.cbf_file_to_basis_dict"]], "copy_cbf_header() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.copy_cbf_header"]], "env_dxtbx_from_slac_metrology() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.env_dxtbx_from_slac_metrology"]], "format_object_from_data() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.format_object_from_data"]], "get_calib_file_path() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_calib_file_path"]], "get_cspad_cbf_handle() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_cspad_cbf_handle"]], "map_detector_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.map_detector_to_basis_dict"]], "metro_phil_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.metro_phil_to_basis_dict"]], "metrology2phil() (in module xfel.cftbx.detector.metrology2phil)": [[339, "xfel.cftbx.detector.metrology2phil.metrology2phil"]], "read_optical_metrology_from_flat_file() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.read_optical_metrology_from_flat_file"]], "sections2phil() (in module xfel.cftbx.detector.metrology2phil)": [[339, "xfel.cftbx.detector.metrology2phil.sections2phil"]], "write_cspad_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.write_cspad_cbf"]], "xfel.cftbx.detector": [[339, "module-xfel.cftbx.detector"]], "xfel.cftbx.detector.cspad_cbf_tbx": [[339, "module-xfel.cftbx.detector.cspad_cbf_tbx"]], "xfel.cftbx.detector.metrology2phil": [[339, "module-xfel.cftbx.detector.metrology2phil"]], "angstroms_to_ev (xfel.clustering.singleframe.singleframe attribute)": [[340, "xfel.clustering.singleframe.SingleFrame.ANGSTROMS_TO_EV"]], "cluster (class in xfel.clustering.cluster)": [[340, "xfel.clustering.cluster.Cluster"]], "singleframe (class in xfel.clustering.singleframe)": [[340, "xfel.clustering.singleframe.SingleFrame"]], "__dict__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__dict__"]], "__init__() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.__init__"]], "__init__() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.__init__"]], "__len__() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.__len__"]], "__module__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__module__"]], "__module__ (xfel.clustering.singleframe.singleframe attribute)": [[340, "xfel.clustering.singleframe.SingleFrame.__module__"]], "__weakref__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__weakref__"]], "ab_cluster() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.ab_cluster"]], "all_frames_intensity_stats() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.all_frames_intensity_stats"]], "best_by_cc() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.best_by_CC"]], "distance_from() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.distance_from"]], "dump_as_mtz() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_as_mtz"]], "dump_file_list() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_file_list"]], "filter_negative_intensities() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.filter_negative_intensities"]], "from_crystal_symmetries() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_crystal_symmetries"]], "from_directories() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_directories"]], "from_expts() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_expts"]], "from_files() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_files"]], "from_iterable() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_iterable"]], "from_list() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_list"]], "init_calc_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.init_calc_wilson"]], "intensity_statistics() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.intensity_statistics"]], "make_g6() (xfel.clustering.singleframe.singleframe static method)": [[340, "xfel.clustering.singleframe.SingleFrame.make_g6"]], "make_sub_cluster() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.make_sub_cluster"]], "merge_dict() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.merge_dict"]], "n_reflections_by_sigi() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.n_reflections_by_sigi"]], "plot_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.plot_wilson"]], "point_group_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.point_group_filter"]], "polarization_correction() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.polarization_correction"]], "prime_postrefine() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.prime_postrefine"]], "print_ucs() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.print_ucs"]], "to_panda() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.to_panda"]], "to_pandas() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.to_pandas"]], "total_intensity_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.total_intensity_filter"]], "trim_res_limit() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.trim_res_limit"]], "uc_feature_vector() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.uc_feature_vector"]], "unit_cell_info() (in module xfel.clustering.cluster_groups)": [[340, "xfel.clustering.cluster_groups.unit_cell_info"]], "visualise_orientational_distribution() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.visualise_orientational_distribution"]], "xfel.clustering.cluster": [[340, "module-xfel.clustering.cluster"]], "xfel.clustering.cluster_groups": [[340, "module-xfel.clustering.cluster_groups"]], "xfel.clustering.singleframe": [[340, "module-xfel.clustering.singleframe"]], "outliercellerror": [[341, "xfel.command_line.cxi_merge.OutlierCellError"]], "pixelfiterror": [[341, "xfel.command_line.view_pixel_histograms.PixelFitError"]], "wrongbravaiserror": [[341, "xfel.command_line.cxi_merge.WrongBravaisError"]], "add_cell() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cell"]], "add_cells() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cells"]], "add_frame() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.add_frame"]], "apply_sub_pixel_metrology() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.apply_sub_pixel_metrology"]], "check_image() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.check_image"]], "check_pixel_histogram_fit() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.check_pixel_histogram_fit"]], "consistent_set_and_model() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.consistent_set_and_model"]], "convert_2x2() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.convert_2x2"]], "convert_detector() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.convert_detector"]], "convert_detector() (in module xfel.command_line.convert_gain_map_cbf)": [[341, "xfel.command_line.convert_gain_map_cbf.convert_detector"]], "crystfel_to_cctbx_coord_system() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.crystfel_to_cctbx_coord_system"]], "data() (xfel.command_line.convert_gain_map.fake_cspad_elementv2 method)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2.data"]], "determine_mean_i_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.determine_mean_I_mproc"]], "distance() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.distance"]], "estimate_signal_to_noise() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.estimate_signal_to_noise"]], "estimate_signal_to_noise() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.estimate_signal_to_noise"]], "fake_config (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_config"]], "fake_cspad_elementv2 (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2"]], "fake_env (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_env"]], "fake_evt (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_evt"]], "fake_get_config() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_get_config"]], "finalize_and_save_data() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.finalize_and_save_data"]], "fit_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.fit_one_histogram"]], "fourier_filter() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.fourier_filter"]], "full_width_half_max() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.full_width_half_max"]], "generate_data_from_streams() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_data_from_streams"]], "generate_streams_from_path() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_streams_from_path"]], "getconfig() (xfel.command_line.convert_gain_map.fake_env method)": [[341, "xfel.command_line.convert_gain_map.fake_env.getConfig"]], "getcspadquads() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getCsPadQuads"]], "gettime() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getTime"]], "get_average_cell_dimensions() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.get_average_cell_dimensions"]], "get_boundaries_from_sensor_id() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_boundaries_from_sensor_ID"]], "get_observations() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_observations"]], "get_overall_correlation() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.get_overall_correlation"]], "get_phil() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.get_phil"]], "get_plot_statistics() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.get_plot_statistics"]], "get_tile_center() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_center"]], "get_tile_coords() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_coords"]], "get_tile_id() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_id"]], "hist_outline() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.hist_outline"]], "image_template() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.image_template"]], "interpolate() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.interpolate"]], "keywise_printout() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.keywise_printout"]], "load_result() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.load_result"]], "make_int_pickle() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.make_int_pickle"]], "match_runs() (in module xfel.command_line.auto_submit)": [[341, "xfel.command_line.auto_submit.match_runs"]], "pixel_histograms (class in xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms"]], "pixels() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.pixels"]], "plot() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot"]], "plot_gaussians() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_gaussians"]], "plot_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_one_histogram"]], "plot_overall_completeness() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_overall_completeness"]], "plot_statistics (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_statistics"]], "plot_statistics_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_statistics_histograms"]], "plot_unit_cell_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_unit_cell_histograms"]], "point_in_polygon() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_in_polygon"]], "point_inside_circle() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_inside_circle"]], "postrefine_by_frame_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.postrefine_by_frame_mproc"]], "pyplot_label_axes() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.pyplot_label_axes"]], "quad() (xfel.command_line.convert_gain_map.fake_cspad_elementv2 method)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2.quad"]], "quadmask() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.quadMask"]], "read_all_mysql() (xfel.command_line.cxi_xmerge.xscaling_manager method)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager.read_all_mysql"]], "read_input() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.read_input"]], "reset() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.reset"]], "resolution_bin (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.resolution_bin"]], "roimask() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.roiMask"]], "run() (in module xfel.command_line.auto_submit)": [[341, "xfel.command_line.auto_submit.run"]], "run() (in module xfel.command_line.brehm_diederichs)": [[341, "xfel.command_line.brehm_diederichs.run"]], "run() (in module xfel.command_line.cbf_average)": [[341, "xfel.command_line.cbf_average.run"]], "run() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.run"]], "run() (in module xfel.command_line.convert_gain_map_cbf)": [[341, "xfel.command_line.convert_gain_map_cbf.run"]], "run() (in module xfel.command_line.cxi_cspad_pinwheel)": [[341, "xfel.command_line.cxi_cspad_pinwheel.run"]], "run() (in module xfel.command_line.cxi_diff)": [[341, "xfel.command_line.cxi_diff.run"]], "run() (in module xfel.command_line.cxi_lsf)": [[341, "xfel.command_line.cxi_lsf.run"]], "run() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.run"]], "run() (in module xfel.command_line.cxi_pbs)": [[341, "xfel.command_line.cxi_pbs.run"]], "run() (in module xfel.command_line.cxi_plotcv)": [[341, "xfel.command_line.cxi_plotcv.run"]], "run() (in module xfel.command_line.cxi_psana)": [[341, "xfel.command_line.cxi_psana.run"]], "run() (in module xfel.command_line.cxi_pyana)": [[341, "xfel.command_line.cxi_pyana.run"]], "run() (in module xfel.command_line.cxi_xmerge)": [[341, "xfel.command_line.cxi_xmerge.run"]], "run() (in module xfel.command_line.list_db_metadata)": [[341, "xfel.command_line.list_db_metadata.run"]], "run() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.run"]], "run() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.run"]], "run() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.run"]], "run() (in module xfel.command_line.plot_to_subpixel)": [[341, "xfel.command_line.plot_to_subpixel.run"]], "run() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.run"]], "run() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.run"]], "run() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.run"]], "run() (in module xfel.command_line.trial_stats)": [[341, "xfel.command_line.trial_stats.run"]], "run() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.run"]], "scale_all() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_all"]], "scale_all() (xfel.command_line.cxi_xmerge.xscaling_manager method)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager.scale_all"]], "scale_frame() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_frame"]], "scale_frame_by_mean_i_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.scale_frame_by_mean_I_mproc"]], "scale_frame_detail() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_frame_detail"]], "scaling_manager (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.scaling_manager"]], "scaling_result (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.scaling_result"]], "sections() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.sections"]], "show_all_pyplot() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.show_all_pyplot"]], "show_histograms() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.show_histograms"]], "show_overall_observations() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.show_overall_observations"]], "show_tiles() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.show_tiles"]], "show_unit_cell_histograms() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.show_unit_cell_histograms"]], "signal_to_noise_statistical() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.signal_to_noise_statistical"]], "single_peak_fit() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.single_peak_fit"]], "single_reflection_histograms() (xfel.command_line.cxi_merge.scaling_manager static method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.single_reflection_histograms"]], "sliding_average() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.sliding_average"]], "subtract_background() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.subtract_background"]], "sum_intensities() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.sum_intensities"]], "unit_cell_distribution (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution"]], "unit_cell_to_symetry_object() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.unit_cell_to_symetry_object"]], "validate_phil() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.validate_phil"]], "view_raw_image() (in module xfel.command_line.quadrants)": [[341, "xfel.command_line.quadrants.view_raw_image"]], "xfel.command_line": [[341, "module-xfel.command_line"]], "xfel.command_line.auto_submit": [[341, "module-xfel.command_line.auto_submit"]], "xfel.command_line.brehm_diederichs": [[341, "module-xfel.command_line.brehm_diederichs"]], "xfel.command_line.cbf_average": [[341, "module-xfel.command_line.cbf_average"]], "xfel.command_line.convert_gain_map": [[341, "module-xfel.command_line.convert_gain_map"]], "xfel.command_line.convert_gain_map_cbf": [[341, "module-xfel.command_line.convert_gain_map_cbf"]], "xfel.command_line.cxi_apply_metrology": [[341, "module-xfel.command_line.cxi_apply_metrology"]], "xfel.command_line.cxi_cspad_pinwheel": [[341, "module-xfel.command_line.cxi_cspad_pinwheel"]], "xfel.command_line.cxi_diff": [[341, "module-xfel.command_line.cxi_diff"]], "xfel.command_line.cxi_display_metrology": [[341, "module-xfel.command_line.cxi_display_metrology"]], "xfel.command_line.cxi_generate_circular_gain_mask": [[341, "module-xfel.command_line.cxi_generate_circular_gain_mask"]], "xfel.command_line.cxi_index": [[341, "module-xfel.command_line.cxi_index"]], "xfel.command_line.cxi_lsf": [[341, "module-xfel.command_line.cxi_lsf"]], "xfel.command_line.cxi_merge": [[341, "module-xfel.command_line.cxi_merge"]], "xfel.command_line.cxi_optical2cbfheader": [[341, "module-xfel.command_line.cxi_optical2cbfheader"]], "xfel.command_line.cxi_pbs": [[341, "module-xfel.command_line.cxi_pbs"]], "xfel.command_line.cxi_pickle2cbf": [[341, "module-xfel.command_line.cxi_pickle2cbf"]], "xfel.command_line.cxi_plotcv": [[341, "module-xfel.command_line.cxi_plotcv"]], "xfel.command_line.cxi_psana": [[341, "module-xfel.command_line.cxi_psana"]], "xfel.command_line.cxi_pyana": [[341, "module-xfel.command_line.cxi_pyana"]], "xfel.command_line.cxi_spots": [[341, "module-xfel.command_line.cxi_spots"]], "xfel.command_line.cxi_stream_to_pickle": [[341, "module-xfel.command_line.cxi_stream_to_pickle"]], "xfel.command_line.cxi_view": [[341, "module-xfel.command_line.cxi_view"]], "xfel.command_line.cxi_xmerge": [[341, "module-xfel.command_line.cxi_xmerge"]], "xfel.command_line.histogram_finalise": [[341, "module-xfel.command_line.histogram_finalise"]], "xfel.command_line.list_db_metadata": [[341, "module-xfel.command_line.list_db_metadata"]], "xfel.command_line.make_mask": [[341, "module-xfel.command_line.make_mask"]], "xfel.command_line.metrology": [[341, "module-xfel.command_line.metrology"]], "xfel.command_line.monitor_detectors": [[341, "module-xfel.command_line.monitor_detectors"]], "xfel.command_line.monitor_trials": [[341, "module-xfel.command_line.monitor_trials"]], "xfel.command_line.overlay_spectra": [[341, "module-xfel.command_line.overlay_spectra"]], "xfel.command_line.plot_to_subpixel": [[341, "module-xfel.command_line.plot_to_subpixel"]], "xfel.command_line.postrefine": [[341, "module-xfel.command_line.postrefine"]], "xfel.command_line.print_pickle": [[341, "module-xfel.command_line.print_pickle"]], "xfel.command_line.quadrants": [[341, "module-xfel.command_line.quadrants"]], "xfel.command_line.radial_average": [[341, "module-xfel.command_line.radial_average"]], "xfel.command_line.smooth_spectrum": [[341, "module-xfel.command_line.smooth_spectrum"]], "xfel.command_line.subtract_background": [[341, "module-xfel.command_line.subtract_background"]], "xfel.command_line.trial_stats": [[341, "module-xfel.command_line.trial_stats"]], "xfel.command_line.view_pixel_histograms": [[341, "module-xfel.command_line.view_pixel_histograms"]], "xfel.command_line.xes_finalise": [[341, "module-xfel.command_line.xes_finalise"]], "xfel.command_line.xes_histograms": [[341, "module-xfel.command_line.xes_histograms"]], "xscaling_manager (class in xfel.command_line.cxi_xmerge)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager"]], "imagefactory() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.ImageFactory"]], "imagefactory() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.ImageFactory"]], "apply_gaussian_noise() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.apply_gaussian_noise"]], "binned_correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.binned_correlation"]], "correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.correlation"]], "display() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.display"]], "display_with_callback() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.display_with_callback"]], "empty (class in xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.empty"]], "get_cursor() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_cursor"]], "get_frame_dictionary() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_frame_dictionary"]], "get_mmtbx_icalc() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.get_mmtbx_icalc"]], "img_add() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.img_add"]], "initialize_tables_and_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.initialize_tables_and_insert_command"]], "insert() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.insert"]], "integrate_one_image() (in module xfel.cxi.integrate_image_api)": [[342, "xfel.cxi.integrate_image_api.integrate_one_image"]], "integrate_one_image() (in module xfel.cxi.strong_zulu)": [[342, "xfel.cxi.strong_zulu.integrate_one_image"]], "is_odd_numbered() (in module xfel.cxi.util)": [[342, "xfel.cxi.util.is_odd_numbered"]], "is_pinwheel_region() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.is_pinwheel_region"]], "lines (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.lines"]], "literals() (xfel.cxi.correction_vector_plot.lines method)": [[342, "xfel.cxi.correction_vector_plot.lines.literals"]], "load_cc_data() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.load_cc_data"]], "main() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.main"]], "manage_sql (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.manage_sql"]], "r1_factor() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.r1_factor"]], "r_split() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.r_split"]], "run_cc() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.run_cc"]], "run_correction_vector_plot() (in module xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.run_correction_vector_plot"]], "run_one() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one"]], "run_one_index() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one_index"]], "run_one_index_core() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one_index_core"]], "scale_factor() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.scale_factor"]], "send_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.send_insert_command"]], "split_sigma_test() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.split_sigma_test"]], "spot_add() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.spot_add"]], "superimpose_powder_arcs() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.superimpose_powder_arcs"]], "user_callback() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.user_callback"]], "vectors() (xfel.cxi.correction_vector_plot.lines method)": [[342, "xfel.cxi.correction_vector_plot.lines.vectors"]], "view_raw_image() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.view_raw_image"]], "wrapper_of_callback (class in xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.wrapper_of_callback"]], "xfel.cxi": [[342, "module-xfel.cxi"]], "xfel.cxi.average_spots": [[342, "module-xfel.cxi.average_spots"]], "xfel.cxi.correction_vector_plot": [[342, "module-xfel.cxi.correction_vector_plot"]], "xfel.cxi.cxi_cc": [[342, "module-xfel.cxi.cxi_cc"]], "xfel.cxi.display_powder_arcs": [[342, "module-xfel.cxi.display_powder_arcs"]], "xfel.cxi.display_spots": [[342, "module-xfel.cxi.display_spots"]], "xfel.cxi.integrate_image_api": [[342, "module-xfel.cxi.integrate_image_api"]], "xfel.cxi.strong_zulu": [[342, "module-xfel.cxi.strong_zulu"]], "xfel.cxi.util": [[342, "module-xfel.cxi.util"]], "cspad2x2image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPad2x2Image"]], "cspaddetector() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadDetector"]], "cspadelement() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadElement"]], "section (class in xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section"]], "statusframe_thread (class in xfel.cxi.cspad_ana.mod_daq_status)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread"]], "as_trace() (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis.as_trace"]], "average_mixin (class in xfel.cxi.cspad_ana.average_tbx)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin"]], "begincalibcycle() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.begincalibcycle"]], "beginjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.beginjob"]], "calculate() (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis.calculate"]], "calib2sections() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2sections"]], "calib2tensor3() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2tensor3"]], "cbcaa() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.cbcaa"]], "chebyshev_common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.chebyshev_common_mode"]], "chebyshev_fit() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.chebyshev_fit"]], "commit_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.commit_entries"]], "commit_progress_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.commit_progress_entries"]], "common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.common_mode"]], "common_mode_correction (class in xfel.cxi.cspad_ana.common_mode)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction"]], "corners() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners"]], "corners_asic() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners_asic"]], "cspad2x2_bad_pixel_mask_cxi_run7() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad2x2_bad_pixel_mask_cxi_run7"]], "cspad_unbound_pixel_mask() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad_unbound_pixel_mask"]], "display_calib() (in module xfel.cxi.cspad_ana.display_calib)": [[343, "xfel.cxi.cspad_ana.display_calib.display_calib"]], "distl_filter() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.distl_filter"]], "distl_hitfinder (class in xfel.cxi.cspad_ana.hitfinder_tbx)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder"]], "do_photon_counting() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_photon_counting"]], "do_sigma_scaling() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_sigma_scaling"]], "dpack() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dpack"]], "dwritef() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef"]], "dwritef2() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef2"]], "endjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.endjob"]], "endjob() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.endjob"]], "endjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.endjob"]], "env_distance() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_distance"]], "env_injector_xyz() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_injector_xyz"]], "env_laser_status() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_laser_status"]], "env_sifoil() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_sifoil"]], "env_wavelength_sxr() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_wavelength_sxr"]], "event() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.event"]], "event() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.event"]], "event() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.event"]], "event() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.event"]], "event() (xfel.cxi.cspad_ana.mod_dump.mod_dump method)": [[343, "xfel.cxi.cspad_ana.mod_dump.mod_dump.event"]], "event() (xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap method)": [[343, "xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap.event"]], "event() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.event"]], "event() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.event"]], "event() (xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5 method)": [[343, "xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5.event"]], "event() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.event"]], "event() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.event"]], "event() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.event"]], "event() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.event"]], "event() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.event"]], "event() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.event"]], "event() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.event"]], "event() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.event"]], "evt_beam_charge() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_beam_charge"]], "evt_get_quads() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_get_quads"]], "evt_pulse_energy() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_energy"]], "evt_pulse_length() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_length"]], "evt_repetition_rate() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_repetition_rate"]], "evt_seqno() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_seqno"]], "evt_time() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_time"]], "evt_timestamp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_timestamp"]], "evt_wavelength() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_wavelength"]], "filter_outlying_pixels() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.filter_outlying_pixels"]], "finalise_one_run (class in xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.finalise_one_run"]], "finalise_one_run (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.finalise_one_run"]], "first_moment_analysis (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis"]], "fread_matrix() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_matrix"]], "fread_tensor3() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_tensor3"]], "fread_vector() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_vector"]], "getoptbool() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptBool"]], "getoptevalorstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptEvalOrString"]], "getoptfloat() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptFloat"]], "getoptinteger() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptInteger"]], "getoptroi() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptROI"]], "getoptstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptString"]], "getoptstrings() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptStrings"]], "get_active_data() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.get_active_data"]], "get_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.get_spectrum"]], "hdf5pack() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.hdf5pack"]], "histogram_finalise (class in xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.histogram_finalise"]], "image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image"]], "image_xpp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image_xpp"]], "initialize() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.initialize"]], "iplace() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.iplace"]], "laser_status (class in xfel.cxi.cspad_ana.mod_event_info)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status"]], "mod_average (class in xfel.cxi.cspad_ana.mod_average)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average"]], "mod_daq_status (class in xfel.cxi.cspad_ana.mod_daq_status)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status"]], "mod_dump (class in xfel.cxi.cspad_ana.mod_dump)": [[343, "xfel.cxi.cspad_ana.mod_dump.mod_dump"]], "mod_dump_bitmap (class in xfel.cxi.cspad_ana.mod_dump_bitmap)": [[343, "xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap"]], "mod_event_info (class in xfel.cxi.cspad_ana.mod_event_info)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info"]], "mod_filter (class in xfel.cxi.cspad_ana.mod_filter)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter"]], "mod_hdf5 (class in xfel.cxi.cspad_ana.mod_hdf5)": [[343, "xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5"]], "mod_hitfind (class in xfel.cxi.cspad_ana.mod_hitfind)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind"]], "mod_illumination_filter (class in xfel.cxi.cspad_ana.mod_illumination_filter)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter"]], "mod_mar (class in xfel.cxi.cspad_ana.mod_mar)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar"]], "mod_param (class in xfel.cxi.cspad_ana.mod_param)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param"]], "mod_pulnix_dump (class in xfel.cxi.cspad_ana.mod_pulnix_dump)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump"]], "mod_radial_average (class in xfel.cxi.cspad_ana.mod_radial_average)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average"]], "mod_xes (class in xfel.cxi.cspad_ana.mod_xes)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes"]], "ms_since_last_status_change() (xfel.cxi.cspad_ana.mod_event_info.laser_status method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.ms_since_last_status_change"]], "output_image() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_image"]], "output_matlab_form() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_matlab_form"]], "output_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_spectrum"]], "pathsubst() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.pathsubst"]], "pixel_histograms (class in xfel.cxi.cspad_ana.pixel_histograms)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms"]], "plot_energy() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.plot_energy"]], "q_size (xfel.cxi.cspad_ana.parse_calib.section attribute)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.q_size"]], "qrotate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.qrotate"]], "queue_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.queue_entry"]], "queue_progress_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.queue_progress_entry"]], "rplace() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.rplace"]], "run() (in module xfel.cxi.cspad_ana.xes_histograms)": [[343, "xfel.cxi.cspad_ana.xes_histograms.run"]], "run() (xfel.cxi.cspad_ana.mod_daq_status.statusframe_thread method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread.run"]], "set_status() (xfel.cxi.cspad_ana.mod_event_info.laser_status method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.set_status"]], "set_up_hitfinder() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.set_up_hitfinder"]], "skip_event_flag() (in module xfel.cxi.cspad_ana)": [[343, "xfel.cxi.cspad_ana.skip_event_flag"]], "spec_plot() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.spec_plot"]], "srotate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.srotate"]], "start_local() (xfel.cxi.cspad_ana.mod_daq_status.statusframe_thread method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread.start_local"]], "status (xfel.cxi.cspad_ana.mod_event_info.laser_status property)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status"]], "status_change_timestamp (xfel.cxi.cspad_ana.mod_event_info.laser_status attribute)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status_change_timestamp"]], "translate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.translate"]], "update_histograms() (in module xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.update_histograms"]], "update_plot() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.update_plot"]], "v2calib2sections() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.v2calib2sections"]], "write_tiff() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.write_tiff"]], "xes_finalise (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.xes_finalise"]], "xes_from_histograms (class in xfel.cxi.cspad_ana.xes_histograms)": [[343, "xfel.cxi.cspad_ana.xes_histograms.xes_from_histograms"]], "xfel.cxi.cspad_ana": [[343, "module-xfel.cxi.cspad_ana"]], "xfel.cxi.cspad_ana.average_tbx": [[343, "module-xfel.cxi.cspad_ana.average_tbx"]], "xfel.cxi.cspad_ana.common_mode": [[343, "module-xfel.cxi.cspad_ana.common_mode"]], "xfel.cxi.cspad_ana.cspad_tbx": [[343, "module-xfel.cxi.cspad_ana.cspad_tbx"]], "xfel.cxi.cspad_ana.display_calib": [[343, "module-xfel.cxi.cspad_ana.display_calib"]], "xfel.cxi.cspad_ana.histogram_finalise": [[343, "module-xfel.cxi.cspad_ana.histogram_finalise"]], "xfel.cxi.cspad_ana.hitfinder_tbx": [[343, "module-xfel.cxi.cspad_ana.hitfinder_tbx"]], "xfel.cxi.cspad_ana.mod_average": [[343, "module-xfel.cxi.cspad_ana.mod_average"]], "xfel.cxi.cspad_ana.mod_daq_status": [[343, "module-xfel.cxi.cspad_ana.mod_daq_status"]], "xfel.cxi.cspad_ana.mod_dump": [[343, "module-xfel.cxi.cspad_ana.mod_dump"]], "xfel.cxi.cspad_ana.mod_dump_bitmap": [[343, "module-xfel.cxi.cspad_ana.mod_dump_bitmap"]], "xfel.cxi.cspad_ana.mod_event_info": [[343, "module-xfel.cxi.cspad_ana.mod_event_info"]], "xfel.cxi.cspad_ana.mod_filter": [[343, "module-xfel.cxi.cspad_ana.mod_filter"]], "xfel.cxi.cspad_ana.mod_hdf5": [[343, "module-xfel.cxi.cspad_ana.mod_hdf5"]], "xfel.cxi.cspad_ana.mod_hitfind": [[343, "module-xfel.cxi.cspad_ana.mod_hitfind"]], "xfel.cxi.cspad_ana.mod_illumination_filter": [[343, "module-xfel.cxi.cspad_ana.mod_illumination_filter"]], "xfel.cxi.cspad_ana.mod_mar": [[343, "module-xfel.cxi.cspad_ana.mod_mar"]], "xfel.cxi.cspad_ana.mod_param": [[343, "module-xfel.cxi.cspad_ana.mod_param"]], "xfel.cxi.cspad_ana.mod_pulnix_dump": [[343, "module-xfel.cxi.cspad_ana.mod_pulnix_dump"]], "xfel.cxi.cspad_ana.mod_radial_average": [[343, "module-xfel.cxi.cspad_ana.mod_radial_average"]], "xfel.cxi.cspad_ana.mod_xes": [[343, "module-xfel.cxi.cspad_ana.mod_xes"]], "xfel.cxi.cspad_ana.parse_calib": [[343, "module-xfel.cxi.cspad_ana.parse_calib"]], "xfel.cxi.cspad_ana.pixel_histograms": [[343, "module-xfel.cxi.cspad_ana.pixel_histograms"]], "xfel.cxi.cspad_ana.xes_finalise": [[343, "module-xfel.cxi.cspad_ana.xes_finalise"]], "xfel.cxi.cspad_ana.xes_histograms": [[343, "module-xfel.cxi.cspad_ana.xes_histograms"]], "detectorplot (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot"]], "detectorplotframe (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame"]], "onpan() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnPan"]], "onsave() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.OnSave"]], "onsaveimage() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnSaveImage"]], "onsetrunnumber() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnSetRunNumber"]], "ontimelockcheck() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnTimeLockCheck"]], "ontimer() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnTimer"]], "ontimer() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.OnTimer"]], "onupdate() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnUpdate"]], "onzoom() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnZoom"]], "run (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.Run"]], "runnumberevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.RunNumberEvent"]], "saveimageevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.SaveImageEvent"]], "statusframe (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame"]], "statusplot (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusPlot"]], "trialsplot (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlot"]], "trialsplotframe (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame"]], "updateevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.UpdateEvent"]], "create_plot_panel() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.create_plot_panel"]], "create_plot_panel() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.create_plot_panel"]], "create_plot_panel() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.create_plot_panel"]], "cull_braggs() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.cull_braggs"]], "cull_braggs() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.cull_braggs"]], "draw_plot() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot"]], "draw_plot_to_file() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot_to_file"]], "find_logs() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.find_logs"]], "format_time() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.format_time"]], "load_data() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.load_data"]], "max() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.max"]], "min() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.min"]], "recalc_hits() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.recalc_hits"]], "run() (in module xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.run"]], "run() (in module xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.run"]], "save_png() (xfel.cxi.gfx.wx_detectors.detectorplot method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot.save_png"]], "set_params() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.set_params"]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplot method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot.set_run_id"]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_run_id"]], "set_watch_dir() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_watch_dir"]], "show_controls_default (xfel.cxi.gfx.status_plot.statusframe attribute)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.show_controls_default"]], "show_controls_default (xfel.cxi.gfx.trials_plot.trialsplotframe attribute)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.show_controls_default"]], "show_controls_default (xfel.cxi.gfx.wx_detectors.detectorplotframe attribute)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.show_controls_default"]], "show_plot() (xfel.cxi.gfx.status_plot.statusplot method)": [[344, "xfel.cxi.gfx.status_plot.StatusPlot.show_plot"]], "show_plot() (xfel.cxi.gfx.trials_plot.trialsplot method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlot.show_plot"]], "show_plot() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.show_plot"]], "show_plot() (xfel.cxi.gfx.wx_detectors.detectorplot method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot.show_plot"]], "update_from_logs() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.update_from_logs"]], "update_hit_rate() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.update_hit_rate"]], "width() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.width"]], "xfel.cxi.gfx": [[344, "module-xfel.cxi.gfx"]], "xfel.cxi.gfx.status_plot": [[344, "module-xfel.cxi.gfx.status_plot"]], "xfel.cxi.gfx.trials_plot": [[344, 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"compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_2 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_2.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_3 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_3.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.compute_functional_and_gradients"]], "consistency_controls() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.consistency_controls"]], "correction_vectors (class in xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.correction_vectors"]], "curvatures() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.curvatures"]], "curvatures() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.curvatures"]], "delrsq_functional() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.delrsq_functional"]], "detector_origin_analysis() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.detector_origin_analysis"]], "fit_translation (class in xfel.metrology.mark1)": [[347, "xfel.metrology.mark1.fit_translation"]], "fit_translation2 (class in xfel.metrology.mark3)": [[347, "xfel.metrology.mark3.fit_translation2"]], "fit_translation4 (class in xfel.metrology.mark10)": [[347, "xfel.metrology.mark10.fit_translation4"]], "get_frames_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_frames_from_mysql"]], "get_obs_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_obs_from_mysql"]], "get_phil() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.get_phil"]], "jacobian_frame_rotx (xfel.metrology.mark10.fit_translation4 attribute)": [[347, "xfel.metrology.mark10.fit_translation4.jacobian_frame_rotx"]], "nominal_tile_centers() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.nominal_tile_centers"]], "one_panel (class in xfel.metrology.quadrant)": [[347, "xfel.metrology.quadrant.one_panel"]], "one_sensor (class in xfel.metrology.quadrant)": [[347, "xfel.metrology.quadrant.one_sensor"]], "optimise_rectangle (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle"]], "optimise_rectangle_2 (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle_2"]], "optimise_rectangle_3 (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle_3"]], "parameter_based_model() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.parameter_based_model"]], "parameter_based_model() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.parameter_based_model"]], "parameter_based_model_one_frame_detail() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.parameter_based_model_one_frame_detail"]], "parse_metrology() (in module xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.parse_metrology"]], "post_min_recalc() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.post_min_recalc"]], "post_min_recalc() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.post_min_recalc"]], "print_table() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.print_table"]], "print_table() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.print_table"]], "print_table() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.print_table"]], "print_table() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.print_table"]], "print_table_2() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.print_table_2"]], "print_unit_translations() (xfel.metrology.mark10.fit_translation4 static method)": [[347, "xfel.metrology.mark10.fit_translation4.print_unit_translations"]], "radial_transverse_analysis() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.radial_transverse_analysis"]], "read_data() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.read_data"]], "run() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.run"]], "run() (in module xfel.metrology.mark1)": [[347, "xfel.metrology.mark1.run"]], "run() (in module xfel.metrology.mark3)": [[347, "xfel.metrology.mark3.run"]], "run_cycle_a() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.run_cycle_a"]], "run_cycle_b() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.run_cycle_b"]], "same_sensor_table() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.same_sensor_table"]], "same_sensor_table() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.same_sensor_table"]], "standalone_check() (xfel.metrology.mark0.correction_vectors static method)": [[347, "xfel.metrology.mark0.correction_vectors.standalone_check"]], "tile_weight() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.tile_weight"]], "xfel.metrology": [[347, "module-xfel.metrology"]], "xfel.metrology.flatfile": [[347, "module-xfel.metrology.flatfile"]], "xfel.metrology.mark0": [[347, "module-xfel.metrology.mark0"]], "xfel.metrology.mark1": [[347, "module-xfel.metrology.mark1"]], "xfel.metrology.mark10": [[347, "module-xfel.metrology.mark10"]], "xfel.metrology.mark3": [[347, "module-xfel.metrology.mark3"]], "xfel.metrology.quadrant": [[347, "module-xfel.metrology.quadrant"]], "xfel.metrology.legacy_scale": [[348, "module-xfel.metrology.legacy_scale"]], "contour_plot_deprecated_does_not_apply_subpixel_metrology() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, 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module", "cctbx.maptbx package", "cctbx.maptbx.mem module", "cctbx.maptbx.real_space_refinement module", "cctbx.maptbx.real_space_refinement_simple module", "cctbx.maptbx.real_space_target_and_gradients module", "cctbx.masks package", "cctbx.math_module module", "cctbx.merging package", "cctbx.merging.brehm_diederichs module", "cctbx.miller package", "cctbx.miller.display module", "cctbx.miller.reindexing module", "cctbx.multipolar module", "cctbx.neutron package", "cctbx.omz package", "cctbx.omz.bfgs module", "cctbx.omz.cif_refine module", "cctbx.omz.cod_refine module", "cctbx.omz.cod_select_and_pickle module", "cctbx.omz.dev module", "cctbx.omz.eval_iso_vs_refined module", "cctbx.omz.pdb_dev module", "cctbx.omz.tardy_adaptor module", "cctbx.r_free_utils module", "cctbx.run_examples module", "cctbx.run_tests module", "cctbx.sgtbx package", "cctbx.sgtbx.bravais_types module", "cctbx.sgtbx.cosets module", "cctbx.sgtbx.direct_space_asu package", 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module", "cctbx.web.emma module", "cctbx.web.explore_symmetry module", "cctbx.web.frac_cart module", "cctbx.web.io_utils module", "cctbx.web.iotbx_cif_validate module", "cctbx.web.lattice_symmetry module", "cctbx.web.libtbx_help module", "cctbx.web.multiple_cell module", "cctbx.web.phase_o_phrenia module", "cctbx.web.replay module", "cctbx.web.shelx module", "cctbx.web.structure_factors module", "cctbx.web.structure_factors_pdb module", "cctbx.web.wyckoff module", "cctbx.xray package", "cctbx.xray.ext module", "cctbx.xray.minimization module", "cctbx.xray.observation_types module", "cctbx.xray.observations package", "cctbx.xray.scatterer module", "cctbx.xray.structure module", "cctbx.xray.structure_factors package", "cctbx.xray.structure_factors.from_scatterers module", "cctbx.xray.structure_factors.from_scatterers_direct module", "cctbx.xray.structure_factors.from_scatterers_direct_parallel module", "cctbx.xray.structure_factors.from_scatterers_fft module", 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270, 271, 276, 277, 282, 297, 304, 313, 318, 326, 330, 331, 335, 339], "archaic": 148, "languag": [148, 261, 264, 335], "necessarili": [148, 242, 265, 268, 298, 313, 331, 335], "column": [148, 264, 266, 270, 283, 318, 324, 331, 341, 347], "There": [148, 261, 262, 268, 269, 275, 328, 343], "major": [148, 261, 264, 268, 270, 331, 335], "friedel": [148, 162, 270], "mate": [148, 162, 270], "separ": [148, 242, 261, 266, 270, 277, 282, 293, 325, 326, 327, 330, 341, 343], "present": [148, 262, 264, 266, 268, 269, 273, 277, 282, 286, 298, 299, 309, 318, 326, 328, 331, 335, 339, 340], "becom": [148, 266, 335], "item": [148, 210, 238, 264, 266, 268, 331, 343], "consequ": [148, 298], "behavior": [148, 265, 273, 274, 282, 328, 331, 347], "appear": [148, 257, 293, 298, 302, 335, 344], "doubl": [148, 238, 242, 257, 266, 268, 269, 271, 298, 309, 313, 331, 335, 343], "acentr": [148, 318], "treatment": [148, 327], "sigi": 148, "fwt": 148, "delfwt": 148, "2fofcwt": 148, "ph2fofcwt": 148, 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"module-cctbx.examples.location_part"]], "cctbx.examples.map_skewness module": [[99, "module-cctbx.examples.map_skewness"]], "cctbx.examples.maximum_subgroups module": [[100, "module-cctbx.examples.maximum_subgroups"]], "cctbx.examples.miller_common_sets module": [[101, "module-cctbx.examples.miller_common_sets"]], "cctbx.examples.miller_transform module": [[102, "module-cctbx.examples.miller_transform"]], "cctbx.examples.neutron_structure_factors module": [[103, "module-cctbx.examples.neutron_structure_factors"]], "cctbx.examples.phase_o_phrenia module": [[104, "module-cctbx.examples.phase_o_phrenia"]], "cctbx.examples.quartz_structure module": [[105, "module-cctbx.examples.quartz_structure"]], "cctbx.examples.random_f_calc module": [[106, "module-cctbx.examples.random_f_calc"]], "cctbx.examples.random_puckers module": [[107, "module-cctbx.examples.random_puckers"]], "cctbx.examples.reduced_cell_two_folds module": [[108, "module-cctbx.examples.reduced_cell_two_folds"]], "cctbx.examples.site_symmetry_constraints module": [[109, "module-cctbx.examples.site_symmetry_constraints"]], "cctbx.examples.site_symmetry_table module": [[110, "module-cctbx.examples.site_symmetry_table"]], "cctbx.examples.space_group_matrices module": [[111, "module-cctbx.examples.space_group_matrices"]], "cctbx.examples.space_subgroups module": [[112, "module-cctbx.examples.space_subgroups"]], "cctbx.examples.steve_collins module": [[113, "module-cctbx.examples.steve_collins"]], "cctbx.examples.structure_factor_calculus package": [[114, "cctbx-examples-structure-factor-calculus-package"]], "cctbx.examples.structure_factor_calculus.site_derivatives module": [[115, "module-cctbx.examples.structure_factor_calculus.site_derivatives"]], "cctbx.examples.structure_factor_calculus.sites_derivatives module": [[116, "module-cctbx.examples.structure_factor_calculus.sites_derivatives"]], "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives module": [[117, "module-cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives"]], "cctbx.examples.structure_factor_calculus.u_star_derivatives module": [[118, "module-cctbx.examples.structure_factor_calculus.u_star_derivatives"]], "cctbx.examples.structure_factor_derivatives module": [[119, "module-cctbx.examples.structure_factor_derivatives"]], "cctbx.examples.structure_factor_derivatives_2 module": [[120, "module-cctbx.examples.structure_factor_derivatives_2"]], "cctbx.examples.structure_factor_derivatives_3 module": [[121, "module-cctbx.examples.structure_factor_derivatives_3"]], "cctbx.examples.structure_factor_derivatives_4 module": [[122, "module-cctbx.examples.structure_factor_derivatives_4"]], "cctbx.examples.sub_group_graph module": [[123, "module-cctbx.examples.sub_group_graph"]], "cctbx.examples.symops_530 module": [[124, "module-cctbx.examples.symops_530"]], "cctbx.examples.trigonal_r_vs_tetragonal_i module": [[125, "module-cctbx.examples.trigonal_r_vs_tetragonal_i"]], "cctbx.examples.unit_cell_minimizers module": [[126, "module-cctbx.examples.unit_cell_minimizers"]], "cctbx.examples.unit_cell_refinement module": [[127, "module-cctbx.examples.unit_cell_refinement"]], "cctbx.examples.view_fft_map module": [[128, "cctbx-examples-view-fft-map-module"]], "cctbx.french_wilson module": [[129, "module-cctbx.french_wilson"]], "cctbx.geometry package": [[130, "cctbx-geometry-package"]], "cctbx.geometry_restraints package": [[131, "cctbx-geometry-restraints-package"]], "cctbx.geometry_restraints.energies module": [[132, "module-cctbx.geometry_restraints.energies"]], "cctbx.geometry_restraints.flags module": [[133, "module-cctbx.geometry_restraints.flags"]], "cctbx.geometry_restraints.lbfgs module": [[134, "module-cctbx.geometry_restraints.lbfgs"]], "cctbx.geometry_restraints.manager module": [[135, "module-cctbx.geometry_restraints.manager"]], "cctbx.libtbx_refresh module": [[136, "cctbx-libtbx-refresh-module"]], "cctbx.macro_mol package": [[137, 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input data - practical aspects": [[148, "processing-input-data-practical-aspects"]], "Comparing arrays": [[148, "comparing-arrays"]], "Working with experimental data": [[148, "working-with-experimental-data"]], "From arrays to maps": [[148, "from-arrays-to-maps"]], "The Miller set": [[148, "the-miller-set"]], "The Miller array": [[148, "the-miller-array"]], "Utility classes": [[148, "utility-classes"]], "cctbx.miller.display module": [[149, "module-cctbx.miller.display"]], "cctbx.miller.reindexing module": [[150, "module-cctbx.miller.reindexing"]], "cctbx.multipolar module": [[151, "module-cctbx.multipolar"]], "cctbx.neutron package": [[152, "cctbx-neutron-package"]], "cctbx.omz package": [[153, "cctbx-omz-package"]], "cctbx.omz.bfgs module": [[154, "module-cctbx.omz.bfgs"]], "cctbx.omz.cif_refine module": [[155, "module-cctbx.omz.cif_refine"]], "cctbx.omz.cod_refine module": [[156, "module-cctbx.omz.cod_refine"]], "cctbx.omz.cod_select_and_pickle module": [[157, "module-cctbx.omz.cod_select_and_pickle"]], "cctbx.omz.dev module": [[158, "module-cctbx.omz.dev"]], "cctbx.omz.eval_iso_vs_refined module": [[159, "module-cctbx.omz.eval_iso_vs_refined"]], "cctbx.omz.pdb_dev module": [[160, "module-cctbx.omz.pdb_dev"]], "cctbx.omz.tardy_adaptor module": [[161, "module-cctbx.omz.tardy_adaptor"]], "cctbx.r_free_utils module": [[162, "module-cctbx.r_free_utils"]], "cctbx.run_examples module": [[163, "module-cctbx.run_examples"]], "cctbx.run_tests module": [[164, "module-cctbx.run_tests"]], "cctbx.sgtbx package": [[165, "cctbx-sgtbx-package"]], "cctbx.sgtbx.bravais_types module": [[166, "module-cctbx.sgtbx.bravais_types"]], "cctbx.sgtbx.cosets module": [[167, "module-cctbx.sgtbx.cosets"]], "cctbx.sgtbx.direct_space_asu package": [[168, "cctbx-sgtbx-direct-space-asu-package"]], "cctbx.sgtbx.direct_space_asu.check_redundancies module": [[169, "module-cctbx.sgtbx.direct_space_asu.check_redundancies"]], "cctbx.sgtbx.direct_space_asu.cut_plane module": [[170, "module-cctbx.sgtbx.direct_space_asu.cut_plane"]], "cctbx.sgtbx.direct_space_asu.facet_analysis module": [[171, "module-cctbx.sgtbx.direct_space_asu.facet_analysis"]], "cctbx.sgtbx.direct_space_asu.plane_group_reference_table module": [[172, "module-cctbx.sgtbx.direct_space_asu.plane_group_reference_table"]], "cctbx.sgtbx.direct_space_asu.proto package": [[173, "cctbx-sgtbx-direct-space-asu-proto-package"]], "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module": [[174, "module-cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table"]], "cctbx.sgtbx.direct_space_asu.reference_table module": [[175, "module-cctbx.sgtbx.direct_space_asu.reference_table"]], "cctbx.sgtbx.direct_space_asu.short_cuts module": [[176, "module-cctbx.sgtbx.direct_space_asu.short_cuts"]], "cctbx.sgtbx.harker module": [[177, "module-cctbx.sgtbx.harker"]], "cctbx.sgtbx.lattice_symmetry module": [[178, "module-cctbx.sgtbx.lattice_symmetry"]], "cctbx.sgtbx.literal_description module": [[179, "module-cctbx.sgtbx.literal_description"]], "cctbx.sgtbx.plane_groups module": [[180, "module-cctbx.sgtbx.plane_groups"]], "cctbx.sgtbx.pointgroup_tools module": [[181, "module-cctbx.sgtbx.pointgroup_tools"]], "cctbx.sgtbx.rational_matrices_point_groups module": [[182, "module-cctbx.sgtbx.rational_matrices_point_groups"]], "cctbx.sgtbx.reticular_pg_tools module": [[183, "module-cctbx.sgtbx.reticular_pg_tools"]], "cctbx.sgtbx.reticular_twin_laws module": [[184, "module-cctbx.sgtbx.reticular_twin_laws"]], "cctbx.sgtbx.show_cosets module": [[185, "module-cctbx.sgtbx.show_cosets"]], "cctbx.sgtbx.sub_lattice_tools module": [[186, "module-cctbx.sgtbx.sub_lattice_tools"]], "cctbx.sgtbx.subgroups module": [[187, "module-cctbx.sgtbx.subgroups"]], "cctbx.sgtbx.symbol_confidence module": [[188, "module-cctbx.sgtbx.symbol_confidence"]], "cctbx.sgtbx.sys_abs_equiv module": [[189, "module-cctbx.sgtbx.sys_abs_equiv"]], "cctbx.source_generators package": [[190, "cctbx-source-generators-package"]], "cctbx.source_generators.eltbx package": [[191, "cctbx-source-generators-eltbx-package"]], "cctbx.source_generators.eltbx.generate_henke_cpp module": [[192, "module-cctbx.source_generators.eltbx.generate_henke_cpp"]], "cctbx.source_generators.eltbx.generate_sasaki_cpp module": [[193, "module-cctbx.source_generators.eltbx.generate_sasaki_cpp"]], "cctbx.source_generators.flex_fwd_h module": [[194, "module-cctbx.source_generators.flex_fwd_h"]], "cctbx.statistics module": [[195, "module-cctbx.statistics"]], "cctbx.symmetry_search module": [[196, "module-cctbx.symmetry_search"]], "cctbx.translation_search module": [[197, "module-cctbx.translation_search"]], "cctbx.uctbx package": [[198, "cctbx-uctbx-package"]], "The unit cell": [[198, "the-unit-cell"]], "cctbx.uctbx.determine_unit_cell package": [[199, "cctbx-uctbx-determine-unit-cell-package"]], "cctbx.uctbx.gruber_1973 module": [[200, "module-cctbx.uctbx.gruber_1973"]], "cctbx.uctbx.gruber_1973_table_1 module": [[201, "module-cctbx.uctbx.gruber_1973_table_1"]], "cctbx.uctbx.krivy_gruber_1976 module": [[202, "module-cctbx.uctbx.krivy_gruber_1976"]], "cctbx.uctbx.reduction_base module": [[203, "module-cctbx.uctbx.reduction_base"]], "cctbx.web package": [[204, "cctbx-web-package"]], "cctbx.web.all_axes module": [[205, "module-cctbx.web.all_axes"]], "cctbx.web.asu_gallery package": [[206, "cctbx-web-asu-gallery-package"]], "cctbx.web.asu_gallery.guide_to_notation module": [[207, "module-cctbx.web.asu_gallery.guide_to_notation"]], "cctbx.web.asu_gallery.jv_asu module": [[208, "module-cctbx.web.asu_gallery.jv_asu"]], "cctbx.web.asu_gallery.jv_index module": [[209, "module-cctbx.web.asu_gallery.jv_index"]], "cctbx.web.asu_gallery.jvx module": [[210, "module-cctbx.web.asu_gallery.jvx"]], "cctbx.web.asu_gallery.web_links module": [[211, "module-cctbx.web.asu_gallery.web_links"]], "cctbx.web.browse_settings module": [[212, "module-cctbx.web.browse_settings"]], "cctbx.web.cgi_utils module": [[213, "module-cctbx.web.cgi_utils"]], "cctbx.web.change_basis module": [[214, "module-cctbx.web.change_basis"]], "cctbx.web.change_hand module": [[215, "module-cctbx.web.change_hand"]], "cctbx.web.change_setting module": [[216, "module-cctbx.web.change_setting"]], "cctbx.web.dispatcher module": [[217, "module-cctbx.web.dispatcher"]], "cctbx.web.emma module": [[218, "module-cctbx.web.emma"]], "cctbx.web.explore_symmetry module": [[219, "module-cctbx.web.explore_symmetry"]], "cctbx.web.frac_cart module": [[220, "module-cctbx.web.frac_cart"]], "cctbx.web.io_utils module": [[221, "module-cctbx.web.io_utils"]], "cctbx.web.iotbx_cif_validate module": [[222, "module-cctbx.web.iotbx_cif_validate"]], "cctbx.web.lattice_symmetry module": [[223, "module-cctbx.web.lattice_symmetry"]], "cctbx.web.libtbx_help module": [[224, "module-cctbx.web.libtbx_help"]], "cctbx.web.multiple_cell module": [[225, "module-cctbx.web.multiple_cell"]], "cctbx.web.phase_o_phrenia module": [[226, "module-cctbx.web.phase_o_phrenia"]], "cctbx.web.replay module": [[227, "module-cctbx.web.replay"]], "cctbx.web.shelx module": [[228, "module-cctbx.web.shelx"]], "cctbx.web.structure_factors module": [[229, "module-cctbx.web.structure_factors"]], "cctbx.web.structure_factors_pdb module": [[230, "module-cctbx.web.structure_factors_pdb"]], "cctbx.web.wyckoff module": [[231, "module-cctbx.web.wyckoff"]], "cctbx.xray package": [[232, "cctbx-xray-package"]], "cctbx.xray.ext module": [[233, "module-cctbx.xray.ext"]], "cctbx.xray.minimization module": [[234, "module-cctbx.xray.minimization"]], "cctbx.xray.observation_types module": [[235, "module-cctbx.xray.observation_types"]], "cctbx.xray.observations package": [[236, "cctbx-xray-observations-package"]], "cctbx.xray.scatterer module": [[237, "module-cctbx.xray.scatterer"]], "cctbx.xray.structure module": [[238, "module-cctbx.xray.structure"]], "cctbx.xray.structure_factors package": [[239, "cctbx-xray-structure-factors-package"]], "cctbx.xray.structure_factors.from_scatterers module": [[240, "module-cctbx.xray.structure_factors.from_scatterers"]], "cctbx.xray.structure_factors.from_scatterers_direct module": [[241, "module-cctbx.xray.structure_factors.from_scatterers_direct"]], "cctbx.xray.structure_factors.from_scatterers_direct_parallel module": [[242, "module-cctbx.xray.structure_factors.from_scatterers_direct_parallel"]], "cctbx.xray.structure_factors.from_scatterers_fft module": [[243, "module-cctbx.xray.structure_factors.from_scatterers_fft"]], "cctbx.xray.structure_factors.global_counters module": [[244, "module-cctbx.xray.structure_factors.global_counters"]], "cctbx.xray.structure_factors.gradient_flags module": [[245, "module-cctbx.xray.structure_factors.gradient_flags"]], "cctbx.xray.structure_factors.gradients module": [[246, "module-cctbx.xray.structure_factors.gradients"]], "cctbx.xray.structure_factors.gradients_base module": [[247, "module-cctbx.xray.structure_factors.gradients_base"]], "cctbx.xray.structure_factors.gradients_direct module": [[248, "module-cctbx.xray.structure_factors.gradients_direct"]], "cctbx.xray.structure_factors.gradients_fft module": [[249, "module-cctbx.xray.structure_factors.gradients_fft"]], "cctbx.xray.structure_factors.manager module": [[250, "module-cctbx.xray.structure_factors.manager"]], "cctbx.xray.structure_factors.misc module": [[251, "module-cctbx.xray.structure_factors.misc"]], "cctbx.xray.target_functors module": [[252, "module-cctbx.xray.target_functors"]], "cctbx.xray.targets package": [[253, "cctbx-xray-targets-package"]], "cctbx.xray.targets.r1 module": [[254, "module-cctbx.xray.targets.r1"]], "cctbx.xray.weighting_schemes module": [[255, "module-cctbx.xray.weighting_schemes"]], "cctbx": [[256, "cctbx"], [261, "cctbx"]], "dxtbx.model": [[257, "dxtbx-model"]], "Table of Contents": [[257, "table-of-contents"], [258, "table-of-contents"], [261, "table-of-contents"], [262, "table-of-contents"], [264, "table-of-contents"], [266, "table-of-contents"], [271, "table-of-contents"], [272, "table-of-contents"], [309, "table-of-contents"], [335, "table-of-contents"]], "dxtbx.model.detector": [[257, "module-dxtbx.model.detector"]], "dxtbx.model.beam": [[257, "module-dxtbx.model.beam"]], "dxtbx.model.scan": [[257, "module-dxtbx.model.scan"]], "dxtbx.model.goniometer": [[257, "module-dxtbx.model.goniometer"]], "dxtbx.model.crystal": [[257, "module-dxtbx.model.crystal"]], "dxtbx.serialize": [[258, "dxtbx-serialize"]], "dxtbx.serialize.load": [[258, "module-dxtbx.serialize.load"]], "dxtbx.serialize.dump": [[258, "dxtbx-serialize-dump"]], "dxtbx.serialize.xds": [[258, "module-dxtbx.serialize.xds"]], "dxtbx package": [[259, "dxtbx-package"]], "CCTBX development history": [[260, "cctbx-development-history"]], "eltbx - Element Toolbox": [[260, "eltbx-element-toolbox"]], "sgtbx - Space Group Toolbox": [[260, "sgtbx-space-group-toolbox"]], "Computational Crystallography Toolbox": [[261, "computational-crystallography-toolbox"]], "Welcome to CCTBX\u2019s documentation!": [[261, "welcome-to-cctbx-s-documentation"]], "High level organization": [[261, "high-level-organization"]], "libtbx": [[261, "libtbx"]], "boost_adaptbx": [[261, "boost-adaptbx"]], "scitbx": [[261, "scitbx"]], "iotbx": [[261, "iotbx"]], "mmtbx": [[261, "mmtbx"], [329, "mmtbx"]], "xfel": [[261, "xfel"], [336, "xfel"]], "smtbx": [[261, "smtbx"]], "dxtbx": [[261, "dxtbx"]], "Tour": [[261, "tour"]], "Tutorials": [[261, "tutorials"]], "Installation": [[261, "installation"]], "Reference Documentation": [[261, "reference-documentation"]], "Links": [[261, "links"]], "Contact": [[261, "contact"]], "Indices and tables": [[261, "indices-and-tables"]], "Installation overview": [[262, "installation-overview"]], "Manually building from sources under Linux and macOS": [[262, "manually-building-from-sources-under-linux-and-macos"]], "Manually building from sources under Windows 2000 or higher": [[262, "manually-building-from-sources-under-windows-2000-or-higher"]], "iotbx - file readers and writers": [[263, "iotbx-file-readers-and-writers"]], "iotbx.cif": [[264, "iotbx-cif"]], "Overview": [[264, "overview"], [266, "overview"], [269, "overview"], [271, "overview"], [272, "overview"]], "Reading a CIF file": [[264, "reading-a-cif-file"]], "Python representation of a CIF file": [[264, "python-representation-of-a-cif-file"]], "Dictionary validation": [[264, "dictionary-validation"]], "Creating a standalone C++ CIF parser": [[264, "creating-a-standalone-c-cif-parser"]], "API documentation": [[264, "api-documentation"], [265, "module-iotbx.file_reader"], [266, "module-iotbx.map_manager"], [268, "api-documentation"], [271, "module-iotbx.shelx"], [272, "module-iotbx.xds.xds_inp"], [282, "module-mmtbx.command_line"], [288, "module-mmtbx.f_model"], [310, "module-mmtbx.pdbtools"], [331, "module-scitbx.array_family.flex"], [332, "module-scitbx.lbfgs"], [333, "module-scitbx.lstbx.normal_eqns"], [334, "api-documentation"]], "iotbx.cif objects": [[264, "iotbx-cif-objects"]], "Accessory classes and functions": [[264, "accessory-classes-and-functions"], [268, "accessory-classes-and-functions"]], "iotbx.file_reader - generic file input": [[265, "iotbx-file-reader-generic-file-input"]], "iotbx.managers": [[266, "iotbx-managers"]], "Parameters:": [[266, "parameters"], [266, "id1"]], "Summary:": [[266, "summary"]], "iotbx.ncs package": [[267, "iotbx-ncs-package"]], "iotbx.ncs.ncs_preprocess module": [[267, "iotbx-ncs-ncs-preprocess-module"]], "iotbx.pdb": [[268, "iotbx-pdb"]], "Input methods and objects": [[268, "input-methods-and-objects"]], "Arguments:": [[268, "arguments"]], "Returns:": [[268, "returns"]], "PDB hierarchy objects": [[268, "pdb-hierarchy-objects"]], "iotbx.pdb.multimer_reconstruction module": [[268, "iotbx-pdb-multimer-reconstruction-module"]], "iotbx.pdb tutorial: pdb_truncate_to_ala": [[269, "iotbx-pdb-tutorial-pdb-truncate-to-ala"]], "Use print and help()!": 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"pool-map-parallel-map-function-for-unix-linux-systems"]], "parallel_map: parallel map() function for multiple architectures": [[274, "parallel-map-parallel-map-function-for-multiple-architectures"]], "libtbx.program_template: Standard Program Template for CCTBX Programs": [[275, "libtbx-program-template-standard-program-template-for-cctbx-programs"]], "Program Template": [[275, "program-template"]], "mmtbx - macromolecular crystallography": [[276, "mmtbx-macromolecular-crystallography"]], "mmtbx.building package": [[277, "mmtbx-building-package"]], "mmtbx.building.extend_sidechains module": [[277, "module-mmtbx.building.extend_sidechains"]], "mmtbx.building.make_library module": [[277, "module-mmtbx.building.make_library"]], "mmtbx.bulk_solvent package": [[278, "mmtbx-bulk-solvent-package"]], "mmtbx.bulk_solvent.bulk_solvent_and_scaling module": [[278, "module-mmtbx.bulk_solvent.bulk_solvent_and_scaling"]], "mmtbx.bulk_solvent.scaler module": [[278, 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"module-mmtbx.cablam.fingerprints.how_to"]], "mmtbx.cablam.fingerprints.parallel_beta module": [[280, "module-mmtbx.cablam.fingerprints.parallel_beta"]], "mmtbx.cablam.fingerprints.regular_helix_definitions module": [[280, "module-mmtbx.cablam.fingerprints.regular_helix_definitions"]], "mmtbx.chemical_components package": [[281, "mmtbx-chemical-components-package"]], "mmtbx.chemical_components.cif_parser module": [[281, "module-mmtbx.chemical_components.cif_parser"]], "mmtbx.command_line package": [[282, "mmtbx-command-line-package"]], "mmtbx.conformation_dependent_library package": [[283, "mmtbx-conformation-dependent-library-package"]], "mmtbx.conformation_dependent_library.altloc_weighting module": [[283, "module-mmtbx.conformation_dependent_library.altloc_weighting"]], "mmtbx.conformation_dependent_library.bond_angle_registry module": [[283, "module-mmtbx.conformation_dependent_library.bond_angle_registry"]], "mmtbx.conformation_dependent_library.cdl_database module": [[283, "module-mmtbx.conformation_dependent_library.cdl_database"]], "mmtbx.conformation_dependent_library.rdl_database module": [[283, "module-mmtbx.conformation_dependent_library.rdl_database"]], "mmtbx.conformation_dependent_library.rotamers module": [[283, "mmtbx-conformation-dependent-library-rotamers-module"]], "mmtbx.conformation_dependent_library.tst_cdl module": [[283, "module-mmtbx.conformation_dependent_library.tst_cdl"]], "mmtbx.conformation_dependent_library.test_interpolation module": [[283, "mmtbx-conformation-dependent-library-test-interpolation-module"]], "mmtbx.conformation_dependent_library.tst_rdl module": [[283, "mmtbx-conformation-dependent-library-tst-rdl-module"]], "mmtbx.conformation_dependent_library.utils module": [[283, "module-mmtbx.conformation_dependent_library.utils"]], "mmtbx.den package": [[284, "mmtbx-den-package"]], "mmtbx.den.plot_weights module": [[284, "module-mmtbx.den.plot_weights"]], "mmtbx.den.refinement module": [[284, 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"mmtbx.geometry_restraints.hbond module": [[290, "mmtbx-geometry-restraints-hbond-module"]], "mmtbx.geometry_restraints.ramachandran module": [[290, "module-mmtbx.geometry_restraints.ramachandran"]], "mmtbx.geometry_restraints.reference module": [[290, "module-mmtbx.geometry_restraints.reference"]], "mmtbx.geometry_restraints.rotamer module": [[290, "mmtbx-geometry-restraints-rotamer-module"]], "mmtbx.hydrogens package": [[291, "mmtbx-hydrogens-package"]], "mmtbx.hydrogens.build_hydrogens module": [[291, "module-mmtbx.hydrogens.build_hydrogens"]], "mmtbx.hydrogens.find module": [[291, "module-mmtbx.hydrogens.find"]], "mmtbx.ias package": [[292, "mmtbx-ias-package"]], "mmtbx.ions package": [[293, "mmtbx-ions-package"]], "mmtbx.ions.build module": [[294, "module-mmtbx.ions.build"]], "mmtbx.ions.environment module": [[295, "module-mmtbx.ions.environment"]], "mmtbx.ions.geometry module": [[296, "module-mmtbx.ions.geometry"]], "mmtbx.ions.halides module": [[297, "module-mmtbx.ions.halides"]], "mmtbx.ions.identify module": [[298, "module-mmtbx.ions.identify"]], "mmtbx.ions.svm package": [[299, "mmtbx-ions-svm-package"]], "mmtbx.ions.svm.dump_sites module": [[300, "module-mmtbx.ions.svm.dump_sites"]], "mmtbx.ions.svm.utils module": [[301, "module-mmtbx.ions.svm.utils"]], "mmtbx.ions.utils module": [[302, "module-mmtbx.ions.utils"]], "mmtbx.kinemage package": [[303, "mmtbx-kinemage-package"]], "mmtbx.kinemage.validation module": [[303, "module-mmtbx.kinemage.validation"]], "mmtbx.ligands package": [[304, "mmtbx-ligands-package"]], "mmtbx.ligands.xtal_screens module": [[304, "module-mmtbx.ligands.xtal_screens"]], "mmtbx.maps package": [[305, "mmtbx-maps-package"]], "mmtbx.maps.composite_omit_map module": [[305, "module-mmtbx.maps.composite_omit_map"]], "mmtbx.maps.fem module": [[305, "module-mmtbx.maps.fem"]], "mmtbx.maps.fobs_minus_fobs_map module": [[305, "module-mmtbx.maps.fobs_minus_fobs_map"]], "mmtbx.maps.kick module": [[305, "module-mmtbx.maps.kick"]], "mmtbx.maps.superpose module": [[305, "module-mmtbx.maps.superpose"]], "mmtbx.maps.utils module": [[305, "module-mmtbx.maps.utils"]], "mmtbx.masks package": [[306, "mmtbx-masks-package"]], "mmtbx.max_lik package": [[307, "mmtbx-max-lik-package"]], "mmtbx.max_lik.max_like_non_uniform module": [[307, "module-mmtbx.max_lik.max_like_non_uniform"]], "mmtbx.max_lik.maxlik module": [[307, "module-mmtbx.max_lik.maxlik"]], "mmtbx.monomer_library package": [[308, "mmtbx-monomer-library-package"]], "mmtbx.monomer_library.bondlength_defaults module": [[308, "module-mmtbx.monomer_library.bondlength_defaults"]], "mmtbx.monomer_library.cif_triage module": [[308, "module-mmtbx.monomer_library.cif_triage"]], "mmtbx.monomer_library.cif_types module": [[308, "module-mmtbx.monomer_library.cif_types"]], "mmtbx.monomer_library.conformation_dependent_restraints module": [[308, "module-mmtbx.monomer_library.conformation_dependent_restraints"]], "mmtbx.monomer_library.conv_v2_v3 module": [[308, "module-mmtbx.monomer_library.conv_v2_v3"]], "mmtbx.monomer_library.correct_hydrogen_geometries module": [[308, "module-mmtbx.monomer_library.correct_hydrogen_geometries"]], "mmtbx.monomer_library.glyco_chiral_values module": [[308, "module-mmtbx.monomer_library.glyco_chiral_values"]], "mmtbx.monomer_library.glyco_utils module": [[308, "module-mmtbx.monomer_library.glyco_utils"]], "mmtbx.monomer_library.hydrogen_restrictions module": [[308, "module-mmtbx.monomer_library.hydrogen_restrictions"]], "mmtbx.monomer_library.idealized_aa module": [[308, "module-mmtbx.monomer_library.idealized_aa"]], "mmtbx.monomer_library.linking_mixins module": [[308, "module-mmtbx.monomer_library.linking_mixins"]], "mmtbx.monomer_library.linking_setup module": [[308, "module-mmtbx.monomer_library.linking_setup"]], "mmtbx.monomer_library.linking_utils module": [[308, "module-mmtbx.monomer_library.linking_utils"]], "mmtbx.monomer_library.pdb_interpretation module": [[308, "module-mmtbx.monomer_library.pdb_interpretation"]], "mmtbx.monomer_library.rna_sugar_pucker_analysis module": [[308, "module-mmtbx.monomer_library.rna_sugar_pucker_analysis"]], "mmtbx.monomer_library.rotamer_utils module": [[308, "module-mmtbx.monomer_library.rotamer_utils"]], "mmtbx.monomer_library.server module": [[308, "module-mmtbx.monomer_library.server"]], "mmtbx.ncs": [[309, "mmtbx-ncs"]], "mmtbx.ncs.ligands module": [[309, "module-mmtbx.ncs.ligands"]], "mmtbx.ncs.ncs module": [[309, "module-mmtbx.ncs.ncs"]], "mmtbx.ncs.restraints module": [[309, "mmtbx-ncs-restraints-module"]], "mmtbx.ncs.ncs_search module": [[309, "module-mmtbx.ncs.ncs_search"]], "mmtbx.ncs.ncs_utils module": [[309, "module-mmtbx.ncs.ncs_utils"]], "mmtbx.pdbtools - model manipulation utilities": [[310, "mmtbx-pdbtools-model-manipulation-utilities"]], "mmtbx.polygon package": [[311, "mmtbx-polygon-package"]], "mmtbx.polygon.output module": [[311, "module-mmtbx.polygon.output"]], "mmtbx.real_space package": [[312, "mmtbx-real-space-package"]], "mmtbx.refinement package": [[313, "mmtbx-refinement-package"]], "mmtbx.refinement.adp_refinement module": [[313, "module-mmtbx.refinement.adp_refinement"]], "mmtbx.refinement.anomalous_scatterer_groups module": [[313, "module-mmtbx.refinement.anomalous_scatterer_groups"]], "mmtbx.refinement.fit_rotamers module": [[313, "mmtbx-refinement-fit-rotamers-module"]], "mmtbx.refinement.flip_peptides module": [[313, "mmtbx-refinement-flip-peptides-module"]], "mmtbx.refinement.geometry_minimization module": [[313, "module-mmtbx.refinement.geometry_minimization"]], "mmtbx.refinement.group module": [[313, "module-mmtbx.refinement.group"]], "mmtbx.refinement.inspect_tardy_trajectory module": [[313, "module-mmtbx.refinement.inspect_tardy_trajectory"]], "mmtbx.refinement.minimization module": [[313, "module-mmtbx.refinement.minimization"]], "mmtbx.refinement.minimization_ncs_constraints module": [[313, "module-mmtbx.refinement.minimization_ncs_constraints"]], "mmtbx.refinement.occupancies module": [[313, "module-mmtbx.refinement.occupancies"]], "mmtbx.refinement.orca module": [[313, "module-mmtbx.refinement.orca"]], "mmtbx.refinement.print_statistics module": [[313, "module-mmtbx.refinement.print_statistics"]], "mmtbx.refinement.refinement_flags module": [[313, "module-mmtbx.refinement.refinement_flags"]], "mmtbx.refinement.rigid_body module": [[313, "module-mmtbx.refinement.rigid_body"]], "mmtbx.refinement.select_best_starting_model module": [[313, "module-mmtbx.refinement.select_best_starting_model"]], "mmtbx.refinement.tardy module": [[313, "module-mmtbx.refinement.tardy"]], "mmtbx.refinement.targets module": [[313, "module-mmtbx.refinement.targets"]], "mmtbx.refinement.weights_params module": [[313, "module-mmtbx.refinement.weights_params"]], "mmtbx.refinement.wx_tardy_pdb module": [[313, "mmtbx-refinement-wx-tardy-pdb-module"]], "mmtbx.refinement.ensemble_refinement package": [[314, "mmtbx-refinement-ensemble-refinement-package"]], "mmtbx.refinement.ensemble_refinement.ensemble_utils module": [[314, "module-mmtbx.refinement.ensemble_refinement.ensemble_utils"]], "mmtbx.refinement.real_space package": [[315, "mmtbx-refinement-real-space-package"]], "mmtbx.refinement.real_space.fit_residue module": [[315, "module-mmtbx.refinement.real_space.fit_residue"]], "mmtbx.refinement.real_space.fit_residues module": [[315, "module-mmtbx.refinement.real_space.fit_residues"]], "mmtbx.refinement.real_space.fit_water module": [[315, "module-mmtbx.refinement.real_space.fit_water"]], "mmtbx.refinement.real_space.individual_sites module": [[315, "module-mmtbx.refinement.real_space.individual_sites"]], "mmtbx.refinement.real_space.rigid_body module": [[315, "module-mmtbx.refinement.real_space.rigid_body"]], "mmtbx.refinement.real_space.weight module": [[315, "module-mmtbx.refinement.real_space.weight"]], "mmtbx.rotamer package": [[316, "mmtbx-rotamer-package"]], "mmtbx.rotamer.graphics module": [[316, "module-mmtbx.rotamer.graphics"]], "mmtbx.rotamer.n_dim_table module": [[316, "module-mmtbx.rotamer.n_dim_table"]], "mmtbx.rotamer.ramachandran_eval module": [[316, "module-mmtbx.rotamer.ramachandran_eval"]], "mmtbx.rotamer.rotamer_eval module": [[316, "module-mmtbx.rotamer.rotamer_eval"]], "mmtbx.rotamer.sidechain_angles module": [[316, "module-mmtbx.rotamer.sidechain_angles"]], "mmtbx.rsr package": [[317, "mmtbx-rsr-package"]], "mmtbx.scaling package": [[318, "mmtbx-scaling-package"]], "mmtbx.scaling.absence_likelihood module": [[318, "module-mmtbx.scaling.absence_likelihood"]], "mmtbx.scaling.absences module": [[318, "module-mmtbx.scaling.absences"]], "mmtbx.scaling.absolute_scaling module": [[318, "module-mmtbx.scaling.absolute_scaling"]], "mmtbx.scaling.basic_analyses module": [[318, "module-mmtbx.scaling.basic_analyses"]], "mmtbx.scaling.data_statistics module": [[318, "module-mmtbx.scaling.data_statistics"]], "mmtbx.scaling.fa_estimation module": [[318, "module-mmtbx.scaling.fa_estimation"]], "mmtbx.scaling.fest module": [[318, "module-mmtbx.scaling.fest"]], "mmtbx.scaling.make_param module": [[318, "module-mmtbx.scaling.make_param"]], "mmtbx.scaling.massage_twin_detwin_data module": [[318, "module-mmtbx.scaling.massage_twin_detwin_data"]], "mmtbx.scaling.matthews module": [[318, "module-mmtbx.scaling.matthews"]], "mmtbx.scaling.outlier_plots module": [[318, "module-mmtbx.scaling.outlier_plots"]], "mmtbx.scaling.outlier_rejection module": [[318, "module-mmtbx.scaling.outlier_rejection"]], "mmtbx.scaling.pair_analyses module": [[318, "module-mmtbx.scaling.pair_analyses"]], "mmtbx.scaling.pre_scale module": [[318, "module-mmtbx.scaling.pre_scale"]], "mmtbx.scaling.random_omit module": [[318, "module-mmtbx.scaling.random_omit"]], "mmtbx.scaling.relative_scaling module": [[318, "module-mmtbx.scaling.relative_scaling"]], "mmtbx.scaling.relative_wilson module": [[318, "module-mmtbx.scaling.relative_wilson"]], "mmtbx.scaling.remove_outliers module": [[318, "module-mmtbx.scaling.remove_outliers"]], "mmtbx.scaling.rip_scale module": [[318, "module-mmtbx.scaling.rip_scale"]], "mmtbx.scaling.sad_scale module": [[318, "module-mmtbx.scaling.sad_scale"]], "mmtbx.scaling.sigmaa_estimation module": [[318, "module-mmtbx.scaling.sigmaa_estimation"]], "mmtbx.scaling.sir_scale module": [[318, "module-mmtbx.scaling.sir_scale"]], "mmtbx.scaling.siras_scale module": [[318, "module-mmtbx.scaling.siras_scale"]], "mmtbx.scaling.ta_alpha_beta_calc module": [[318, "module-mmtbx.scaling.ta_alpha_beta_calc"]], "mmtbx.scaling.thorough_outlier_test module": [[318, "module-mmtbx.scaling.thorough_outlier_test"]], "mmtbx.scaling.twin_analyses module": [[318, "module-mmtbx.scaling.twin_analyses"]], "mmtbx.scaling.twmad_scale module": [[318, "module-mmtbx.scaling.twmad_scale"]], "mmtbx.scaling.xtriage module": [[318, "module-mmtbx.scaling.xtriage"]], "mmtbx.secondary_structure package": [[319, "mmtbx-secondary-structure-package"]], "mmtbx.secondary_structure.base_pairing module": [[319, "mmtbx-secondary-structure-base-pairing-module"]], "mmtbx.secondary_structure.dssp module": [[319, "mmtbx-secondary-structure-dssp-module"]], "mmtbx.secondary_structure.proteins module": [[319, "module-mmtbx.secondary_structure.proteins"]], "mmtbx.secondary_structure.utils module": [[319, "module-mmtbx.secondary_structure.utils"]], "mmtbx.secondary_structure.build package": [[320, "mmtbx-secondary-structure-build-package"]], "mmtbx.solvent package": [[321, "mmtbx-solvent-package"]], "mmtbx.solvent.ensemble_ordered_solvent module": [[321, "module-mmtbx.solvent.ensemble_ordered_solvent"]], "mmtbx.solvent.ordered_solvent module": [[321, "module-mmtbx.solvent.ordered_solvent"]], "mmtbx.tls package": [[322, "mmtbx-tls-package"]], "mmtbx.tls.command_line module": [[322, "module-mmtbx.tls.command_line"]], "mmtbx.tls.ladp module": [[322, "module-mmtbx.tls.ladp"]], "mmtbx.tls.tls_as_xyz module": [[322, "module-mmtbx.tls.tls_as_xyz"]], "mmtbx.tls.tools module": [[322, "module-mmtbx.tls.tools"]], "mmtbx.torsion_restraints package": [[323, "mmtbx-torsion-restraints-package"]], "mmtbx.torsion_restraints.reference_model module": [[323, "mmtbx-torsion-restraints-reference-model-module"]], "mmtbx.torsion_restraints.rotamer_search module": [[323, "mmtbx-torsion-restraints-rotamer-search-module"]], "mmtbx.torsion_restraints.torsion_ncs module": [[323, "mmtbx-torsion-restraints-torsion-ncs-module"]], "mmtbx.torsion_restraints.utils module": [[323, "mmtbx-torsion-restraints-utils-module"]], "mmtbx.twinning package": [[324, "mmtbx-twinning-package"]], "mmtbx.twinning.probabalistic_detwinning module": [[324, "module-mmtbx.twinning.probabalistic_detwinning"]], "mmtbx.twinning.twin_f_model module": [[324, "module-mmtbx.twinning.twin_f_model"]], "mmtbx.twinning.twin_map_utils module": [[324, "mmtbx-twinning-twin-map-utils-module"]], "mmtbx.utils package": [[325, "mmtbx-utils-package"]], "mmtbx.utils.fab_elbow_angle module": [[325, "module-mmtbx.utils.fab_elbow_angle"]], "mmtbx.utils.ncs_utils module": [[325, "mmtbx-utils-ncs-utils-module"]], "mmtbx.utils.rotatable_bonds module": [[325, "module-mmtbx.utils.rotatable_bonds"]], "mmtbx.validation package": [[326, "mmtbx-validation-package"]], "Base classes": [[326, "base-classes"]], "Rotalyze - protein sidechain rotamer analysis": [[326, "rotalyze-protein-sidechain-rotamer-analysis"]], "Ramalyze - Ramachandran plot analysis": [[326, "ramalyze-ramachandran-plot-analysis"]], "Clashscore - all-atom contacts using Reduce and Probe": [[326, "clashscore-all-atom-contacts-using-reduce-and-probe"]], "C-beta deviations": [[326, "c-beta-deviations"]], "mmtbx.validation.restraints module": [[326, "module-mmtbx.validation.restraints"]], "mmtbx.validation.rna_validate module": [[326, "module-mmtbx.validation.rna_validate"]], "mmtbx.validation.analyze_peptides module": [[326, "module-mmtbx.validation.analyze_peptides"]], "mmtbx.validation.experimental module": [[326, "module-mmtbx.validation.experimental"]], "mmtbx.validation.graphics module": [[326, "module-mmtbx.validation.graphics"]], "mmtbx.validation.ligands module": [[326, "module-mmtbx.validation.ligands"]], "mmtbx.validation.model_properties module": [[326, "module-mmtbx.validation.model_properties"]], "mmtbx.validation.sequence module": [[326, "module-mmtbx.validation.sequence"]], "mmtbx.validation.utils module": [[326, "module-mmtbx.validation.utils"]], "mmtbx.validation.waters module": [[326, "module-mmtbx.validation.waters"]], "mmtbx.validation.molprobity package": [[327, "mmtbx-validation-molprobity-package"]], "mmtbx.validation.molprobity.mp_geo module": [[327, "module-mmtbx.validation.molprobity.mp_geo"]], "mmtbx.validation.molprobity.nqh_minimize module": [[327, "module-mmtbx.validation.molprobity.nqh_minimize"]], "mmtbx.wwpdb package": [[328, "mmtbx-wwpdb-package"]], "mmtbx.wwpdb.rcsb_web_services module": [[328, "module-mmtbx.wwpdb.rcsb_web_services"]], "mmtbx.wwpdb.standard_geometry_cif module": [[328, "module-mmtbx.wwpdb.standard_geometry_cif"]], "mmtbx.wwpdb.utils module": [[328, "module-mmtbx.wwpdb.utils"]], "scitbx - general-purpose scientific programming infrastructure": [[330, "scitbx-general-purpose-scientific-programming-infrastructure"]], "scitbx.array_family.flex": [[331, "scitbx-array-family-flex"], [335, "scitbx-array-family-flex"]], "Multidimensional arrays: flex.grid": [[331, "multidimensional-arrays-flex-grid"]], "Working with selections": [[331, "working-with-selections"]], "scitbx.lbfgs": [[332, "scitbx-lbfgs"]], "scitbx.lstbx": [[333, "scitbx-lstbx"]], "scitbx.matrix": [[334, "module-scitbx.matrix"]], "Tour of the cctbx": [[335, "tour-of-the-cctbx"]], "The beach in the box": [[335, "the-beach-in-the-box"]], "At the very bottom": [[335, "at-the-very-bottom"]], "cctbx.array_family.flex": [[335, "cctbx-array-family-flex"]], "A balancing act": [[335, "a-balancing-act"]], "Hybrid systems": [[335, "hybrid-systems"]], "Building bridges": [[335, "building-bridges"]], "Thinking hybrid": [[335, "thinking-hybrid"]], "xfel package": [[337, "xfel-package"]], "xfel.detector_formats module": [[337, "xfel-detector-formats-module"]], "xfel.phil_preferences module": [[337, "module-xfel.phil_preferences"]], "xfel.cftbx package": [[338, "xfel-cftbx-package"]], "xfel.cftbx.detector package": [[339, "xfel-cftbx-detector-package"]], "xfel.cftbx.detector.cspad_cbf_tbx module": [[339, "module-xfel.cftbx.detector.cspad_cbf_tbx"]], "xfel.cftbx.detector.cspad_detector module": [[339, "xfel-cftbx-detector-cspad-detector-module"]], "xfel.cftbx.detector.generic_detector module": [[339, "xfel-cftbx-detector-generic-detector-module"]], "xfel.cftbx.detector.metrology module": [[339, "xfel-cftbx-detector-metrology-module"]], "xfel.cftbx.detector.metrology2phil module": [[339, "module-xfel.cftbx.detector.metrology2phil"]], "xfel.clustering package": [[340, "xfel-clustering-package"]], "xfel.clustering.cluster module": [[340, "module-xfel.clustering.cluster"]], "cluster.Cluster": [[340, "cluster-cluster"]], "xfel.clustering.cluster_groups module": [[340, "module-xfel.clustering.cluster_groups"]], "xfel.clustering.singleframe module": [[340, "module-xfel.clustering.singleframe"]], "singleframe.SingleFrame": [[340, "singleframe-singleframe"]], "xfel.command_line package": [[341, "xfel-command-line-package"]], "xfel.command_line.auto_submit module": [[341, "module-xfel.command_line.auto_submit"]], "xfel.command_line.brehm_diederichs module": [[341, "module-xfel.command_line.brehm_diederichs"]], "xfel.command_line.cbf_average module": [[341, "module-xfel.command_line.cbf_average"]], "xfel.command_line.cluster_42 module": [[341, "xfel-command-line-cluster-42-module"]], "xfel.command_line.cluster_intensity_statistics module": [[341, "xfel-command-line-cluster-intensity-statistics-module"]], "xfel.command_line.cluster_per_frame_wilson module": [[341, "xfel-command-line-cluster-per-frame-wilson-module"]], "xfel.command_line.cluster_unit_cell module": [[341, "xfel-command-line-cluster-unit-cell-module"]], "xfel.command_line.cluster_visualise_orientations module": [[341, "xfel-command-line-cluster-visualise-orientations-module"]], "xfel.command_line.convert_gain_map module": [[341, "module-xfel.command_line.convert_gain_map"]], "xfel.command_line.convert_gain_map_cbf module": [[341, "module-xfel.command_line.convert_gain_map_cbf"]], "xfel.command_line.cxi_apply_metrology module": [[341, "module-xfel.command_line.cxi_apply_metrology"]], "xfel.command_line.cxi_cspad_pinwheel module": [[341, "module-xfel.command_line.cxi_cspad_pinwheel"]], "xfel.command_line.cxi_diff module": [[341, "module-xfel.command_line.cxi_diff"]], "xfel.command_line.cxi_display_metrology module": [[341, "module-xfel.command_line.cxi_display_metrology"]], "xfel.command_line.cxi_generate_circular_gain_mask module": [[341, "module-xfel.command_line.cxi_generate_circular_gain_mask"]], "xfel.command_line.cxi_image2pickle module": [[341, "xfel-command-line-cxi-image2pickle-module"]], "xfel.command_line.cxi_index module": [[341, "module-xfel.command_line.cxi_index"]], "xfel.command_line.cxi_lsf module": [[341, "module-xfel.command_line.cxi_lsf"]], "xfel.command_line.cxi_merge module": [[341, "module-xfel.command_line.cxi_merge"]], "xfel.command_line.cxi_optical2cbfheader module": [[341, "module-xfel.command_line.cxi_optical2cbfheader"]], "xfel.command_line.cxi_pbs module": [[341, "module-xfel.command_line.cxi_pbs"]], "xfel.command_line.cxi_pickle2cbf module": [[341, "module-xfel.command_line.cxi_pickle2cbf"]], "xfel.command_line.cxi_plotcv module": [[341, "module-xfel.command_line.cxi_plotcv"]], "xfel.command_line.cxi_psana module": [[341, "module-xfel.command_line.cxi_psana"]], "xfel.command_line.cxi_pyana module": [[341, "module-xfel.command_line.cxi_pyana"]], "xfel.command_line.cxi_spots module": [[341, "module-xfel.command_line.cxi_spots"]], "xfel.command_line.cxi_stream_to_pickle module": [[341, "module-xfel.command_line.cxi_stream_to_pickle"]], "xfel.command_line.cxi_view module": [[341, "module-xfel.command_line.cxi_view"]], "xfel.command_line.cxi_xmerge module": [[341, "module-xfel.command_line.cxi_xmerge"]], "xfel.command_line.get_next_trial_id module": [[341, "xfel-command-line-get-next-trial-id-module"]], "xfel.command_line.grid_index module": [[341, "xfel-command-line-grid-index-module"]], "xfel.command_line.histogram_finalise module": [[341, "module-xfel.command_line.histogram_finalise"]], "xfel.command_line.list_db_metadata module": [[341, "module-xfel.command_line.list_db_metadata"]], "xfel.command_line.make_mask module": [[341, "module-xfel.command_line.make_mask"]], "xfel.command_line.metrology module": [[341, "module-xfel.command_line.metrology"]], "xfel.command_line.monitor_detectors module": [[341, "module-xfel.command_line.monitor_detectors"]], "xfel.command_line.monitor_trials module": [[341, "module-xfel.command_line.monitor_trials"]], "xfel.command_line.overlay_spectra module": [[341, "module-xfel.command_line.overlay_spectra"]], "xfel.command_line.plot_to_subpixel module": [[341, "module-xfel.command_line.plot_to_subpixel"]], "xfel.command_line.postrefine module": [[341, "module-xfel.command_line.postrefine"]], "xfel.command_line.print_pickle module": [[341, "module-xfel.command_line.print_pickle"]], "xfel.command_line.quadrants module": [[341, "module-xfel.command_line.quadrants"]], "xfel.command_line.radial_average module": [[341, "module-xfel.command_line.radial_average"]], "xfel.command_line.smooth_spectrum module": [[341, "module-xfel.command_line.smooth_spectrum"]], "xfel.command_line.subtract_background module": [[341, "module-xfel.command_line.subtract_background"]], "xfel.command_line.trial_stats module": [[341, "module-xfel.command_line.trial_stats"]], "xfel.command_line.view_pixel_histograms module": [[341, "module-xfel.command_line.view_pixel_histograms"]], "xfel.command_line.xes_finalise module": [[341, "module-xfel.command_line.xes_finalise"]], "xfel.command_line.xes_histograms module": [[341, "module-xfel.command_line.xes_histograms"]], "xfel.cxi package": [[342, "xfel-cxi-package"]], "xfel.cxi.average_spots module": [[342, "module-xfel.cxi.average_spots"]], "xfel.cxi.completeness_plot module": [[342, "xfel-cxi-completeness-plot-module"]], "xfel.cxi.correction_vector_plot module": [[342, "module-xfel.cxi.correction_vector_plot"]], "xfel.cxi.cxi_cc module": [[342, "module-xfel.cxi.cxi_cc"]], "xfel.cxi.display_powder_arcs module": [[342, "module-xfel.cxi.display_powder_arcs"]], "xfel.cxi.display_spots module": [[342, "module-xfel.cxi.display_spots"]], "xfel.cxi.integrate_image_api module": [[342, "module-xfel.cxi.integrate_image_api"]], "xfel.cxi.merging_database module": [[342, "xfel-cxi-merging-database-module"]], "xfel.cxi.merging_database_fs module": [[342, "xfel-cxi-merging-database-fs-module"]], "xfel.cxi.merging_database_sqlite3 module": [[342, "xfel-cxi-merging-database-sqlite3-module"]], "xfel.cxi.strong_zulu module": [[342, "module-xfel.cxi.strong_zulu"]], "xfel.cxi.util module": [[342, "module-xfel.cxi.util"]], "xfel.cxi.cspad_ana package": [[343, "xfel-cxi-cspad-ana-package"]], "xfel.cxi.cspad_ana.average_tbx module": [[343, "module-xfel.cxi.cspad_ana.average_tbx"]], "xfel.cxi.cspad_ana.common_mode module": [[343, "module-xfel.cxi.cspad_ana.common_mode"]], "xfel.cxi.cspad_ana.cspad_tbx module": [[343, "module-xfel.cxi.cspad_ana.cspad_tbx"]], "xfel.cxi.cspad_ana.display_calib module": [[343, "module-xfel.cxi.cspad_ana.display_calib"]], "xfel.cxi.cspad_ana.histogram_finalise module": [[343, "module-xfel.cxi.cspad_ana.histogram_finalise"]], "xfel.cxi.cspad_ana.hitfinder_tbx module": [[343, "module-xfel.cxi.cspad_ana.hitfinder_tbx"]], "xfel.cxi.cspad_ana.mod_average module": [[343, "module-xfel.cxi.cspad_ana.mod_average"]], "xfel.cxi.cspad_ana.mod_average_cbf module": [[343, "xfel-cxi-cspad-ana-mod-average-cbf-module"]], "xfel.cxi.cspad_ana.mod_cbf_hitfind module": [[343, "xfel-cxi-cspad-ana-mod-cbf-hitfind-module"]], "xfel.cxi.cspad_ana.mod_cbf_index module": [[343, "xfel-cxi-cspad-ana-mod-cbf-index-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_daq_status module": [[343, "module-xfel.cxi.cspad_ana.mod_daq_status"]], "xfel.cxi.cspad_ana.mod_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_dump"]], "xfel.cxi.cspad_ana.mod_dump_bitmap module": [[343, "module-xfel.cxi.cspad_ana.mod_dump_bitmap"]], "xfel.cxi.cspad_ana.mod_event_info module": [[343, "module-xfel.cxi.cspad_ana.mod_event_info"]], "xfel.cxi.cspad_ana.mod_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_filter"]], "xfel.cxi.cspad_ana.mod_hdf5 module": [[343, "module-xfel.cxi.cspad_ana.mod_hdf5"]], "xfel.cxi.cspad_ana.mod_hitfind module": [[343, "module-xfel.cxi.cspad_ana.mod_hitfind"]], "xfel.cxi.cspad_ana.mod_illumination_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_illumination_filter"]], "xfel.cxi.cspad_ana.mod_ledge module": [[343, "xfel-cxi-cspad-ana-mod-ledge-module"]], "xfel.cxi.cspad_ana.mod_mar module": [[343, "module-xfel.cxi.cspad_ana.mod_mar"]], "xfel.cxi.cspad_ana.mod_param module": [[343, "module-xfel.cxi.cspad_ana.mod_param"]], "xfel.cxi.cspad_ana.mod_pickle2cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-pickle2cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_pulnix_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_pulnix_dump"]], "xfel.cxi.cspad_ana.mod_radial_average module": [[343, "module-xfel.cxi.cspad_ana.mod_radial_average"]], "xfel.cxi.cspad_ana.mod_spectra module": [[343, "xfel-cxi-cspad-ana-mod-spectra-module"]], "xfel.cxi.cspad_ana.mod_spectra_view module": [[343, "xfel-cxi-cspad-ana-mod-spectra-view-module"]], "xfel.cxi.cspad_ana.mod_view module": [[343, "xfel-cxi-cspad-ana-mod-view-module"]], "xfel.cxi.cspad_ana.mod_xes module": [[343, "module-xfel.cxi.cspad_ana.mod_xes"]], "xfel.cxi.cspad_ana.parse_calib module": [[343, "module-xfel.cxi.cspad_ana.parse_calib"]], "xfel.cxi.cspad_ana.pixel_histograms module": [[343, "module-xfel.cxi.cspad_ana.pixel_histograms"]], "xfel.cxi.cspad_ana.xes_finalise module": [[343, "module-xfel.cxi.cspad_ana.xes_finalise"]], "xfel.cxi.cspad_ana.xes_histograms module": [[343, "module-xfel.cxi.cspad_ana.xes_histograms"]], "xfel.cxi.gfx package": [[344, "xfel-cxi-gfx-package"]], "xfel.cxi.gfx.status_plot module": [[344, "module-xfel.cxi.gfx.status_plot"]], "xfel.cxi.gfx.trials_plot module": [[344, "module-xfel.cxi.gfx.trials_plot"]], "xfel.cxi.gfx.wx_detectors module": [[344, "module-xfel.cxi.gfx.wx_detectors"]], "xfel.cxi.merging package": [[345, "xfel-cxi-merging-package"]], "xfel.cxi.merging.general_fcalc module": [[345, "xfel-cxi-merging-general-fcalc-module"]], "xfel.cxi.merging.phil_validation module": [[345, "xfel-cxi-merging-phil-validation-module"]], "xfel.cxi.merging.refine module": [[345, "xfel-cxi-merging-refine-module"]], "xfel.cxi.postrefine package": [[346, "xfel-cxi-postrefine-package"]], "xfel.cxi.postrefine.justsum module": [[346, "xfel-cxi-postrefine-justsum-module"]], "xfel.cxi.postrefine.mod_energy module": [[346, "xfel-cxi-postrefine-mod-energy-module"]], "xfel.cxi.postrefine.mod_graddesc module": [[346, "xfel-cxi-postrefine-mod-graddesc-module"]], "xfel.cxi.postrefine.mod_leastsqr module": [[346, "xfel-cxi-postrefine-mod-leastsqr-module"]], "xfel.cxi.postrefine.mod_normal_eqns module": [[346, "xfel-cxi-postrefine-mod-normal-eqns-module"]], "xfel.cxi.postrefine.mod_partiality module": [[346, "xfel-cxi-postrefine-mod-partiality-module"]], "xfel.cxi.postrefine.mod_pdb module": [[346, "xfel-cxi-postrefine-mod-pdb-module"]], "xfel.cxi.postrefine.mod_polar module": [[346, "xfel-cxi-postrefine-mod-polar-module"]], "xfel.cxi.postrefine.mod_results module": [[346, "xfel-cxi-postrefine-mod-results-module"]], "xfel.cxi.postrefine.mod_util module": [[346, "xfel-cxi-postrefine-mod-util-module"]], "xfel.cxi.postrefine.postrefine module": [[346, "xfel-cxi-postrefine-postrefine-module"]], "xfel.cxi.postrefine.probe module": [[346, "xfel-cxi-postrefine-probe-module"]], "xfel.cxi.postrefine.probe_best module": [[346, "xfel-cxi-postrefine-probe-best-module"]], "xfel.cxi.postrefine.read_serial_and_img module": [[346, "xfel-cxi-postrefine-read-serial-and-img-module"]], "xfel.cxi.postrefine.test_energy_model module": [[346, "xfel-cxi-postrefine-test-energy-model-module"]], "xfel.cxi.postrefine.test_rs module": [[346, "xfel-cxi-postrefine-test-rs-module"]], "xfel.metrology package": [[347, "xfel-metrology-package"]], "xfel.metrology.flatfile module": [[347, "module-xfel.metrology.flatfile"]], "xfel.metrology.mark0 module": [[347, "module-xfel.metrology.mark0"]], "xfel.metrology.mark1 module": [[347, "module-xfel.metrology.mark1"]], "xfel.metrology.mark10 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"module-xfel.metrology.quadrant"], [348, "module-xfel.metrology.legacy_scale"], [349, "module-xfel.mono_simulation"], [349, "module-xfel.mono_simulation.mono_treatment"]], "adp_aniso_restraints (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.adp_aniso_restraints"]], "cctbx.adp_restraints": [[2, "module-cctbx.adp_restraints"]], "energies_iso (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.energies_iso"]], "adp_similarity_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.adp_similarity_deviation"]], "cctbx.adp_restraints.energies": [[3, "module-cctbx.adp_restraints.energies"]], "energies (class in cctbx.adp_restraints.energies)": [[3, "cctbx.adp_restraints.energies.energies"]], "finalize_target_and_gradients() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.finalize_target_and_gradients"]], "isotropic_adp_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.isotropic_adp_deviation"]], "rigid_bond_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.rigid_bond_deviation"]], "show() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.show"]], "cctbx.adp_restraints.flags": [[4, "module-cctbx.adp_restraints.flags"]], "flags (class in cctbx.adp_restraints.flags)": [[4, "cctbx.adp_restraints.flags.flags"]], "show() (cctbx.adp_restraints.flags.flags method)": [[4, "cctbx.adp_restraints.flags.flags.show"]], "cctbx.adptbx": [[5, "module-cctbx.adptbx"]], "debye_waller_factor_u_star_curvatures() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.debye_waller_factor_u_star_curvatures"]], "debye_waller_factor_u_star_gradients() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.debye_waller_factor_u_star_gradients"]], "intersection() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.intersection"]], "random_rotate_ellipsoid() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_rotate_ellipsoid"]], "random_traceless_symmetry_constrained_b_cart() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_traceless_symmetry_constrained_b_cart"]], "random_u_cart() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.random_u_cart"]], "cctbx.array_family": [[6, "module-cctbx.array_family"]], "cctbx.array_family.flex": [[7, "module-cctbx.array_family.flex"]], "cctbx.command_line": [[8, "module-cctbx.command_line"]], "cctbx.command_line.brehm_diederichs": [[9, "module-cctbx.command_line.brehm_diederichs"]], "run() (in module cctbx.command_line.brehm_diederichs)": [[9, "cctbx.command_line.brehm_diederichs.run"]], "cctbx.command_line.cod_select_and_pickle": [[10, "module-cctbx.command_line.cod_select_and_pickle"]], "cctbx.command_line.euclidean_model_matching": [[12, "module-cctbx.command_line.euclidean_model_matching"]], "match_record (class in cctbx.command_line.euclidean_model_matching)": [[12, "cctbx.command_line.euclidean_model_matching.match_record"]], "run() (in module cctbx.command_line.euclidean_model_matching)": [[12, "cctbx.command_line.euclidean_model_matching.run"]], "cctbx.command_line.find_reticular_twin_laws": [[13, "module-cctbx.command_line.find_reticular_twin_laws"]], "run() (in module cctbx.command_line.find_reticular_twin_laws)": [[13, "cctbx.command_line.find_reticular_twin_laws.run"]], "cctbx.command_line.form_factor_query": [[14, "module-cctbx.command_line.form_factor_query"]], "run() (in module cctbx.command_line.form_factor_query)": [[14, "cctbx.command_line.form_factor_query.run"]], "getsize() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.GetSize"]], "getsize() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.GetSize"]], "cctbx.command_line.precession_view": [[15, "module-cctbx.command_line.precession_view"]], "draw_filled_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_filled_circle"]], "draw_filled_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_filled_circle"]], "draw_line() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_line"]], "draw_line() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_line"]], "draw_open_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_open_circle"]], "draw_open_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_open_circle"]], "draw_text() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_text"]], "draw_text() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_text"]], "frac2int() (in module cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.frac2int"]], "get_scale_factor() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.get_scale_factor"]], "get_scale_factor() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.get_scale_factor"]], "paint() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.paint"]], "render_pil (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_pil"]], "render_postscript (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_postscript"]], "run() (in module cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.run"]], "cctbx.command_line.space_group_info": [[16, "module-cctbx.command_line.space_group_info"]], "run() (in module cctbx.command_line.space_group_info)": [[16, "cctbx.command_line.space_group_info.run"]], "cctbx.command_line.structure_factor_timings": [[17, "module-cctbx.command_line.structure_factor_timings"]], "read_structure() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.read_structure"]], "run() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.run"]], "timings() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.timings"]], "cctbx.command_line.subgroups": [[18, "module-cctbx.command_line.subgroups"]], "run() (in module cctbx.command_line.subgroups)": [[18, "cctbx.command_line.subgroups.run"]], "cctbx.command_line.version": [[19, "module-cctbx.command_line.version"]], "run() (in module cctbx.command_line.version)": [[19, "cctbx.command_line.version.run"]], "cctbx.command_line.wavelength_units": [[20, "module-cctbx.command_line.wavelength_units"]], "raise_usage() (in module cctbx.command_line.wavelength_units)": [[20, "cctbx.command_line.wavelength_units.raise_usage"]], "run() (in module cctbx.command_line.wavelength_units)": [[20, "cctbx.command_line.wavelength_units.run"]], "cctbx.covariance": [[22, "module-cctbx.covariance"]], "as_cif_block() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_cif_block"]], "as_pdb_remark_290() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_pdb_remark_290"]], "as_py_code() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_py_code"]], "as_reference_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_reference_setting"]], "as_str() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.as_str"]], "assert_min_distance_sym_equiv() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.assert_min_distance_sym_equiv"]], "asu_mappings() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.asu_mappings"]], "asu_mappings() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.asu_mappings"]], "average_b_cart() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.average_b_cart"]], "average_u_cart() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.average_u_cart"]], "best_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.best_cell"]], "build_miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.build_miller_set"]], "calculate_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_angles"]], "calculate_dihedrals (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_dihedrals"]], "calculate_distances (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_distances"]], "cctbx.crystal": [[23, "module-cctbx.crystal"]], "cell_equivalent_p1() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.cell_equivalent_p1"]], "change_basis() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.change_basis"]], "change_basis() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_basis"]], "change_of_basis_op_to_best_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_best_cell"]], "change_of_basis_op_to_inverse_hand() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_inverse_hand"]], "change_of_basis_op_to_minimum_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_minimum_cell"]], "change_of_basis_op_to_niggli_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_niggli_cell"]], "change_of_basis_op_to_primitive_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_primitive_setting"]], "change_of_basis_op_to_reference_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.change_of_basis_op_to_reference_setting"]], "cluster_erosion() (in module cctbx.crystal)": [[23, "cctbx.crystal.cluster_erosion"]], "correct_special_position() (in module cctbx.crystal)": [[23, "cctbx.crystal.correct_special_position"]], "customized_copy() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.customized_copy"]], "dihedral_angle_def (class in cctbx.crystal)": [[23, "cctbx.crystal.dihedral_angle_def"]], "direct_space_asu() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.direct_space_asu"]], "distance_based_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.distance_based_clustering"]], "distances_info (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.distances_info"]], "expand_to_p1() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.expand_to_p1"]], "gridding() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.gridding"]], "have_sym (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.have_sym"]], "i_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.i_seq"]], "i_seqs() (cctbx.crystal.sym_pair method)": [[23, "cctbx.crystal.sym_pair.i_seqs"]], "incremental_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.incremental_clustering"]], "incremental_pairs() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.incremental_pairs"]], "inverse_hand() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.inverse_hand"]], "is_compatible_unit_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_compatible_unit_cell"]], "is_empty() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_empty"]], "is_identical_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_identical_symmetry"]], "is_incomplete() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_incomplete"]], "is_nonsense() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_nonsense"]], "is_patterson_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_patterson_symmetry"]], "is_similar_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_similar_symmetry"]], "j_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.j_seq"]], "join_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.join_symmetry"]], "miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.miller_set"]], "min_distance_sym_equiv() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.min_distance_sym_equiv"]], "minimum_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.minimum_cell"]], "next() (cctbx.crystal.calculate_dihedrals method)": [[23, "cctbx.crystal.calculate_dihedrals.next"]], "niggli_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.niggli_cell"]], "non_crystallographic_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.non_crystallographic_symmetry"]], "pair_asu_table (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.pair_asu_table"]], "pair_asu_table() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.pair_asu_table"]], "pair_generator() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.pair_generator"]], "patterson_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.patterson_symmetry"]], "primitive_setting() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.primitive_setting"]], "reflection_intensity_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.reflection_intensity_symmetry"]], "rt_mx_ji (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.rt_mx_ji"]], "select_crystal_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.select_crystal_symmetry"]], "show_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.show_angles"]], "show_dihedral_angles (class in cctbx.crystal)": [[23, "cctbx.crystal.show_dihedral_angles"]], "show_distances (class in cctbx.crystal)": [[23, "cctbx.crystal.show_distances"]], "show_summary() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.show_summary"]], "site_cluster_analysis() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_cluster_analysis"]], "site_symmetry() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry"]], "site_symmetry_table() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry_table"]], "space_group() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group"]], "space_group_info() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group_info"]], "space_group_number() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.space_group_number"]], "special_position_settings (class in cctbx.crystal)": [[23, "cctbx.crystal.special_position_settings"]], "special_position_settings() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.special_position_settings"]], "subtract_continuous_allowed_origin_shifts() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.subtract_continuous_allowed_origin_shifts"]], "sym_equiv_sites() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.sym_equiv_sites"]], "sym_pair (class in cctbx.crystal)": [[23, "cctbx.crystal.sym_pair"]], "symmetry (class in cctbx.crystal)": [[23, "cctbx.crystal.symmetry"]], "u_star_tolerance() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.u_star_tolerance"]], "unit_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.unit_cell"]], "unit_crystal_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.unit_crystal_symmetry"]], "xray_structure() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.xray_structure"]], "latticecharacter (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter"]], "metriccriteria (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria"]], "all() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.all"]], "apply_sign_correction() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.apply_sign_correction"]], "best() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best"]], "best_bravais__() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best_bravais__"]], "cctbx.crystal.burzlaff_zimmermann_dewolff": [[24, "module-cctbx.crystal.burzlaff_zimmermann_dewolff"]], "character_tests() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.character_tests"]], "counterexamples() (in module cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.counterexamples"]], "equal() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal"]], "equal_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal_penalty"]], "penalty_scores() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.penalty_scores"]], "run() (in module cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.run"]], "show_summary() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.show_summary"]], "show_summary_labelit_format() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.show_summary_labelit_format"]], "zero() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.zero"]], "zero_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.zero_penalty"]], "cctbx.crystal.close_packing": [[25, "module-cctbx.crystal.close_packing"]], "hexagonal_sampling() (in module cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.hexagonal_sampling"]], "setup_hexagonal_sampling (class in cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.setup_hexagonal_sampling"]], "cctbx.crystal.coordination_sequences": [[26, "module-cctbx.crystal.coordination_sequences"]], "find_node() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.find_node"]], "get_kriber_coseq_file() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.get_kriber_coseq_file"]], "node (class in cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.node"]], "show_terms() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.show_terms"]], "simple_and_slow() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.simple_and_slow"]], "add_buffer() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.add_buffer"]], "as_float_asu() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.as_float_asu"]], "cctbx.crystal.direct_space_asu": [[27, "module-cctbx.crystal.direct_space_asu"]], "direct_space_asu (class in cctbx.crystal.direct_space_asu)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu"]], "minimum_covering_sphere() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.minimum_covering_sphere"]], "non_crystallographic_asu_mappings() (in module cctbx.crystal.direct_space_asu)": [[27, "cctbx.crystal.direct_space_asu.non_crystallographic_asu_mappings"]], "build_simple_two_way_bond_sets() (in module cctbx.crystal.distance_based_connectivity)": [[28, "cctbx.crystal.distance_based_connectivity.build_simple_two_way_bond_sets"]], "cctbx.crystal.distance_based_connectivity": [[28, "module-cctbx.crystal.distance_based_connectivity"]], "all_cells() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.all_cells"]], "alternative_find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell"]], "cb_op() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.cb_op"]], "cctbx.crystal.find_best_cell": [[29, "module-cctbx.crystal.find_best_cell"]], "exercise() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise"]], "exercise_alternative() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise_alternative"]], "find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.find_best_cell"]], "find_it() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.find_it"]], "order_check() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.order_check"]], "return_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_best_cell"]], "return_best_xs() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_best_xs"]], "return_change_of_basis_op_to_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.return_change_of_basis_op_to_best_cell"]], "symmetry() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.symmetry"]], "cb_ops_in_niggli_setting() (cctbx.crystal.reindex.reindexing_operators method)": [[30, "cctbx.crystal.reindex.reindexing_operators.cb_ops_in_niggli_setting"]], "cctbx.crystal.reindex": [[30, "module-cctbx.crystal.reindex"]], "combined_cb_ops() (cctbx.crystal.reindex.reindexing_operators method)": [[30, "cctbx.crystal.reindex.reindexing_operators.combined_cb_ops"]], "reindexing_operators (class in cctbx.crystal.reindex)": [[30, "cctbx.crystal.reindex.reindexing_operators"]], "basis_type (class in cctbx.crystal_orientation)": [[31, "cctbx.crystal_orientation.basis_type"]], "cctbx.crystal_orientation": [[31, "module-cctbx.crystal_orientation"]], "direct (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.direct"]], "reciprocal (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.reciprocal"]], "cctbx.development": [[32, "module-cctbx.development"]], "cctbx.development.cns_density_modification": [[33, "module-cctbx.development.cns_density_modification"]], "do_dirty_work() (in module cctbx.development.cns_density_modification)": [[33, "cctbx.development.cns_density_modification.do_dirty_work"]], "run() (in module cctbx.development.cns_density_modification)": [[33, "cctbx.development.cns_density_modification.run"]], "cctbx.development.debug_utils": [[34, "module-cctbx.development.debug_utils"]], "get_test_space_group_symbols() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.get_test_space_group_symbols"]], "loop_space_groups() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.loop_space_groups"]], "parse_options_loop_space_groups() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.parse_options_loop_space_groups"]], "random_origin_shift() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.random_origin_shift"]], "cctbx.development.direct_or_fft": [[35, "module-cctbx.development.direct_or_fft"]], "dummy_miller_set() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_miller_set"]], "dummy_structure() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_structure"]], "get_times() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.get_times"]], "run() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.run"]], "run_call_back() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.run_call_back"]], "cctbx.development.electron_density_sampling": [[36, "module-cctbx.development.electron_density_sampling"]], "run() (in module cctbx.development.electron_density_sampling)": [[36, "cctbx.development.electron_density_sampling.run"]], "timings() (in module cctbx.development.electron_density_sampling)": [[36, "cctbx.development.electron_density_sampling.timings"]], "mathformmx33() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormMx33"]], "mathformvec3() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormVec3"]], "mathform_adp() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathForm_adp"]], "cctbx.development.fmt_utils": [[37, "module-cctbx.development.fmt_utils"]], "dot6fdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot"]], "dot6fdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot_list"]], "dot6g_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6g_list"]], "dot6gdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot"]], "dot6gdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot_list"]], "xtal6g() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.xtal6g"]], "xtal6g_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.xtal6g_list"]], "cctbx.development.make_cns_input": [[38, "module-cctbx.development.make_cns_input"]], "coordinates() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.coordinates"]], "exercise() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.exercise"]], "parameter_nbonds (class in cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.parameter_nbonds"]], "parameter_nonb (class in cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.parameter_nonb"]], "run() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.run"]], "run_call_back() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.run_call_back"]], "script_predict_methods_comparison() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_predict_methods_comparison"]], "script_vdw_energy() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_vdw_energy"]], "script_xray_gradients() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.script_xray_gradients"]], "topology() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.topology"]], "tst_run_requiring_cns() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.tst_run_requiring_cns"]], "write() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.write"]], "xray_anomalous() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_anomalous"]], "xray_declare() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_declare"]], "xray_generate() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_generate"]], "xray_gradients() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_gradients"]], "xray_mapresolution() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_mapresolution"]], "xray_method() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_method"]], "xray_predict() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_predict"]], "xray_reflection() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_reflection"]], "xray_structure() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_structure"]], "xray_symmetry() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_symmetry"]], "xray_unit_cell() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.xray_unit_cell"]], "cctbx.development.make_settings": [[39, "module-cctbx.development.make_settings"]], "run() (in module cctbx.development.make_settings)": [[39, "cctbx.development.make_settings.run"]], "build_scatterers() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.build_scatterers"]], "cctbx.development.random_structure": [[40, "module-cctbx.development.random_structure"]], "have_suitable_hetero_distance() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.have_suitable_hetero_distance"]], "loop() (cctbx.development.random_structure.wyckoff_pair_generator method)": [[40, "cctbx.development.random_structure.wyckoff_pair_generator.loop"]], "random_elements() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_elements"]], "random_modify_adp_and_adp_flags() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_adp_and_adp_flags"]], "random_modify_adp_and_adp_flags_2() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_adp_and_adp_flags_2"]], "random_modify_fdp() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_fdp"]], "random_modify_fp() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_fp"]], "random_modify_occupancy() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_occupancy"]], "random_modify_parameters() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_parameters"]], "random_modify_site() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_site"]], "random_modify_site() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_modify_site"]], "random_modify_u_iso() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_iso"]], "random_modify_u_star() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_star"]], "random_site() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_site"]], "random_sites() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.random_sites"]], "wyckoff_pair_generator (class in cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.wyckoff_pair_generator"]], "xray_structure (class in cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.xray_structure"]], "fix() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.FIX"]], "hklf() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.HKLF"]], "nofix() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.NOFIX"]], "sfac_disp_unit() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.SFAC_DISP_UNIT"]], "atoms() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.atoms"]], "calculate_cell_content() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.calculate_cell_content"]], "cctbx.development.run_shelx": [[41, "module-cctbx.development.run_shelx"]], "check_anisou() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_anisou"]], "check_r1() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_r1"]], "exercise() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.exercise"]], "pre_check() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.pre_check"]], "run() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run"]], "run_call_back() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run_call_back"]], "run_shelx() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.run_shelx"]], "atoms() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.atoms"]], "cctbx.development.run_shelx76": [[42, "module-cctbx.development.run_shelx76"]], "exercise() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.exercise"]], "run() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run"]], "run_call_back() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run_call_back"]], "run_shelx76() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.run_shelx76"]], "sfac_unit() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.sfac_unit"]], "write_shelx76_ls() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.write_shelx76_ls"]], "cctbx.development.space_group_option_parser": [[43, "module-cctbx.development.space_group_option_parser"]], "loop_over_space_groups() (cctbx.development.space_group_option_parser.space_group_processed_options method)": [[43, "cctbx.development.space_group_option_parser.space_group_processed_options.loop_over_space_groups"]], "process() (cctbx.development.space_group_option_parser.space_group_option_parser method)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.process"]], "processed_options_type (cctbx.development.space_group_option_parser.space_group_option_parser attribute)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.processed_options_type"]], "space_group_option_parser (class in cctbx.development.space_group_option_parser)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser"]], "space_group_processed_options (class in cctbx.development.space_group_option_parser)": [[43, "cctbx.development.space_group_option_parser.space_group_processed_options"]], "space_group_sets (cctbx.development.space_group_option_parser.space_group_option_parser attribute)": [[43, "cctbx.development.space_group_option_parser.space_group_option_parser.space_group_sets"]], "add() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.add"]], "cctbx.development.structure_factor_utils": [[44, "module-cctbx.development.structure_factor_utils"]], "check_correlation() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_correlation"]], "check_phase_restrictions() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_phase_restrictions"]], "check_regression() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_regression"]], "collector (class in cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.collector"]], "report() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.report"]], "cctbx.dmtbx": [[45, "module-cctbx.dmtbx"]], "triplet_generator() (in module cctbx.dmtbx)": [[45, "cctbx.dmtbx.triplet_generator"]], "cctbx.eltbx": [[46, "module-cctbx.eltbx"]], "atomic_number() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number"]], "atomic_number_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number_list"]], "cctbx.eltbx.attenuation_coefficient": [[47, "module-cctbx.eltbx.attenuation_coefficient"]], "chemlex() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.chemlex"]], "get_table() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.get_table"]], "nist_elements (class in cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements"]], "symbol() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.symbol"]], "symbol_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.symbol_list"]], "cctbx.eltbx.chemical_elements": [[48, "module-cctbx.eltbx.chemical_elements"]], "cctbx.eltbx.covalent_radii": [[49, "module-cctbx.eltbx.covalent_radii"]], "cctbx.eltbx.development": [[50, "module-cctbx.eltbx.development"]], "cctbx.eltbx.development.combine_fits": [[51, "module-cctbx.eltbx.development.combine_fits"]], "main() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.main"]], "pick_nicest_fit() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.pick_nicest_fit"]], "reset_max_error() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.reset_max_error"]], "cctbx.eltbx.development.create_n_gaussian_raw_cpp": [[52, "module-cctbx.eltbx.development.create_n_gaussian_raw_cpp"]], "identifier() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.identifier"]], "run() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.run"]], "write_fit_group() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_fit_group"]], "write_header() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_header"]], "write_labels() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_labels"]], "write_module_info() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_module_info"]], "write_table() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_table"]], "write_tail() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_tail"]], "cctbx.eltbx.development.e_scattering_plots": [[53, "module-cctbx.eltbx.development.e_scattering_plots"]], "run() (in module cctbx.eltbx.development.e_scattering_plots)": [[53, "cctbx.eltbx.development.e_scattering_plots.run"]], "cctbx.eltbx.development.format_gaussian_fits": [[54, "module-cctbx.eltbx.development.format_gaussian_fits"]], "cross_check() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.cross_check"]], "expected_labels() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.expected_labels"]], "labeled_fit (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.labeled_fit"]], "main() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.main"]], "read_pickled_fits (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.read_pickled_fits"]], "run() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.run"]], "cctbx.eltbx.development.hydrogen_plots": [[55, "module-cctbx.eltbx.development.hydrogen_plots"]], "fit_input (class in cctbx.eltbx.development.hydrogen_plots)": [[55, "cctbx.eltbx.development.hydrogen_plots.fit_input"]], "run() (in module cctbx.eltbx.development.hydrogen_plots)": [[55, "cctbx.eltbx.development.hydrogen_plots.run"]], "cctbx.eltbx.development.itvc_approx": [[56, "module-cctbx.eltbx.development.itvc_approx"]], "main() (in module cctbx.eltbx.development.itvc_approx)": [[56, "cctbx.eltbx.development.itvc_approx.main"]], "run() (in module cctbx.eltbx.development.itvc_approx)": [[56, "cctbx.eltbx.development.itvc_approx.run"]], "cctbx.eltbx.development.itvc_cross_validation": [[57, "module-cctbx.eltbx.development.itvc_cross_validation"]], "main() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.main"]], "run() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.run"]], "show_differences_if_any() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.show_differences_if_any"]], "cctbx.eltbx.development.itvc_fits": [[58, "module-cctbx.eltbx.development.itvc_fits"]], "main() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.main"]], "run() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.run"]], "run_and_time() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.run_and_time"]], "cctbx.eltbx.development.itvc_section61_io": [[60, "module-cctbx.eltbx.development.itvc_section61_io"]], "enter_block() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_block"]], "enter_entry() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_entry"]], "read_table6111() (in module cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.read_table6111"]], "table6111 (class in cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111"]], "table6111_entry (class in cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111_entry"]], "cctbx.eltbx.development.kissel_fits": [[61, "module-cctbx.eltbx.development.kissel_fits"]], "main() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.main"]], "run() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.run"]], "run_and_time() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.run_and_time"]], "cctbx.eltbx.development.kissel_io": [[62, "module-cctbx.eltbx.development.kissel_io"]], "itvc_sampling_selection() (cctbx.eltbx.development.kissel_io.table method)": [[62, "cctbx.eltbx.development.kissel_io.table.itvc_sampling_selection"]], "main() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.main"]], "read_table() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.read_table"]], "table (class in cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.table"]], "cctbx.eltbx.development.rez_rez_grant": [[63, "module-cctbx.eltbx.development.rez_rez_grant"]], "run() (in module cctbx.eltbx.development.rez_rez_grant)": [[63, "cctbx.eltbx.development.rez_rez_grant.run"]], "build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.build_edge_list"]], "cctbx.eltbx.distance_based_connectivity": [[64, "module-cctbx.eltbx.distance_based_connectivity"]], "tst_build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.tst_build_edge_list"]], "cctbx.eltbx.e_scattering": [[65, "module-cctbx.eltbx.e_scattering"]], "ito_vol_c_2011_table_4_3_2_2_elements() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_elements"]], "ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian"]], "cctbx.eltbx.formula": [[66, "module-cctbx.eltbx.formula"]], "formula (class in cctbx.eltbx.formula)": [[66, "cctbx.eltbx.formula.formula"]], "sorted_as_c_h_then_by_increasing_atomic_number() (cctbx.eltbx.formula.formula method)": [[66, "cctbx.eltbx.formula.formula.sorted_as_c_h_then_by_increasing_atomic_number"]], "cctbx.eltbx.fp_fdp": [[67, "module-cctbx.eltbx.fp_fdp"]], "cctbx.eltbx.gaussian_fit": [[68, "module-cctbx.eltbx.gaussian_fit"]], "decremental_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.decremental_fits"]], "fit_parameters (class in cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.fit_parameters"]], "incremental_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.incremental_fits"]], "quick() (cctbx.eltbx.gaussian_fit.fit_parameters method)": [[68, "cctbx.eltbx.gaussian_fit.fit_parameters.quick"]], "show_fit_summary() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.show_fit_summary"]], "show_literature_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.show_literature_fits"]], "write_plot() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.write_plot"]], "write_plots() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.write_plots"]], "zig_zag_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.zig_zag_fits"]], "cctbx.eltbx.henke": [[69, "module-cctbx.eltbx.henke"]], "cctbx.eltbx.icsd_radii": [[70, "module-cctbx.eltbx.icsd_radii"]], "cctbx.eltbx.neutron": [[71, "module-cctbx.eltbx.neutron"]], "cctbx.eltbx.sasaki": [[72, "module-cctbx.eltbx.sasaki"]], "cctbx.eltbx.tiny_pse": [[73, "module-cctbx.eltbx.tiny_pse"]], "cctbx.eltbx.van_der_waals_radii": [[74, "module-cctbx.eltbx.van_der_waals_radii"]], "table (cctbx.eltbx.van_der_waals_radii.vdw attribute)": [[74, "cctbx.eltbx.van_der_waals_radii.vdw.table"]], "vdw (class in cctbx.eltbx.van_der_waals_radii)": [[74, "cctbx.eltbx.van_der_waals_radii.vdw"]], "cctbx.eltbx.wavelengths": [[75, "module-cctbx.eltbx.wavelengths"]], "best_approximation() (in module cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.best_approximation"]], "cctbx.eltbx.xray_scattering": [[76, "module-cctbx.eltbx.xray_scattering"]], "fitted_gaussian (class in cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.fitted_gaussian"]], "get_element_and_charge_symbols() (in module cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.get_element_and_charge_symbols"]], "one_gaussian_agarwal_1978 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(cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2_target_d_params"]], "d2_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params"]], "d2_target_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2_target_d_params_diag"]], "d2_target_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params_diag"]], "d2_target_d_params_diag_cpp() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d2_target_d_params_diag_cpp"]], "d2f_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2f_d_params"]], "d2f_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d2f_d_params_diag"]], "d_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.d_target_d_params"]], "d_target_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.d_target_d_params"]], "df_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.df_d_params"]], "f() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.f"]], "f() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.f"]], "fs() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.fs"]], "structure_factor (class in cctbx.examples.structure_factor_derivatives_4)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor"]], "structure_factors (class in cctbx.examples.structure_factor_derivatives_4)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors"]], "cctbx.examples.sub_group_graph": [[123, "module-cctbx.examples.sub_group_graph"]], "run() (in module cctbx.examples.sub_group_graph)": [[123, "cctbx.examples.sub_group_graph.run"]], "cctbx.examples.symops_530": [[124, "module-cctbx.examples.symops_530"]], "run() (in module cctbx.examples.symops_530)": [[124, "cctbx.examples.symops_530.run"]], "cctbx.examples.trigonal_r_vs_tetragonal_i": [[125, "module-cctbx.examples.trigonal_r_vs_tetragonal_i"]], "run() (in module cctbx.examples.trigonal_r_vs_tetragonal_i)": [[125, "cctbx.examples.trigonal_r_vs_tetragonal_i.run"]], "cctbx.examples.unit_cell_minimizers": [[126, "module-cctbx.examples.unit_cell_minimizers"]], "functional() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.functional"]], "gradients() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.gradients"]], "gradients() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.gradients"]], "hessian() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.hessian"]], "hessian() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.hessian"]], "refinery (class in cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.refinery"]], "residual() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.residual"]], "run() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.run"]], "run_lbfgs_raw() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.run_lbfgs_raw"]], "run_lbfgsb() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.run_lbfgsb"]], "show_fit() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.show_fit"]], "unit_cell() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.unit_cell"]], "callback_after_step() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.callback_after_step"]], "cctbx.examples.unit_cell_refinement": [[127, "module-cctbx.examples.unit_cell_refinement"]], "compute_functional_and_gradients() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.compute_functional_and_gradients"]], "gradients() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.gradients"]], "refinery (class in cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.refinery"]], "residual() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.residual"]], "run() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.run"]], "show_fit() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.show_fit"]], "unit_cell() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, "cctbx.examples.unit_cell_refinement.refinery.unit_cell"]], "calculate_mean_intensities() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.calculate_mean_intensities"]], "cctbx.french_wilson": [[129, "module-cctbx.french_wilson"]], "f_w_binning() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.f_w_binning"]], "french_wilson_scale() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.french_wilson_scale"]], "fw_acentric() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.fw_acentric"]], "fw_centric() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.fw_centric"]], "get_bin_centers() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_bin_centers"]], "get_mean_intensity() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_mean_intensity"]], "interpolate() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.interpolate"]], "show_rejected_summary() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.show_rejected_summary"]], "cctbx.geometry": [[130, "module-cctbx.geometry"]], "add_if_not_duplicated() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.chirality_proxy_registry method)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.parallelity_proxy_registry method)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry.add_if_not_duplicated"]], "add_if_not_duplicated() (cctbx.geometry_restraints.planarity_proxy_registry method)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry.add_if_not_duplicated"]], "angle_delta_deg() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_delta_deg"]], "angle_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_proxy_registry"]], "append_custom_proxy() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.append_custom_proxy"]], "bond_simple_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry"]], "cctbx.geometry_restraints": [[131, "module-cctbx.geometry_restraints"]], "chirality_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry"]], "dihedral_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry"]], "discard_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.discard_table"]], "initialize_table() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.initialize_table"]], "initialize_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.initialize_table"]], "is_any_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_any_proxy_set"]], "is_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_proxy_set"]], "lookup_i_proxy() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.lookup_i_proxy"]], "lookup_i_proxy() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.lookup_i_proxy"]], "pair_proxies (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.pair_proxies"]], "parallelity_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry"]], "planarity_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry"]], "process() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.process"]], "process() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.process"]], "process() (cctbx.geometry_restraints.chirality_proxy_registry method)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry.process"]], "process() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.process"]], "process() (cctbx.geometry_restraints.parallelity_proxy_registry method)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry.process"]], "process() (cctbx.geometry_restraints.planarity_proxy_registry method)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry.process"]], "proxy_registry_base (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.proxy_registry_base"]], "proxy_registry_process_result (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.proxy_registry_process_result"]], "resid_to_pymol() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.resid_to_pymol"]], "sigma_as_weight() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.sigma_as_weight"]], "weight_as_sigma() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.weight_as_sigma"]], "angle_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations"]], "angle_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_weighted"]], "angle_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_z"]], "bond_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations"]], "bond_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_weighted"]], "bond_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_z"]], "cctbx.geometry_restraints.energies": [[132, "module-cctbx.geometry_restraints.energies"]], "chirality_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.chirality_deviations"]], "dihedral_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.dihedral_deviations"]], "energies (class in cctbx.geometry_restraints.energies)": [[132, "cctbx.geometry_restraints.energies.energies"]], "get_angle_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_angle_outliers"]], "get_bond_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_bond_outliers"]], "get_chirality_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_chirality_outliers"]], "get_dihedral_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_dihedral_outliers"]], "get_filtered_n_angle_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_angle_proxies"]], "get_filtered_n_bond_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_bond_proxies"]], "get_filtered_n_dihedral_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_dihedral_proxies"]], "get_filtered_n_planarity_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_planarity_proxies"]], "nonbonded_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.nonbonded_deviations"]], "nonbonded_distances() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.nonbonded_distances"]], "parallelity_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.parallelity_deviations"]], "planarity_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.planarity_deviations"]], "reference_dihedral_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.reference_dihedral_deviations"]], "show() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.show"]], "cctbx.geometry_restraints.flags": [[133, "module-cctbx.geometry_restraints.flags"]], "flags (class in cctbx.geometry_restraints.flags)": [[133, "cctbx.geometry_restraints.flags.flags"]], "show() (cctbx.geometry_restraints.flags.flags method)": [[133, "cctbx.geometry_restraints.flags.flags.show"]], "apply_shifts() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.apply_shifts"]], "cctbx.geometry_restraints.lbfgs": [[134, "module-cctbx.geometry_restraints.lbfgs"]], "compute_functional_and_gradients() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.compute_functional_and_gradients"]], "compute_target() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.compute_target"]], "empty (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.empty"]], "lbfgs (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs"]], "add_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_angles_in_place"]], "add_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_chi_torsion_restraints_in_place"]], "add_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_dihedrals_in_place"]], "add_new_bond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_bond_restraints_in_place"]], "add_new_hbond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_hbond_restraints_in_place"]], "add_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_parallelities_in_place"]], "add_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_planarities_in_place"]], "add_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_reference_coordinate_restraints_in_place"]], "adopt_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_den_manager"]], "adopt_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_coordinate_restraints_in_place"]], "adopt_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_dihedral_manager"]], "append_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.append_reference_coordinate_restraints_in_place"]], "cctbx.geometry_restraints.manager": [[135, "module-cctbx.geometry_restraints.manager"]], "construct_non_crystallographic_conserving_bonds_and_angles() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.construct_non_crystallographic_conserving_bonds_and_angles"]], "construct_tardy_tree() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.construct_tardy_tree"]], "create_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.create_den_manager"]], "discard_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.discard_symmetry"]], "energies_sites() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.energies_sites"]], "format_distances_for_error_message() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.format_distances_for_error_message"]], "get_all_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_angle_proxies"]], "get_all_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_bond_proxies"]], "get_angle_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_angle_proxies_without_user_supplied"]], "get_bond_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_bond_proxies_without_user_supplied"]], "get_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_c_beta_torsion_proxies"]], "get_chi_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_chi_torsion_proxies"]], "get_cif_link_entries() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_cif_link_entries"]], "get_covalent_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_angle_proxies"]], "get_covalent_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_bond_proxies"]], "get_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies"]], "get_dihedral_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies_without_user_supplied"]], "get_hbond_proxies_iseqs() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_hbond_proxies_iseqs"]], "get_n_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_angle_proxies"]], "get_n_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_bond_proxies"]], "get_n_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_c_beta_torsion_proxies"]], "get_n_chi_torsion_proixes() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_chi_torsion_proixes"]], "get_n_den_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_den_proxies"]], "get_n_hangle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hangle_proxies"]], "get_n_hbond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hbond_proxies"]], "get_n_parallelity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_parallelity_bp_proxies"]], "get_n_planarity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_bp_proxies"]], "get_n_planarity_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_proxies"]], "get_n_ramachandran_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_ramachandran_proxies"]], "get_n_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_coordinate_proxies"]], "get_n_reference_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_dihedral_proxies"]], "get_n_stacking_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_stacking_proxies"]], "get_parallelity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_parallelity_proxies_without_user_supplied"]], "get_planarity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_planarity_proxies_without_user_supplied"]], "get_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_reference_coordinate_proxies"]], "get_struct_conn_mmcif() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_struct_conn_mmcif"]], "get_user_supplied_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_user_supplied_restraints"]], "harmonic_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.harmonic_restraints"]], "is_bonded_atoms() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.is_bonded_atoms"]], "manager (class in cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.manager"]], "new_included_bonded_atoms() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.new_included_bonded_atoms"]], "new_including_isolated_sites() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.new_including_isolated_sites"]], "nonbonded_model_distances() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.nonbonded_model_distances"]], "pair_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.pair_proxies"]], "reduce_for_tardy() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reduce_for_tardy"]], "remove_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_angles_in_place"]], "remove_c_beta_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_c_beta_torsion_restraints_in_place"]], "remove_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chi_torsion_restraints_in_place"]], "remove_chiralities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chiralities_in_place"]], "remove_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_dihedrals_in_place"]], "remove_ncs_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ncs_dihedrals_in_place"]], "remove_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_parallelities_in_place"]], "remove_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_planarities_in_place"]], "remove_ramachandran_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ramachandran_in_place"]], "remove_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_coordinate_restraints_in_place"]], "remove_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedral_manager"]], "remove_reference_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedrals_in_place"]], "remove_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_secondary_structure_restraints"]], "remove_user_supplied_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_user_supplied_restraints_in_place"]], "replace_site_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.replace_site_symmetry"]], "reset_internals() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reset_internals"]], "rigid_clusters_due_to_dihedrals_and_planes() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.rigid_clusters_due_to_dihedrals_and_planes"]], "select() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.select"]], "set_external_energy_function() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_external_energy_function"]], "set_ramachandran_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_ramachandran_restraints"]], "set_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_secondary_structure_restraints"]], "shift_sites_cart() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.shift_sites_cart"]], "show_sorted() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.show_sorted"]], "simple_edge_list() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.simple_edge_list"]], "sites_cart_used_for_pair_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.sites_cart_used_for_pair_proxies"]], "sync_reference_dihedral_with_ncs() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.sync_reference_dihedral_with_ncs"]], "ta_harmonic_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.ta_harmonic_restraints"]], "update_atom_nonbonded_type() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_atom_nonbonded_type"]], "update_dihedral_ncs_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_dihedral_ncs_restraints"]], "update_plain_pair_sym_table() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_plain_pair_sym_table"]], "update_ramachandran_restraints_phi_psi_targets() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.update_ramachandran_restraints_phi_psi_targets"]], "write_geo_file() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.write_geo_file"]], "cctbx.macro_mol": [[137, "module-cctbx.macro_mol"]], "adjust_cosine() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.adjust_cosine"]], "amore_alpha_beta_gamma (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma"]], "amore_alpha_beta_gamma_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_as_matrix"]], "amore_alpha_beta_gamma_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_from_matrix"]], "amore_alpha_beta_gamma_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_normalize"]], "amore_kappa_l_m_n (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n"]], "amore_kappa_l_m_n_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_as_matrix"]], "amore_kappa_l_m_n_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_from_matrix"]], "amore_kappa_l_m_n_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_normalize"]], "ccp4_alpha_beta_gamma_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs"]], "ccp4_alpha_beta_gamma_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc"]], "ccp4_phi_omega_kappa_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs"]], "ccp4_phi_omega_kappa_fcalc_fobs_params_to_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs_params_to_matrix"]], "ccp4_phi_omega_kappa_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc"]], "ccp4_phi_omega_kappa_fobs_fcalc_matrix_to_params() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc_matrix_to_params"]], "cctbx.macro_mol.rotation_parameters": [[138, "module-cctbx.macro_mol.rotation_parameters"]], "cns_axis_x_axis_y_axis_z_axis_kappa (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa"]], "cns_psi_phi_kappa (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa"]], "cns_theta1_theta2_theta3 (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3"]], "cns_theta_123_as_p2m() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_123_as_p2m"]], "cns_theta_123_from_p2m() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_123_from_p2m"]], "cns_theta_plus_theta2_theta_minus (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus"]], "converter_base (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.converter_base"]], "degree_as_radians() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.degree_as_radians"]], "degree_from_radians() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.degree_from_radians"]], "det() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.det"]], "fmod_positive() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.fmod_positive"]], "generic_polar_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.generic_polar_normalize"]], "get_converter_by_docstring() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converter_by_docstring"]], "get_converters() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converters"]], "index1d() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.index1d"]], "matrix33 (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.matrix_to_params"]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.matrix_to_params"]], "normalize() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.normalize"]], "normalize() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.normalize"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.params_to_matrix"]], "params_to_matrix() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.params_to_matrix"]], "preprocess_angles() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.preprocess_angles"]], "safe_atan2() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.safe_atan2"]], "trace() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.trace"]], "all() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all"]], "all_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_site_cluster_analysis"]], "all_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_with_effective_resolution"]], "append_fixed_site() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.append_fixed_site"]], "as_cobjectzyx() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.as_CObjectZYX"]], "assert_equal() (cctbx.maptbx.positivity_constrained_density_modification method)": [[139, "cctbx.maptbx.positivity_constrained_density_modification.assert_equal"]], "assert_same_gridding() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.assert_same_gridding"]], "atom_curves (class in cctbx.maptbx)": [[139, "cctbx.maptbx.atom_curves"]], "atom_radius_as_central_peak_width() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.atom_radius_as_central_peak_width"]], "bcr_approx() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.bcr_approx"]], "boxes (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes"]], "boxes_by_dimension (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes_by_dimension"]], "cc_peak() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.cc_peak"]], "cctbx.maptbx": [[139, "module-cctbx.maptbx"]], "ccv() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.ccv"]], "change_space_group() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.change_space_group"]], "cluster_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.cluster_height_fraction"]], "cluster_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.cluster_height_fraction"]], "cluster_site_info (class in cctbx.maptbx)": [[139, "cctbx.maptbx.cluster_site_info"]], "crystal_gridding (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding"]], "crystal_gridding_tags (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding_tags"]], "crystal_symmetry() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.crystal_symmetry"]], "d99 (class in cctbx.maptbx)": [[139, "cctbx.maptbx.d99"]], "d_min() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.d_min"]], "d_min_corner() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.d_min_corner"]], "d_min_from_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.d_min_from_map"]], "discard_last() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.discard_last"]], "effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.effective_resolution"]], "effective_resolution() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.effective_resolution"]], "exact_density() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density"]], "exact_density_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density_at_r"]], "exact_gradient_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_gradient_at_r"]], "fixed_site_indices() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.fixed_site_indices"]], "form_factor() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.form_factor"]], "general_positions_only() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.general_positions_only"]], "general_positions_only() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.general_positions_only"]], "get_diff_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_diff_score_towards_periodic"]], "get_edge_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_edge_score_towards_periodic"]], "get_relative_cc() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_relative_cc"]], "get_resolution_where_significant_data_present() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_resolution_where_significant_data_present"]], "get_xray_structure() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.get_xray_structure"]], "heights() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.heights"]], "image() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image"]], "image_from_3d() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_3d"]], "image_from_miller_indices() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_miller_indices"]], "integrand() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.integrand"]], "interpolate() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.interpolate"]], "is_bounded_by_constant() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_bounded_by_constant"]], "is_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_periodic"]], "loc_res() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.loc_res"]], "local_scale (class in cctbx.maptbx)": [[139, "cctbx.maptbx.local_scale"]], "mandatory_factors() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.mandatory_factors"]], "map_accumulator() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_accumulator"]], "map_coefficients_to_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_coefficients_to_map"]], "map_peak_3d_as_2d() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_peak_3d_as_2d"]], "map_to_map_coefficients() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_to_map_coefficients"]], "map_values_along_line_connecting_two_points() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_values_along_line_connecting_two_points"]], "mask() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.mask"]], "max_clusters() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_clusters"]], "max_clusters() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_clusters"]], "max_grid_height() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_grid_height"]], "max_peaks() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_peaks"]], "max_prime() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.max_prime"]], "min_cross_distance() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.min_cross_distance"]], "min_cross_distance() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cross_distance"]], "min_cubicle_edge() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cubicle_edge"]], "min_distance_sym_equiv() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_distance_sym_equiv"]], "n_grid_points() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.n_grid_points"]], "n_real() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.n_real"]], "next() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next"]], "next_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next_site_cluster_analysis"]], "next_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.next_with_effective_resolution"]], "one_gaussian_approximation() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.one_gaussian_approximation"]], "one_gaussian_exact() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.one_gaussian_exact"]], "peak_cluster_analysis (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_cluster_analysis"]], "peak_cutoff() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.peak_cutoff"]], "peak_list (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_list"]], "peak_list() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.peak_list"]], "peak_list_indices() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.peak_list_indices"]], "peak_search() (cctbx.maptbx.crystal_gridding_tags method)": [[139, "cctbx.maptbx.crystal_gridding_tags.peak_search"]], "peak_search_level() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.peak_search_level"]], "peak_search_parameters (class in cctbx.maptbx)": [[139, "cctbx.maptbx.peak_search_parameters"]], "peak_volume_estimate() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.peak_volume_estimate"]], "positivity_constrained_density_modification (class in cctbx.maptbx)": [[139, "cctbx.maptbx.positivity_constrained_density_modification"]], "principal_axes_of_inertia() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.principal_axes_of_inertia"]], "region_density_correlation() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.region_density_correlation"]], "relative_sd_on_edges() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.relative_sd_on_edges"]], "resolution_factor() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.resolution_factor"]], "sharpen2() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sharpen2"]], "shift_origin_if_needed() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.shift_origin_if_needed"]], "show() (cctbx.maptbx.d99 method)": [[139, "cctbx.maptbx.d99.show"]], "show() (cctbx.maptbx.spherical_variance_around_point method)": [[139, "cctbx.maptbx.spherical_variance_around_point.show"]], "significant_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.significant_height_fraction"]], "significant_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.significant_height_fraction"]], "site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.site_cluster_analysis"]], "sites() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.sites"]], "smooth_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.smooth_map"]], "space_group() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.space_group"]], "space_group_info() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.space_group_info"]], "special_position_settings() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.special_position_settings"]], "spherical_variance_around_point (class in cctbx.maptbx)": [[139, "cctbx.maptbx.spherical_variance_around_point"]], "sphericity_by_heuristics() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sphericity_by_heuristics"]], "statistics (class in cctbx.maptbx)": [[139, "cctbx.maptbx.statistics"]], "symmetry_flags() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.symmetry_flags"]], "tags() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.tags"]], "tags() (cctbx.maptbx.crystal_gridding_tags method)": [[139, "cctbx.maptbx.crystal_gridding_tags.tags"]], "truncate() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.truncate"]], "unit_cell() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.unit_cell"]], "value_at_closest_grid_point() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.value_at_closest_grid_point"]], "hn() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hn"]], "hw() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hw"]], "q_x() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Q_X"]], "cctbx.maptbx.mem": [[140, "module-cctbx.maptbx.mem"]], "is_converged() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.is_converged"]], "iterations() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.iterations"]], "map_coefficients() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.map_coefficients"]], "normalize_start_map() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.normalize_start_map"]], "r_factor() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.r_factor"]], "run (class in cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.run"]], "scale() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.scale"]], "show() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.show"]], "show_map_stat() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.show_map_stat"]], "update_metrics() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.update_metrics"]], "write_mtz_file() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.write_mtz_file"]], "cctbx.maptbx.real_space_refinement_simple": [[142, "module-cctbx.maptbx.real_space_refinement_simple"]], "compute_functional_and_gradients() (cctbx.maptbx.real_space_refinement_simple.lbfgs method)": [[142, "cctbx.maptbx.real_space_refinement_simple.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization method)": [[142, "cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization.compute_functional_and_gradients"]], "lbfgs (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.lbfgs"]], "local_standard_deviations_gradients() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_gradients"]], "local_standard_deviations_target() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target"]], "local_standard_deviations_target_per_site() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target_per_site"]], "magnification_anisotropic_minimization (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization"]], "cctbx.masks": [[144, "module-cctbx.masks"]], "show() (cctbx.masks.vdw_radii method)": [[144, "cctbx.masks.vdw_radii.show"]], "vdw_radii (class in cctbx.masks)": [[144, "cctbx.masks.vdw_radii"]], "vdw_radii_from_xray_structure() (in module cctbx.masks)": [[144, "cctbx.masks.vdw_radii_from_xray_structure"]], "basis_of_mirror_plane_with_normal() (in module cctbx.math_module)": [[145, "cctbx.math_module.basis_of_mirror_plane_with_normal"]], "cctbx.math_module": [[145, "module-cctbx.math_module"]], "cctbx.merging": [[146, "module-cctbx.merging"]], "algorithm2 (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.algorithm2"]], "cctbx.merging.brehm_diederichs": [[147, "module-cctbx.merging.brehm_diederichs"]], "compute_functional_and_gradients() (cctbx.merging.brehm_diederichs.minimize method)": [[147, "cctbx.merging.brehm_diederichs.minimize.compute_functional_and_gradients"]], "compute_functional_and_gradients() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.compute_functional_and_gradients"]], "curvatures() (cctbx.merging.brehm_diederichs.minimize method)": [[147, "cctbx.merging.brehm_diederichs.minimize.curvatures"]], "functional_only() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.functional_only"]], "generate_comparison_selections() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_comparison_selections"]], "generate_reindex_sets() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_reindex_sets"]], "generate_twin_operators() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_twin_operators"]], "minimize (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize"]], "minimize_divide (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide"]], "mp_reassemble() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.mp_reassemble"]], "one_lattice_slice() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.one_lattice_slice"]], "plus_minus() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.plus_minus"]], "reassemble() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.reassemble"]], "report() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.report"]], "run() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.run"]], "run_core_algorithm() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.run_core_algorithm"]], "run_multiprocess() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.run_multiprocess"]], "test_reassembly() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.test_reassembly"]], "adopt_set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.adopt_set"]], "all_selection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.all_selection"]], "amplitude_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_normalisations"]], "amplitude_normalisations() (cctbx.miller.set method)": [[148, "cctbx.miller.set.amplitude_normalisations"]], "amplitude_quasi_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_quasi_normalisations"]], "amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitudes"]], "analyze_intensity_statistics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.analyze_intensity_statistics"]], "anomalous_completeness() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_completeness"]], "anomalous_differences() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_differences"]], "anomalous_flag() (cctbx.miller.set method)": [[148, "cctbx.miller.set.anomalous_flag"]], "anomalous_probability_plot() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_probability_plot"]], "anomalous_signal() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_signal"]], "apply_change_of_basis() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_change_of_basis"]], "apply_debye_waller_factors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_debye_waller_factors"]], "apply_scaling() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_scaling"]], "apply_shelxl_extinction_correction() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_shelxl_extinction_correction"]], "arg() (cctbx.miller.array method)": [[148, "cctbx.miller.array.arg"]], "array (class in cctbx.miller)": [[148, "cctbx.miller.array"]], "array() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.array"]], "array() (cctbx.miller.set method)": [[148, "cctbx.miller.set.array"]], "array_info (class in cctbx.miller)": [[148, "cctbx.miller.array_info"]], "as_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_amplitude_array"]], "as_anomalous_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_anomalous_array"]], "as_anomalous_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.as_anomalous_set"]], "as_cif_block() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_cif_block"]], "as_cif_simple() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_cif_simple"]], "as_double() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_double"]], "as_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_intensity_array"]], "as_map_manager() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_map_manager"]], "as_mtz_dataset() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_mtz_dataset"]], "as_non_anomalous_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_non_anomalous_array"]], "as_non_anomalous_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.as_non_anomalous_set"]], "as_phases_phs() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_phases_phs"]], "as_xray_observations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.as_xray_observations"]], "at_first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.at_first_index"]], "auto_anomalous() (cctbx.miller.set method)": [[148, "cctbx.miller.set.auto_anomalous"]], "average_bijvoet_mates() (cctbx.miller.array method)": [[148, "cctbx.miller.array.average_bijvoet_mates"]], "average_neighbors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.average_neighbors"]], "bijvoet_ratios() (cctbx.miller.array method)": [[148, "cctbx.miller.array.bijvoet_ratios"]], "binner (class in cctbx.miller)": [[148, "cctbx.miller.binner"]], "binner() (cctbx.miller.set method)": 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"cctbx.miller.array.convert_to_non_anomalous_if_ratio_pairs_lone_less_than"]], "copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.copy"]], "copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.copy"]], "correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.correlation"]], "count_and_fraction_in_bins() (cctbx.miller.array method)": [[148, "cctbx.miller.array.count_and_fraction_in_bins"]], "crystal_gridding() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_gridding"]], "crystal_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_symmetry"]], "crystal_symmetry_is_compatible_with_symmetry_from_file (class in cctbx.miller)": [[148, "cctbx.miller.crystal_symmetry_is_compatible_with_symmetry_from_file"]], "crystal_symmetry_is_compatible_with_symmetry_from_file() (cctbx.miller.array method)": [[148, "cctbx.miller.array.crystal_symmetry_is_compatible_with_symmetry_from_file"]], "customized_copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.customized_copy"]], "customized_copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.customized_copy"]], "d_max_min() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_max_min"]], "d_min() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_min"]], "d_min_along_a_b_c_star() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_min_along_a_b_c_star"]], "d_min_from_fsc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.d_min_from_fsc"]], "d_spacings() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_spacings"]], "d_star_cubed() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_star_cubed"]], "d_star_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.d_star_sq"]], "data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.data"]], "data_at_first_index() (cctbx.miller.array method)": [[148, "cctbx.miller.array.data_at_first_index"]], "debye_waller_factors() (cctbx.miller.set method)": [[148, "cctbx.miller.set.debye_waller_factors"]], "deep_copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.deep_copy"]], "deep_copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.deep_copy"]], "delete_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.delete_index"]], "delete_indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.delete_indices"]], "detwin_data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.detwin_data"]], "direct_summation_at_point() (cctbx.miller.array method)": [[148, "cctbx.miller.array.direct_summation_at_point"]], "disagreeable_reflections() (cctbx.miller.array method)": [[148, "cctbx.miller.array.disagreeable_reflections"]], "discard_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.discard_sigmas"]], "double_step_filtration() (cctbx.miller.array method)": [[148, "cctbx.miller.array.double_step_filtration"]], "eliminate_sys_absent() (cctbx.miller.array method)": [[148, "cctbx.miller.array.eliminate_sys_absent"]], "ellipsoidal_resolutions_and_indices_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_resolutions_and_indices_by_sigma"]], "ellipsoidal_truncation_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_truncation_by_sigma"]], "enforce_positive_amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_amplitudes"]], "enforce_positive_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_sigmas"]], "epsilons() (cctbx.miller.set method)": [[148, "cctbx.miller.set.epsilons"]], "expand_to_p1() (cctbx.miller.array method)": [[148, "cctbx.miller.array.expand_to_p1"]], "expand_to_p1() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1"]], "expand_to_p1_iselection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1_iselection"]], "export_as_cns_hkl() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_cns_hkl"]], "export_as_scalepack_unmerged() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_scalepack_unmerged"]], "export_as_shelx_hklf() (cctbx.miller.array method)": [[148, "cctbx.miller.array.export_as_shelx_hklf"]], "f_as_f_sq() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_as_f_sq"]], "f_obs_f_calc_fan_outlier_selection() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_obs_f_calc_fan_outlier_selection"]], "f_obs_minus_f_calc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_obs_minus_f_calc"]], "f_obs_minus_xray_structure_f_calc() (cctbx.miller.set method)": [[148, "cctbx.miller.set.f_obs_minus_xray_structure_f_calc"]], "f_sq_as_f() (cctbx.miller.array method)": [[148, "cctbx.miller.array.f_sq_as_f"]], "fft_map (class in cctbx.miller)": [[148, "cctbx.miller.fft_map"]], "fft_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fft_map"]], "first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.first_index"]], "french_wilson() (cctbx.miller.array method)": [[148, "cctbx.miller.array.french_wilson"]], "from_cif() (cctbx.miller.array class method)": [[148, "cctbx.miller.array.from_cif"]], "fsc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fsc"]], "g_function() (cctbx.miller.array method)": [[148, "cctbx.miller.array.g_function"]], "generate_bijvoet_mates() (cctbx.miller.array method)": [[148, "cctbx.miller.array.generate_bijvoet_mates"]], "generate_bivoet_mates() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_bivoet_mates"]], "generate_r_free_flags() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags"]], "generate_r_free_flags_basic() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_basic"]], "generate_r_free_flags_on_lattice_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_on_lattice_symmetry"]], "half_dataset_anomalous_correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.half_dataset_anomalous_correlation"]], "has_twinning() (cctbx.miller.array method)": [[148, "cctbx.miller.array.has_twinning"]], "hemisphere_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemisphere_acentrics"]], "hemispheres_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemispheres_acentrics"]], "hoppe_gassmann_modification() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hoppe_gassmann_modification"]], "i_over_sig_i() (cctbx.miller.array method)": [[148, "cctbx.miller.array.i_over_sig_i"]], "index_span() (cctbx.miller.set method)": [[148, "cctbx.miller.set.index_span"]], "indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.indices"]], "info() (cctbx.miller.array method)": [[148, "cctbx.miller.array.info"]], "intensities() (cctbx.miller.array method)": [[148, "cctbx.miller.array.intensities"]], "intensity_quasi_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.intensity_quasi_normalisations"]], "is_bool_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_bool_array"]], "is_complex_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_complex_array"]], "is_hendrickson_lattman_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_hendrickson_lattman_array"]], "is_in_asu() (cctbx.miller.set method)": [[148, "cctbx.miller.set.is_in_asu"]], "is_integer_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_integer_array"]], "is_real_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_real_array"]], "is_string_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_string_array"]], "is_unique_set_under_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.is_unique_set_under_symmetry"]], "is_unmerged_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_unmerged_intensity_array"]], "is_xray_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_amplitude_array"]], "is_xray_data_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_data_array"]], "is_xray_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_intensity_array"]], "is_xray_reconstructed_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_reconstructed_amplitude_array"]], "local_overlap_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_overlap_map"]], "local_standard_deviation_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_standard_deviation_map"]], "log_binning() (cctbx.miller.set method)": [[148, "cctbx.miller.set.log_binning"]], "lone_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_set"]], "lone_sets() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_sets"]], "make_up_hl_coeffs() (cctbx.miller.array method)": [[148, "cctbx.miller.array.make_up_hl_coeffs"]], "map_correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.map_correlation"]], "map_to_asu() (cctbx.miller.array method)": [[148, "cctbx.miller.array.map_to_asu"]], "map_to_asu() (cctbx.miller.set method)": [[148, "cctbx.miller.set.map_to_asu"]], "match_bijvoet_mates() (cctbx.miller.set method)": [[148, "cctbx.miller.set.match_bijvoet_mates"]], "match_indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.match_indices"]], "matching_set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.matching_set"]], "mean() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean"]], "mean_of_intensity_divided_by_epsilon() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_of_intensity_divided_by_epsilon"]], "mean_of_squared_sigma_divided_by_epsilon() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_of_squared_sigma_divided_by_epsilon"]], "mean_phase_error() (cctbx.miller.array method)": [[148, 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"cctbx.miller.set.minimum_wavelength_based_on_d_min"]], "multiplicities() (cctbx.miller.set method)": [[148, "cctbx.miller.set.multiplicities"]], "multiscale() (cctbx.miller.array method)": [[148, "cctbx.miller.array.multiscale"]], "n_bijvoet_pairs() (cctbx.miller.set method)": [[148, "cctbx.miller.set.n_bijvoet_pairs"]], "norm() (cctbx.miller.array method)": [[148, "cctbx.miller.array.norm"]], "normalised_amplitudes (class in cctbx.miller)": [[148, "cctbx.miller.normalised_amplitudes"]], "normalised_amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.normalised_amplitudes"]], "normalize() (cctbx.miller.array method)": [[148, "cctbx.miller.array.normalize"]], "observation_type() (cctbx.miller.array method)": [[148, "cctbx.miller.array.observation_type"]], "patterson_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.patterson_map"]], "patterson_symmetry() (cctbx.miller.array method)": [[148, "cctbx.miller.array.patterson_symmetry"]], "patterson_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.patterson_symmetry"]], "permute_d_range() (cctbx.miller.array method)": [[148, "cctbx.miller.array.permute_d_range"]], "phase_entropy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_entropy"]], "phase_integrals() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_integrals"]], "phase_transfer() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_transfer"]], "phased_translation_function_coeff() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phased_translation_function_coeff"]], "phases() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phases"]], "quasi_normalize_structure_factors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.quasi_normalize_structure_factors"]], "quasi_normalized_as_normalized() (cctbx.miller.array method)": [[148, "cctbx.miller.array.quasi_normalized_as_normalized"]], "r1_factor() (cctbx.miller.array method)": [[148, "cctbx.miller.array.r1_factor"]], "r_anom() (cctbx.miller.array method)": [[148, "cctbx.miller.array.r_anom"]], "r_free_flags_accumulation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.r_free_flags_accumulation"]], "r_linear() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.r_linear"]], "r_meas() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.r_meas"]], "r_merge() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.r_merge"]], "r_pim() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.r_pim"]], "r_square() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.r_square"]], "random_phases_compatible_with_phase_restrictions() (cctbx.miller.set method)": [[148, "cctbx.miller.set.random_phases_compatible_with_phase_restrictions"]], "randomize_amplitude_and_phase() (cctbx.miller.array method)": [[148, "cctbx.miller.array.randomize_amplitude_and_phase"]], "randomize_phases() (cctbx.miller.array method)": [[148, "cctbx.miller.array.randomize_phases"]], "redundancies() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.redundancies"]], "reflection_intensity_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.reflection_intensity_symmetry"]], "regularize() (cctbx.miller.array method)": [[148, "cctbx.miller.array.regularize"]], "remove_cone() (cctbx.miller.array method)": [[148, "cctbx.miller.array.remove_cone"]], "remove_patterson_origin_peak() (cctbx.miller.array method)": [[148, "cctbx.miller.array.remove_patterson_origin_peak"]], "remove_systematic_absences() (cctbx.miller.set method)": [[148, "cctbx.miller.set.remove_systematic_absences"]], "resolution_filter() (cctbx.miller.set method)": [[148, "cctbx.miller.set.resolution_filter"]], "resolution_filter_selection() (cctbx.miller.set method)": [[148, 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method)": [[148, "cctbx.miller.set.select_acentric"]], "select_centric() (cctbx.miller.set method)": [[148, "cctbx.miller.set.select_centric"]], "select_indices() (cctbx.miller.array method)": [[148, "cctbx.miller.array.select_indices"]], "select_sys_absent() (cctbx.miller.array method)": [[148, "cctbx.miller.array.select_sys_absent"]], "set (class in cctbx.miller)": [[148, "cctbx.miller.set"]], "set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set"]], "set_info() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_info"]], "set_observation_type() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type"]], "set_observation_type_xray_amplitude() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type_xray_amplitude"]], "set_observation_type_xray_intensity() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type_xray_intensity"]], "set_sigmas() (cctbx.miller.array method)": [[148, 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"sigmas_are_sensible() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigmas_are_sensible"]], "sin_theta_over_lambda_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sin_theta_over_lambda_sq"]], "size() (cctbx.miller.array method)": [[148, "cctbx.miller.array.size"]], "size() (cctbx.miller.set method)": [[148, "cctbx.miller.set.size"]], "slice() (cctbx.miller.set method)": [[148, "cctbx.miller.set.slice"]], "sort() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sort"]], "sort_permutation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sort_permutation"]], "sort_permutation() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sort_permutation"]], "statistical_mean() (cctbx.miller.array method)": [[148, "cctbx.miller.array.statistical_mean"]], "structure_factors_from_asu_map() (cctbx.miller.set method)": [[148, "cctbx.miller.set.structure_factors_from_asu_map"]], "structure_factors_from_map() (cctbx.miller.set method)": [[148, "cctbx.miller.set.structure_factors_from_map"]], "structure_factors_from_scatterers() (cctbx.miller.set method)": [[148, "cctbx.miller.set.structure_factors_from_scatterers"]], "sum() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sum"]], "sum_sq() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sum_sq"]], "symmetry_agreement_factor() (cctbx.miller.array method)": [[148, "cctbx.miller.array.symmetry_agreement_factor"]], "sys_absent_flags() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sys_absent_flags"]], "translational_shift() (cctbx.miller.array method)": [[148, "cctbx.miller.array.translational_shift"]], "twin_data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.twin_data"]], "two_theta() (cctbx.miller.set method)": [[148, "cctbx.miller.set.two_theta"]], "unique_under_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.unique_under_symmetry"]], "unique_under_symmetry_selection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.unique_under_symmetry_selection"]], "use_binner_of() (cctbx.miller.set method)": [[148, "cctbx.miller.set.use_binner_of"]], "use_binning() (cctbx.miller.set method)": [[148, "cctbx.miller.set.use_binning"]], "use_binning_of() (cctbx.miller.set method)": [[148, "cctbx.miller.set.use_binning_of"]], "value_at_index() (cctbx.miller.array method)": [[148, "cctbx.miller.array.value_at_index"]], "wilson_plot() (cctbx.miller.array method)": [[148, "cctbx.miller.array.wilson_plot"]], "wilson_ratio() (cctbx.miller.array method)": [[148, "cctbx.miller.array.wilson_ratio"]], "write_mtz() (cctbx.miller.array method)": [[148, "cctbx.miller.array.write_mtz"]], "getsize() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.GetSize"]], "cctbx.miller.display": [[149, "module-cctbx.miller.display"]], "clear_labels() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.clear_labels"]], "draw_filled_circle() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_filled_circle"]], "draw_line() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_line"]], "draw_open_circle() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_open_circle"]], "draw_text() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_text"]], "generate_missing_reflections() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_missing_reflections"]], "generate_systematic_absences() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_systematic_absences"]], "generate_systematic_absences() (in module cctbx.miller.display)": [[149, "cctbx.miller.display.generate_systematic_absences"]], "generate_view_data() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_view_data"]], "get_center_and_radius() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.get_center_and_radius"]], "get_reflection_info() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.get_reflection_info"]], "get_resolution_at_point() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.get_resolution_at_point"]], "get_scale_factor() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.get_scale_factor"]], "process_input_array() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.process_input_array"]], "render() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.render"]], "render_2d (class in cctbx.miller.display)": [[149, "cctbx.miller.display.render_2d"]], "scene (class in cctbx.miller.display)": [[149, "cctbx.miller.display.scene"]], "settings() (in module cctbx.miller.display)": [[149, "cctbx.miller.display.settings"]], "setup_colors() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.setup_colors"]], "assistant (class in cctbx.miller.reindexing)": [[150, "cctbx.miller.reindexing.assistant"]], "cb_ops (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.cb_ops"]], "cctbx.miller.reindexing": [[150, "module-cctbx.miller.reindexing"]], "i_inv_j_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_inv_j_multiplication_table"]], "i_j_inv_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_j_inv_multiplication_table"]], "i_j_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_j_multiplication_table"]], "intensity_group (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.intensity_group"]], "inv_perms (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.inv_perms"]], "lattice_group (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.lattice_group"]], "miller_indices (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.miller_indices"]], "perms (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.perms"]], "show_summary() (cctbx.miller.reindexing.assistant method)": [[150, "cctbx.miller.reindexing.assistant.show_summary"]], "cctbx.multipolar": [[151, "module-cctbx.multipolar"]], "add_scatterer() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterer"]], "add_scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterers"]], "apply_symmetry() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.apply_symmetry"]], "apply_symmetry() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.apply_symmetry"]], "cctbx.neutron": [[152, "module-cctbx.neutron"]], "multiplicity() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.multiplicity"]], "scatterer (class in cctbx.neutron)": [[152, "cctbx.neutron.scatterer"]], "scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.scatterers"]], "show_scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.show_scatterers"]], "show_summary() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.show_summary"]], "special_position_indices() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.special_position_indices"]], "structure (class in cctbx.neutron)": [[152, "cctbx.neutron.structure"]], "structure_factors() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.structure_factors"]], "update_weight() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.update_weight"]], "weight() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.weight"]], "cctbx.omz": [[153, "module-cctbx.omz"]], "b_update() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.b_update"]], "cctbx.omz.bfgs": [[154, "module-cctbx.omz.bfgs"]], "get() (cctbx.omz.bfgs.memory_element method)": [[154, "cctbx.omz.bfgs.memory_element.get"]], "h0_scaling() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.h0_scaling"]], "h_update() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.h_update"]], "hg_two_loop_recursion() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.hg_two_loop_recursion"]], "memory_element (class in cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.memory_element"]], "rho (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.rho"]], "s (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.s"]], "y (cctbx.omz.bfgs.memory_element attribute)": [[154, "cctbx.omz.bfgs.memory_element.y"]], "c_obs (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.c_obs"]], "cctbx.omz.cif_refine": [[155, "module-cctbx.omz.cif_refine"]], "edge_list (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.edge_list"]], "extract_from_cif_files (class in cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files"]], "init_slots_with_none() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.init_slots_with_none"]], "non_hydrogen_iselection (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.non_hydrogen_iselection"]], "non_hydrogen_selection (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.non_hydrogen_selection"]], "process() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.process"]], "process_geom_bond() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.process_geom_bond"]], "report_fraction_of_negative_observations_if_any() (in module cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.report_fraction_of_negative_observations_if_any"]], "run() (in module cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.run"]], "xray_structure (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.xray_structure"]], "cctbx.omz.cod_refine": [[156, "module-cctbx.omz.cod_refine"]], "get_master_phil() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.get_master_phil"]], "process() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.process"]], "process_continue() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.process_continue"]], "remove_tmp_files() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.remove_tmp_files"]], "run() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run"]], "run_shelx76() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_shelx76"]], "run_shelxl() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_shelxl"]], "run_smtbx_ls() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.run_smtbx_ls"]], "shelxl_weights() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.shelxl_weights"]], "shelxl_weights_a_b() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.shelxl_weights_a_b"]], "show_cc_r1() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.show_cc_r1"]], "c_obs (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.c_obs"]], "cctbx.omz.cod_select_and_pickle": [[157, "module-cctbx.omz.cod_select_and_pickle"]], "cod_data (class in cctbx.omz.cod_select_and_pickle)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data"]], "cod_id (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.cod_id"]], "edge_list (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.edge_list"]], "f_obs_and_f_calc_agree_well() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.f_obs_and_f_calc_agree_well"]], "have_bad_sigmas() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_bad_sigmas"]], "have_close_contacts() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_close_contacts"]], "have_redundant_data() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_redundant_data"]], "have_shelxl_compatible_scattering_types() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_shelxl_compatible_scattering_types"]], "have_sys_absent() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_sys_absent"]], "have_zero_occupancies() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_zero_occupancies"]], "is_useful() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.is_useful"]], "non_hydrogen_iselection (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.non_hydrogen_iselection"]], "non_hydrogen_selection (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.non_hydrogen_selection"]], "quick_info() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.quick_info"]], "run() (in module cctbx.omz.cod_select_and_pickle)": [[157, "cctbx.omz.cod_select_and_pickle.run"]], "xray_structure (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.xray_structure"]], "approx_curvs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.approx_curvs"]], "approx_quads (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.approx_quads"]], "build_bfgs_memory() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.build_bfgs_memory"]], "calc_shelxl_wght_ls() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.calc_shelxl_wght_ls"]], "calc_weights_if_needed() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.calc_weights_if_needed"]], "callback_after_step() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.callback_after_step"]], "cctbx.omz.dev": [[158, "module-cctbx.omz.dev"]], "check_strong_wolfe() (cctbx.omz.dev.xfgc_info method)": [[158, "cctbx.omz.dev.xfgc_info.check_strong_wolfe"]], "classic_lbfgs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.classic_lbfgs"]], "compute_functional_and_gradients() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_functional_and_gradients"]], "compute_step() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step"]], "compute_step_just_grads() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_just_grads"]], "compute_step_using_curvs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_using_curvs"]], "curv_est_factor (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.curv_est_factor"]], "curv_est_shift() (cctbx.omz.dev.shift_limit_pair method)": [[158, "cctbx.omz.dev.shift_limit_pair.curv_est_shift"]], "curvs (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.curvs"]], "d_min (cctbx.omz.dev.dynamic_shift_limit_u_iso attribute)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso.d_min"]], "delta_estimation_minus_cos() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.delta_estimation_minus_cos"]], "developmental_algorithms() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.developmental_algorithms"]], "dynamic_shift_limit_site (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site"]], "dynamic_shift_limit_u_iso (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso"]], "format_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.format_rms_info"]], "funcl (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.funcl"]], "get() (cctbx.omz.dev.shift_limit_pair method)": [[158, "cctbx.omz.dev.shift_limit_pair.get"]], "get_active_infos() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_active_infos"]], "get_f_calc() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_calc"]], "get_f_cbs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_cbs"]], "get_master_phil() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.get_master_phil"]], "get_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_rms_info"]], "grads (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.grads"]], "is_iterate (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.is_iterate"]], "lbfgs_emulation() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.lbfgs_emulation"]], "line_search() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.line_search"]], "neg (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.neg"]], "pack_variables() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.pack_variables"]], "pair() (cctbx.omz.dev.dynamic_shift_limit_site method)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site.pair"]], "pair() (cctbx.omz.dev.dynamic_shift_limit_u_iso method)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso.pair"]], "plot_samples() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples"]], "plot_samples_ix() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples_ix"]], "pos (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.pos"]], "r1_factor() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.r1_factor"]], "refinement (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.refinement"]], "run_refinement() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.run_refinement"]], "setup_bulk_solvent_correction() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.setup_bulk_solvent_correction"]], "shift_limit_pair (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.shift_limit_pair"]], "show_dests() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.show_dests"]], "show_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.show_rms_info"]], "sign0() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.sign0"]], "update_dests_using_bfgs_formula() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.update_dests_using_bfgs_formula"]], "update_fgc() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.update_fgc"]], "width (cctbx.omz.dev.dynamic_shift_limit_site attribute)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site.width"]], "x (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.x"]], "xfgc_info (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.xfgc_info"]], "cctbx.omz.eval_iso_vs_refined": [[159, "module-cctbx.omz.eval_iso_vs_refined"]], "eval_logs() (in module cctbx.omz.eval_iso_vs_refined)": [[159, "cctbx.omz.eval_iso_vs_refined.eval_logs"]], "run() (in module cctbx.omz.eval_iso_vs_refined)": [[159, "cctbx.omz.eval_iso_vs_refined.run"]], "cctbx.omz.pdb_dev": [[160, "module-cctbx.omz.pdb_dev"]], "process() (in module cctbx.omz.pdb_dev)": [[160, "cctbx.omz.pdb_dev.process"]], "run() (in module cctbx.omz.pdb_dev)": [[160, "cctbx.omz.pdb_dev.run"]], "cctbx.omz.tardy_adaptor": [[161, "module-cctbx.omz.tardy_adaptor"]], "e_pot() (cctbx.omz.tardy_adaptor.potential_object method)": [[161, "cctbx.omz.tardy_adaptor.potential_object.e_pot"]], "potential_object (class in cctbx.omz.tardy_adaptor)": [[161, "cctbx.omz.tardy_adaptor.potential_object"]], "sample_e_pot() (in module cctbx.omz.tardy_adaptor)": [[161, "cctbx.omz.tardy_adaptor.sample_e_pot"]], "adjust_fraction() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.adjust_fraction"]], "assign_r_free_flags_by_shells() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_r_free_flags_by_shells"]], "assign_random_r_free_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_random_r_free_flags"]], "cctbx.r_free_utils": [[162, "module-cctbx.r_free_utils"]], "export_r_free_flags_for_ccp4() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.export_r_free_flags_for_ccp4"]], "export_r_free_flags_for_shelx() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.export_r_free_flags_for_shelx"]], "extend_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.extend_flags"]], "get_r_free_as_bool() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_as_bool"]], "get_r_free_stats() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_stats"]], "looks_like_ccp4_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.looks_like_ccp4_flags"]], "remediate_mismatches() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.remediate_mismatches"]], "cctbx.run_examples": [[163, "module-cctbx.run_examples"]], "run() (in module cctbx.run_examples)": [[163, "cctbx.run_examples.run"]], "cctbx.run_tests": [[164, "module-cctbx.run_tests"]], "run() (in module cctbx.run_tests)": [[164, "cctbx.run_tests.run"]], "any_compatible_crystal_symmetry() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_crystal_symmetry"]], "any_compatible_unit_cell() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_unit_cell"]], "any_generator_set (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.any_generator_set"]], "any_generator_set() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_generator_set"]], "as_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.as_reference_setting"]], "brick() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.brick"]], "cctbx.sgtbx": [[165, "module-cctbx.sgtbx"]], "change_basis() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_basis"]], "change_hand() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_hand"]], "change_of_basis_op_to() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to"]], "change_of_basis_op_to_other_hand() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_other_hand"]], "change_of_basis_op_to_primitive_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_primitive_setting"]], "change_of_basis_op_to_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.change_of_basis_op_to_reference_setting"]], "cif_symmetry_code() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.cif_symmetry_code"]], "compare_cb_op_as_hkl() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.compare_cb_op_as_hkl"]], "constant (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.constant"]], "direct_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.direct_space_asu"]], "empty (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.empty"]], "get() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.get"]], "group() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.group"]], "i_vars (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.i_vars"]], "is_allowed_origin_shift() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_allowed_origin_shift"]], "is_equivalent() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.is_equivalent"]], "is_identity() (cctbx.sgtbx.special_op_simplified_term method)": [[165, "cctbx.sgtbx.special_op_simplified_term.is_identity"]], "is_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_reference_setting"]], "le_page_1982_delta_details (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.le_page_1982_delta_details"]], "multipliers (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.multipliers"]], "number_of_continuous_allowed_origin_shifts() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.number_of_continuous_allowed_origin_shifts"]], "primitive_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.primitive_setting"]], "reciprocal_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reciprocal_space_asu"]], "reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reference_setting"]], "reference_space_group_infos() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.reference_space_group_infos"]], "reflection_intensity_equivalent_groups() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reflection_intensity_equivalent_groups"]], "registry (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.registry"]], "shelx_fvar_encoding() (cctbx.sgtbx.special_op_simplified method)": [[165, "cctbx.sgtbx.special_op_simplified.shelx_fvar_encoding"]], "show_summary() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.show_summary"]], "site_symmetry_ops_j (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.site_symmetry_ops_j"]], "space_group_info (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.space_group_info"]], "special_op_simplified (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplified"]], "special_op_simplified_term (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplified_term"]], "special_op_simplifier() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.special_op_simplifier"]], "structure_seminvariants() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.structure_seminvariants"]], "subtract_continuous_allowed_origin_shifts() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.subtract_continuous_allowed_origin_shifts"]], "symbol_and_number() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.symbol_and_number"]], "symmetry_equivalent_pair_interactions (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions"]], "terms (cctbx.sgtbx.special_op_simplified attribute)": [[165, "cctbx.sgtbx.special_op_simplified.terms"]], "type() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.type"]], "vec3_rat_from_str() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.vec3_rat_from_str"]], "wyckoff_table() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.wyckoff_table"]], "bravais_lattice (class in cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice"]], "cctbx.sgtbx.bravais_types": [[166, "module-cctbx.sgtbx.bravais_types"]], "crystal_family_symbols (cctbx.sgtbx.bravais_types.bravais_lattice attribute)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice.crystal_family_symbols"]], "exercise() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.exercise"]], "tst_bravais_types() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.tst_bravais_types"]], "best_partition_representatives() (cctbx.sgtbx.cosets.left_decomposition_point_groups_only method)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only.best_partition_representatives"]], "cctbx.sgtbx.cosets": [[167, "module-cctbx.sgtbx.cosets"]], "clear_up_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.clear_up_cosets"]], "construct_nice_cb_op() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.construct_nice_cb_op"]], "double_cosets (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_cosets"]], "double_unique() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_unique"]], "have_duplicates() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.have_duplicates"]], "is_in_coset() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_coset"]], "is_in_list_of_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_list_of_cosets"]], "is_subgroup() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.is_subgroup"]], "left_decomposition (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition"]], "left_decomposition_point_groups_only (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only"]], "partition_t (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.partition_t"]], "run() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.run"]], "show() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.show"]], "show() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.show"]], "sort_cosets() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.sort_cosets"]], "test_double_coset_decomposition() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.test_double_coset_decomposition"]], "test_lattice_translation_aware_left_decomposition() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.test_lattice_translation_aware_left_decomposition"]], "add_buffer() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_buffer"]], "add_plane() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_plane"]], "add_planes() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_planes"]], "box_max() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_max"]], "box_min() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_min"]], "cctbx.sgtbx.direct_space_asu": [[168, "module-cctbx.sgtbx.direct_space_asu"]], "change_basis() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.change_basis"]], "define_metric() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.define_metric"]], "direct_space_asu (class in cctbx.sgtbx.direct_space_asu)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.extract_all_cuts"]], "in_which_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.in_which_cuts"]], "is_inside() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.is_inside"]], "shape_only() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_only"]], "shape_vertices() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_vertices"]], "show_comprehensive_summary() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.show_comprehensive_summary"]], "show_summary() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.show_summary"]], "analyze_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.analyze_redundancies"]], "cctbx.sgtbx.direct_space_asu.check_redundancies": [[169, "module-cctbx.sgtbx.direct_space_asu.check_redundancies"]], "check_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_asu"]], "check_compatibility_with_sampling_grid() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_compatibility_with_sampling_grid"]], "check_multiplicities() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_multiplicities"]], "color_server (class in cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.color_server"]], "colored_grid_point (class in cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.colored_grid_point"]], "compare_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.compare_redundancies"]], "grid_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.grid_asu"]], "iround() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.iround"]], "next() (cctbx.sgtbx.direct_space_asu.check_redundancies.color_server method)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.color_server.next"]], "recolor_grid_points() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.recolor_grid_points"]], "rt_mx_analysis() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_mx_analysis"]], "rt_plus_unit_shifts() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_plus_unit_shifts"]], "rt_times_grid_point() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.rt_times_grid_point"]], "sample_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.sample_asu"]], "slice() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.slice"]], "sort_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.sort_redundancies"]], "str_ev() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.str_ev"]], "test_all() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.test_all"]], "u_index_as_r_index() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.u_index_as_r_index"]], "as_float_cut_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.as_float_cut_plane"]], "as_xyz() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.as_xyz"]], "as_xyz() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.as_xyz"]], "base_symbol() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.base_symbol"]], "c (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.c"]], "cctbx.sgtbx.direct_space_asu.cut_plane": [[170, "module-cctbx.sgtbx.direct_space_asu.cut_plane"]], "change_basis() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.change_basis"]], "change_basis() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.change_basis"]], "cut (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut"]], "cut_expr (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.cut_expr"]], "cut_expr_ops (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expr_ops"]], "cut_expression (class in cctbx.sgtbx.direct_space_asu.cut_plane)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression"]], "evaluate() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.evaluate"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.extract_all_cuts"]], "extract_all_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.extract_all_cuts"]], "get_point_in_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.get_point_in_plane"]], "has_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.has_cuts"]], "inclusive (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.inclusive"]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.is_inside"]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.is_inside"]], "lcm_of_denominators() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.lcm_of_denominators"]], "lhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.lhs"]], "n (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.n"]], "one() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.one"]], "op (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.op"]], "rhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.rhs"]], "strip() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.strip"]], "add() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.add"]], "all_cut_points() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.all_cut_points"]], "all_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.all_points"]], "asu (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.asu"]], "asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.asu_polygons"]], "cctbx.sgtbx.direct_space_asu.facet_analysis": [[171, "module-cctbx.sgtbx.direct_space_asu.facet_analysis"]], "collect_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.collect_cuts"]], "consolidated_edges_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points"]], "cut_point_positions() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.cut_point_positions"]], "cut_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.cut_points"]], "depth1_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.depth1_cuts"]], "edge_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.edge_inclusive_flag"]], "edge_position() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_position"]], "edge_segment (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment"]], "edge_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points"]], "eliminate_outside_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.eliminate_outside_vertices"]], "end_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.end_points"]], "extract_polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.extract_polygon_vertices"]], "face_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_polygons"]], "face_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_vertices"]], "get_all_edge_segments() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_edge_segments"]], "get_all_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_all_segments"]], "get_all_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_vertices"]], "get_edge_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_edge_vertices"]], "get_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_segments"]], "intersection() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.intersection"]], "is_one_of() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.is_one_of"]], "join_edge() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_edge"]], "join_point() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_point"]], "line_sample_point() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.line_sample_point"]], "list (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.list"]], "polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.polygon_vertices"]], "sense_of_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.sense_of_polygon"]], "shape_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.shape_vertices"]], "show_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.show_points"]], "sort_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.sort_cut_points"]], "sorted_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.sorted_cut_points"]], "trace_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.trace_polygon"]], "verify_asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.verify_asu_polygons"]], "verify_edge_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.verify_edge_segments"]], "vertex (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.vertex"]], "vertex_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.vertex_inclusive_flag"]], "asu_01() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_01"]], "asu_02() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_02"]], "asu_03() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_03"]], "asu_04() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_04"]], "asu_05() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_05"]], "asu_06() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_06"]], "asu_07() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_07"]], "asu_08() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_08"]], "asu_09() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_09"]], "asu_10() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_10"]], "asu_11() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_11"]], "asu_12() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_12"]], "asu_13() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_13"]], "asu_14() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_14"]], "asu_15() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_15"]], "asu_16() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_16"]], "asu_17() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_17"]], "cctbx.sgtbx.direct_space_asu.plane_group_reference_table": [[172, "module-cctbx.sgtbx.direct_space_asu.plane_group_reference_table"]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.get_asu"]], "asu_show_() (in module cctbx.sgtbx.direct_space_asu.proto)": [[173, "cctbx.sgtbx.direct_space_asu.proto.asu_show_"]], "cctbx.sgtbx.direct_space_asu.proto": [[173, "module-cctbx.sgtbx.direct_space_asu.proto"]], "base_symbol_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.base_symbol_cpp"]], "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table": [[174, "module-cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table"]], "make_md5() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.make_md5"]], "out_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.out_cpp"]], "run() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.run"]], "show_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.show_cpp"]], "apply_change_of_basis() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.apply_change_of_basis"]], "asu_001() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_001"]], "asu_002() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_002"]], "asu_003() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_003"]], "asu_004() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_004"]], "asu_005() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_005"]], "asu_006() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_006"]], "asu_007() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_007"]], "asu_008() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_008"]], "asu_009() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_009"]], "asu_010() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_010"]], "asu_011() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_011"]], "asu_012() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_012"]], "asu_013() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_013"]], "asu_014() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_014"]], "asu_015() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_015"]], "asu_016() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_016"]], "asu_017() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_017"]], "asu_018() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_018"]], "asu_019() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_019"]], "asu_020() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_020"]], "asu_021() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_021"]], "asu_022() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_022"]], "asu_023() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_023"]], "asu_024() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_024"]], "asu_025() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_025"]], "asu_026() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_026"]], "asu_027() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_027"]], "asu_028() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_028"]], "asu_029() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_029"]], "asu_030() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_030"]], "asu_031() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_031"]], "asu_032() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_032"]], "asu_033() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_033"]], "asu_034() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_034"]], "asu_035() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_035"]], "asu_036() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_036"]], "asu_037() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_037"]], "asu_038() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_038"]], "asu_039() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_039"]], "asu_040() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_040"]], "asu_041() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_041"]], "asu_042() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_042"]], "asu_043() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_043"]], "asu_044() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_044"]], "asu_045() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_045"]], "asu_046() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_046"]], "asu_047() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_047"]], "asu_048() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_048"]], "asu_049() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_049"]], "asu_050() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_050"]], "asu_051() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_051"]], "asu_052() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_052"]], "asu_053() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_053"]], "asu_054() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_054"]], "asu_055() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_055"]], "asu_056() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_056"]], "asu_057() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_057"]], "asu_058() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_058"]], "asu_059() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_059"]], "asu_060() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_060"]], "asu_061() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_061"]], "asu_062() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_062"]], "asu_063() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_063"]], "asu_064() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_064"]], "asu_065() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_065"]], "asu_066() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_066"]], "asu_067() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_067"]], "asu_068() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_068"]], "asu_069() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_069"]], "asu_070() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_070"]], "asu_071() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_071"]], "asu_072() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_072"]], "asu_073() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_073"]], "asu_074() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_074"]], "asu_075() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_075"]], "asu_076() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_076"]], "asu_077() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_077"]], "asu_078() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_078"]], "asu_079() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_079"]], "asu_080() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_080"]], "asu_081() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_081"]], "asu_082() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_082"]], "asu_083() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_083"]], "asu_084() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_084"]], "asu_085() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_085"]], "asu_086() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_086"]], "asu_087() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_087"]], "asu_088() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_088"]], "asu_089() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_089"]], "asu_090() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_090"]], "asu_091() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_091"]], "asu_092() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_092"]], "asu_093() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_093"]], "asu_094() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_094"]], "asu_095() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_095"]], "asu_096() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_096"]], "asu_097() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_097"]], "asu_098() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_098"]], "asu_099() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_099"]], "asu_100() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_100"]], "asu_101() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_101"]], "asu_102() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_102"]], "asu_103() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_103"]], "asu_104() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_104"]], "asu_105() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_105"]], "asu_106() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_106"]], "asu_107() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_107"]], "asu_108() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_108"]], "asu_109() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_109"]], "asu_110() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_110"]], "asu_111() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_111"]], "asu_112() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_112"]], "asu_113() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_113"]], "asu_114() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_114"]], "asu_115() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_115"]], "asu_116() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_116"]], "asu_117() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_117"]], "asu_118() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_118"]], "asu_119() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_119"]], "asu_120() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_120"]], "asu_121() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_121"]], "asu_122() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_122"]], "asu_123() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_123"]], "asu_124() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_124"]], "asu_125() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_125"]], "asu_126() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_126"]], "asu_127() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_127"]], "asu_128() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_128"]], "asu_129() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_129"]], "asu_130() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_130"]], "asu_131() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_131"]], "asu_132() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_132"]], "asu_133() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_133"]], "asu_134() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_134"]], "asu_135() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_135"]], "asu_136() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_136"]], "asu_137() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_137"]], "asu_138() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_138"]], "asu_139() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_139"]], "asu_140() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_140"]], "asu_141() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_141"]], "asu_142() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_142"]], "asu_143() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_143"]], "asu_144() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_144"]], "asu_145() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_145"]], "asu_146() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_146"]], "asu_147() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_147"]], "asu_148() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_148"]], "asu_149() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_149"]], "asu_150() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_150"]], "asu_151() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_151"]], "asu_152() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_152"]], "asu_153() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_153"]], "asu_154() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_154"]], "asu_155() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_155"]], "asu_156() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_156"]], "asu_157() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_157"]], "asu_158() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_158"]], "asu_159() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_159"]], "asu_160() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_160"]], "asu_161() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_161"]], "asu_162() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_162"]], "asu_163() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_163"]], "asu_164() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_164"]], "asu_165() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_165"]], "asu_166() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_166"]], "asu_167() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_167"]], "asu_168() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_168"]], "asu_169() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_169"]], "asu_170() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_170"]], "asu_171() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_171"]], "asu_172() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_172"]], "asu_173() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_173"]], "asu_174() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_174"]], "asu_175() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_175"]], "asu_176() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_176"]], "asu_177() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_177"]], "asu_178() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_178"]], "asu_179() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_179"]], "asu_180() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_180"]], "asu_181() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_181"]], "asu_182() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_182"]], "asu_183() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_183"]], "asu_184() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_184"]], "asu_185() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_185"]], "asu_186() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_186"]], "asu_187() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_187"]], "asu_188() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_188"]], "asu_189() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_189"]], "asu_190() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_190"]], "asu_191() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_191"]], "asu_192() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_192"]], "asu_193() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_193"]], "asu_194() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_194"]], "asu_195() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_195"]], "asu_196() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_196"]], "asu_197() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_197"]], "asu_198() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_198"]], "asu_199() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_199"]], "asu_200() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_200"]], "asu_201() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_201"]], "asu_202() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_202"]], "asu_203() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_203"]], "asu_204() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_204"]], "asu_205() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_205"]], "asu_206() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_206"]], "asu_207() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_207"]], "asu_208() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_208"]], "asu_209() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_209"]], "asu_210() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_210"]], "asu_211() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_211"]], "asu_212() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_212"]], "asu_213() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_213"]], "asu_214() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_214"]], "asu_215() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_215"]], "asu_216() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_216"]], "asu_217() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_217"]], "asu_218() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_218"]], "asu_219() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_219"]], "asu_220() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_220"]], "asu_221() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_221"]], "asu_222() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_222"]], "asu_223() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_223"]], "asu_224() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_224"]], "asu_225() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_225"]], "asu_226() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_226"]], "asu_227() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_227"]], "asu_228() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_228"]], "asu_229() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_229"]], "asu_230() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_230"]], "cctbx.sgtbx.direct_space_asu.reference_table": [[175, "module-cctbx.sgtbx.direct_space_asu.reference_table"]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.get_asu"]], "cctbx.sgtbx.direct_space_asu.short_cuts": [[176, "module-cctbx.sgtbx.direct_space_asu.short_cuts"]], "algebraic() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.algebraic"]], "cctbx.sgtbx.harker": [[177, "module-cctbx.sgtbx.harker"]], "count() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.count"]], "distance() (cctbx.sgtbx.harker.plane_cartesian method)": [[177, "cctbx.sgtbx.harker.plane_cartesian.distance"]], "dot3() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.dot3"]], "min_distance() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.min_distance"]], "mod_positive3() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.mod_positive3"]], "operation() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.operation"]], "plane_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_cartesian"]], "plane_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_fractional"]], "planes_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_cartesian"]], "planes_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_fractional"]], "test() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test"]], "test_call_back() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test_call_back"]], "cctbx.sgtbx.lattice_symmetry": [[178, "module-cctbx.sgtbx.lattice_symmetry"]], "change_input_to_minimum_cell() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.change_input_to_minimum_cell"]], "change_of_basis_op_to_best_cell() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.change_of_basis_op_to_best_cell"]], "derive_result_group_list() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.derive_result_group_list"]], "lattice_group_info() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.lattice_group_info"]], "metric_subgroups (class in cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups"]], "metric_supergroup() (in module cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_supergroup"]], "show() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show"]], "show_groups() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show_groups"]], "show_input() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.show_input"]], "cctbx.sgtbx.literal_description": [[179, "module-cctbx.sgtbx.literal_description"]], "cosets_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.cosets_form"]], "labelit_check_pdb_symmetry_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_form"]], "labelit_check_pdb_symmetry_short() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_short"]], "literal_description (class in cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.literal_description"]], "long_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.long_form"]], "select() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.select"]], "str_ev() (in module cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.str_ev"]], "cctbx.sgtbx.plane_groups": [[180, "module-cctbx.sgtbx.plane_groups"]], "assemble_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.assemble_symops"]], "build_it() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.build_it"]], "cctbx.sgtbx.pointgroup_tools": [[181, "module-cctbx.sgtbx.pointgroup_tools"]], "compare_abs_lists() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.compare_abs_lists"]], "compatible_symmetries() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.compatible_symmetries"]], "coset_lookup() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.coset_lookup"]], "edge_object (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object"]], "find_absent_indices() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.find_absent_indices"]], "find_compatible_space_groups (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups"]], "find_left_over_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.find_left_over_symops"]], "full_sys_abs_mask() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.full_sys_abs_mask"]], "get_maximal_subgroup() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.get_maximal_subgroup"]], "get_space_groups_compatible_with_likely_point_group() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.get_space_groups_compatible_with_likely_point_group"]], "get_symops_from_supergroup_that_are_not_in_subgroup() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.get_symops_from_supergroup_that_are_not_in_subgroup"]], "graphviz_pg_graph() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.graphviz_pg_graph"]], "make_and_place_nodes_and_connections() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.make_and_place_nodes_and_connections"]], "make_sys_abs_list() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.make_sys_abs_list"]], "node_object (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.node_object"]], "point_group_graph (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph"]], "reference_setting_choices() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.reference_setting_choices"]], "remove_point_group_and_its_super_groups_from_graph() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.remove_point_group_and_its_super_groups_from_graph"]], "return_likely_sg_and_cell() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.return_likely_sg_and_cell"]], "return_next_index() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_index"]], "return_next_left_over_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_left_over_set"]], "return_next_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_set"]], "return_next_sg() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.return_next_sg"]], "return_unused() (cctbx.sgtbx.pointgroup_tools.edge_object method)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object.return_unused"]], "return_used() (cctbx.sgtbx.pointgroup_tools.edge_object method)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object.return_used"]], "reverse_dict() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.reverse_dict"]], "show() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.show"]], "show() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.show"]], "show() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.show"]], "space_group_graph_from_cell_and_sg (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg"]], "sub_super_point_group_relations (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations"]], "as_hkl() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.as_hkl"]], "cb_op_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.cb_op_as_rational"]], "cctbx.sgtbx.rational_matrices_point_groups": [[182, "module-cctbx.sgtbx.rational_matrices_point_groups"]], "change_basis() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.change_basis"]], "compare_groups() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.compare_groups"]], "construct_rational_point_group() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.construct_rational_point_group"]], "expand() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.expand"]], "is_in_group() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.is_in_group"]], "rat_rot_group (class in cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group"]], "rt_mx_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rt_mx_as_rational"]], "run() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.run"]], "show() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.show"]], "tst_compare() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_compare"]], "tst_groups() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_groups"]], "as_hkl() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.as_hkl"]], "build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.build_reticular_twin_laws"]], "cb_op_as_rational() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cb_op_as_rational"]], "cctbx.sgtbx.reticular_pg_tools": [[183, "module-cctbx.sgtbx.reticular_pg_tools"]], "change_basis() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.change_basis"]], "compare_groups() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.compare_groups"]], "construct_rational_point_group() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.construct_rational_point_group"]], "cosets() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cosets"]], "expand() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.expand"]], "extra_operators() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.extra_operators"]], "is_in_group() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.is_in_group"]], "is_reticular_polyholohedral() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_reticular_polyholohedral"]], "is_subgroup() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_subgroup"]], "rat_rot_group (class in cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group"]], "recurring_operators() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.recurring_operators"]], "rt_mx_as_rational() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.rt_mx_as_rational"]], "run() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.run"]], "show() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.show"]], "tst_build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_build_reticular_twin_laws"]], "tst_compare() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_compare"]], "tst_groups() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_groups"]], "cctbx.sgtbx.reticular_twin_laws": [[184, "module-cctbx.sgtbx.reticular_twin_laws"]], "construct_twin_laws() (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws.construct_twin_laws"]], "exercise() (in module cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.exercise"]], "make_new_xs() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.make_new_xs"]], "metric_r() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.metric_r"]], "ret_twin_law_info (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info"]], "reticular_twin_laws (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws"]], "show() (cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info method)": [[184, "cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info.show"]], "show() (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method)": [[184, "cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws.show"]], "symmetry_safe_sublattice_xs (class in cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs"]], "cctbx.sgtbx.show_cosets": [[185, "module-cctbx.sgtbx.show_cosets"]], "run() (in module cctbx.sgtbx.show_cosets)": [[185, "cctbx.sgtbx.show_cosets.run"]], "cctbx.sgtbx.sub_lattice_tools": [[186, "module-cctbx.sgtbx.sub_lattice_tools"]], "compare_lattice (class in cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice"]], "divisor() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.divisor"]], "exercise() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.exercise"]], "find_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples"]], "find_triples_slowly() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples_slowly"]], "generate_cb_op_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_cb_op_up_to_order"]], "generate_inverse_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_inverse_matrix_up_to_order"]], "generate_matrix() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix"]], "generate_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix_up_to_order"]], "make_list_of_target_xs_up_to_order (class in cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order"]], "make_new_cell_and_symmetry() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.make_new_cell_and_symmetry"]], "make_new_xs() (cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order method)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order.make_new_xs"]], "make_permutations() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_permutations"]], "make_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_triples"]], "rt_mx_as_rational() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.rt_mx_as_rational"]], "show_basic_info() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.show_basic_info"]], "show_solution() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.show_solution"]], "sort_triple() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.sort_triple"]], "tst_centered_cells() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_centered_cells"]], "tst_compare() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_compare"]], "tst_make_bigger_cell() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_make_bigger_cell"]], "tst_sublattice() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_sublattice"]], "anomalous_reflection_intensity_primitive_cell() (in module cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.anomalous_reflection_intensity_primitive_cell"]], "cctbx.sgtbx.subgroups": [[187, "module-cctbx.sgtbx.subgroups"]], "groups_parent_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_parent_setting"]], "groups_primitive_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_primitive_setting"]], "show() (in module cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.show"]], "subgroups (class in cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.subgroups"]], "cctbx.sgtbx.symbol_confidence": [[188, "module-cctbx.sgtbx.symbol_confidence"]], "level() (in module cctbx.sgtbx.symbol_confidence)": [[188, "cctbx.sgtbx.symbol_confidence.level"]], "cctbx.sgtbx.sys_abs_equiv": [[189, "module-cctbx.sgtbx.sys_abs_equiv"]], "cctbx.source_generators": [[190, "module-cctbx.source_generators"]], "cctbx.source_generators.eltbx": [[191, "module-cctbx.source_generators.eltbx"]], "cctbx.source_generators.eltbx.generate_henke_cpp": [[192, "module-cctbx.source_generators.eltbx.generate_henke_cpp"]], "collect_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_points"]], "collect_tab_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_tab_points"]], "collect_tables() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.collect_tables"]], "compare_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.compare_points"]], "print_ftp_info() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_ftp_info"]], "print_header() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_header"]], "print_henke_cpp() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_henke_cpp"]], "print_table_block() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.print_table_block"]], "run() (in module cctbx.source_generators.eltbx.generate_henke_cpp)": [[192, "cctbx.source_generators.eltbx.generate_henke_cpp.run"]], "cctbx.source_generators.eltbx.generate_sasaki_cpp": [[193, "module-cctbx.source_generators.eltbx.generate_sasaki_cpp"]], "check_first_last() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table.check_first_last"]], "collect_tables() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.collect_tables"]], "combine_tables() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.combine_tables"]], "print_ftp_info() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_ftp_info"]], "print_header() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_header"]], "print_sasaki_cpp() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_sasaki_cpp"]], "print_table_block() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.print_table_block"]], "run() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.run"]], "sasaki_table (class in cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table"]], "table_references (class in cctbx.source_generators.eltbx.generate_sasaki_cpp)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.table_references"]], "validate() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table.validate"]], "cctbx.source_generators.flex_fwd_h": [[194, "module-cctbx.source_generators.flex_fwd_h"]], "run() (in module cctbx.source_generators.flex_fwd_h)": [[194, "cctbx.source_generators.flex_fwd_h.run"]], "cctbx.statistics": [[195, "module-cctbx.statistics"]], "cumulative_intensity_distribution (class in cctbx.statistics)": [[195, "cctbx.statistics.cumulative_intensity_distribution"]], "empty (class in cctbx.statistics)": [[195, "cctbx.statistics.empty"]], "sys_absent_intensity_distribution (class in cctbx.statistics)": [[195, "cctbx.statistics.sys_absent_intensity_distribution"]], "wilson_plot (class in cctbx.statistics)": [[195, "cctbx.statistics.wilson_plot"]], "xy_plot_info() (cctbx.statistics.cumulative_intensity_distribution method)": [[195, "cctbx.statistics.cumulative_intensity_distribution.xy_plot_info"]], "xy_plot_info() (cctbx.statistics.sys_absent_intensity_distribution method)": [[195, "cctbx.statistics.sys_absent_intensity_distribution.xy_plot_info"]], "xy_plot_info() (cctbx.statistics.wilson_plot method)": [[195, "cctbx.statistics.wilson_plot.xy_plot_info"]], "accepted (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.accepted"]], "cctbx.symmetry_search": [[196, "module-cctbx.symmetry_search"]], "centring_translation_peak_sites() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.centring_translation_peak_sites"]], "change_origin() (cctbx.symmetry_search.possible_symmetry method)": [[196, "cctbx.symmetry_search.possible_symmetry.change_origin"]], "compute_functional_and_gradients() (cctbx.symmetry_search.shift_refinement method)": [[196, "cctbx.symmetry_search.shift_refinement.compute_functional_and_gradients"]], "cross_correlation_cutoff_for_centring (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_cutoff_for_centring"]], "cross_correlation_peaks() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_peaks"]], "find_centring_translations() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_centring_translations"]], "find_space_group() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_space_group"]], "fmt3vec (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.fmt3vec"]], "grid_resolution_factor (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.grid_resolution_factor"]], "misfit() (cctbx.symmetry_search.symmetrised_shifted_structure_factors method)": [[196, "cctbx.symmetry_search.symmetrised_shifted_structure_factors.misfit"]], "phi_sym_acceptance_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_acceptance_cutoff"]], "phi_sym_rejection_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_rejection_cutoff"]], "possible_point_group_generators() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.possible_point_group_generators"]], "possible_symmetry (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.possible_symmetry"]], "rejected (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.rejected"]], "set_components_of_global_origin() (cctbx.symmetry_search.possible_symmetry method)": [[196, "cctbx.symmetry_search.possible_symmetry.set_components_of_global_origin"]], "shift_refinement (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.shift_refinement"]], "structure_factor_symmetry (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.structure_factor_symmetry"]], "symmetrised_shifted_structure_factors (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.symmetrised_shifted_structure_factors"]], "symmetrised_structure_factors() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.symmetrised_structure_factors"]], "unsure (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.unsure"]], "cctbx.translation_search": [[197, "module-cctbx.translation_search"]], "unit_cell (class in cctbx.uctbx)": [[198, "cctbx.uctbx.unit_cell"]], "cctbx.uctbx.determine_unit_cell": [[199, "module-cctbx.uctbx.determine_unit_cell"]], "as_gruber_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_gruber_matrix"]], "as_niggli_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_niggli_matrix"]], "as_sym_mat3() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_sym_mat3"]], "as_unit_cell() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.as_unit_cell"]], "b2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b2_action"]], "b2_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b2_action"]], "b3_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b3_action"]], "b3_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b3_action"]], "b4_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b4_action"]], "b4_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b4_action"]], "b5_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.b5_action"]], "b5_action() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.b5_action"]], "cb_update() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.cb_update"]], "cctbx.uctbx.gruber_1973": [[200, "module-cctbx.uctbx.gruber_1973"]], "def_gt_0() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.def_gt_0"]], "def_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.def_test"]], "entier() (in module cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.entier"]], "fast_minimum_reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction"]], "iteration_limit() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.iteration_limit"]], "minimum_reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.minimum_reduction"]], "n1_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n1_action"]], "n2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n2_action"]], "n3_false_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n3_false_action"]], "n3_false_action() (cctbx.uctbx.gruber_1973.minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.minimum_reduction.n3_false_action"]], "n3_true_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n3_true_action"]], "n_iterations() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.n_iterations"]], "r_inv() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.r_inv"]], "reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.reduction"]], "significant_change_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.significant_change_test"]], "step() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.step"]], "step() (cctbx.uctbx.gruber_1973.reduction method)": [[200, "cctbx.uctbx.gruber_1973.reduction.step"]], "type() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.type"]], "cctbx.uctbx.gruber_1973_table_1": [[201, "module-cctbx.uctbx.gruber_1973_table_1"]], "get_mk2_sets() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_mk2_sets"]], "get_type_conditions() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_type_conditions"]], "type_conditions (class in cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.type_conditions"]], "a1_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a1_action"]], "a2_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a2_action"]], "a3_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a3_action"]], "a4_action() (cctbx.uctbx.krivy_gruber_1976.minimum_reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.minimum_reduction.a4_action"]], "a4_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a4_action"]], "a5_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a5_action"]], "a6_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a6_action"]], "a7_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a7_action"]], "a8_action() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.a8_action"]], "cctbx.uctbx.krivy_gruber_1976": [[202, "module-cctbx.uctbx.krivy_gruber_1976"]], "minimum_reduction (class in cctbx.uctbx.krivy_gruber_1976)": [[202, "cctbx.uctbx.krivy_gruber_1976.minimum_reduction"]], "reduction (class in cctbx.uctbx.krivy_gruber_1976)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction"]], "step() (cctbx.uctbx.krivy_gruber_1976.reduction method)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction.step"]], "as_gruber_matrix() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_gruber_matrix"]], "as_niggli_matrix() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_niggli_matrix"]], "as_sym_mat3() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_sym_mat3"]], "as_unit_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.as_unit_cell"]], "cb_update() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.cb_update"]], "cctbx.uctbx.reduction_base": [[203, "module-cctbx.uctbx.reduction_base"]], "change_of_basis_op() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.change_of_basis_op"]], "def_gt_0() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.def_gt_0"]], "def_test() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.def_test"]], "eps_eq() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_eq"]], "eps_eq() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.eps_eq"]], "eps_gt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_gt"]], "eps_lt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_lt"]], "gruber_parameterization (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization"]], "is_buerger_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_buerger_cell"]], "is_niggli_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_niggli_cell"]], "iteration_limit() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.iteration_limit"]], "iteration_limit_exceeded": [[203, "cctbx.uctbx.reduction_base.iteration_limit_exceeded"]], "meets_main_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_main_conditions"]], "meets_primary_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_primary_conditions"]], "minimum_reduction_mixin (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin"]], "n1_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n1_action"]], "n2_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n2_action"]], "n3_false_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n3_false_action"]], "n3_true_action() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n3_true_action"]], "n_iterations() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.n_iterations"]], "r_inv() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.r_inv"]], "reduction_base (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.reduction_base"]], "significant_change_test() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.significant_change_test"]], "type() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.type"]], "cctbx.web": [[204, "module-cctbx.web"]], "cctbx.web.all_axes": [[205, "module-cctbx.web.all_axes"]], "interpret_form_data() (in module cctbx.web.all_axes)": [[205, "cctbx.web.all_axes.interpret_form_data"]], "run() (in module cctbx.web.all_axes)": [[205, "cctbx.web.all_axes.run"]], "cctbx.web.asu_gallery": [[206, "module-cctbx.web.asu_gallery"]], "html_head_title() (in module cctbx.web.asu_gallery)": [[206, "cctbx.web.asu_gallery.html_head_title"]], "cctbx.web.asu_gallery.guide_to_notation": [[207, "module-cctbx.web.asu_gallery.guide_to_notation"]], "write_html() (in module cctbx.web.asu_gallery.guide_to_notation)": [[207, "cctbx.web.asu_gallery.guide_to_notation.write_html"]], "asu_as_jvx() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.asu_as_jvx"]], "basis_vector_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.basis_vector_geometry"]], "cartesian_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.cartesian_polygon"]], "cctbx.web.asu_gallery.jv_asu": [[208, "module-cctbx.web.asu_gallery.jv_asu"]], "edge_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.edge_geometry"]], "get_diagonal_extend() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_diagonal_extend"]], "get_edge_vectors() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_edge_vectors"]], "get_min_fractional() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_min_fractional"]], "orthogonalizer (class in cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.orthogonalizer"]], "run() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.run"]], "select_color() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.select_color"]], "shrink_edge() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_edge"]], "shrink_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_polygon"]], "unit_cell_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.unit_cell_geometry"]], "vertex_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.vertex_geometry"]], "add() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add"]], "add() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.add"]], "add_point_group_type() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add_point_group_type"]], "cctbx.web.asu_gallery.jv_index": [[209, "module-cctbx.web.asu_gallery.jv_index"]], "crystal_system_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table"]], "format_html() (cctbx.web.asu_gallery.jv_index.crystal_system_table method)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.plane_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.format_html"]], "format_html() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.format_html"]], "hermann_mauguin() (cctbx.web.asu_gallery.jv_index.point_group_symbols method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols.hermann_mauguin"]], "number() (cctbx.web.asu_gallery.jv_index.point_group_symbols method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols.number"]], "plane_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table"]], "point_group_symbols (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols"]], "point_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table"]], "symbol_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table"]], "table_format_html() (in module cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.table_format_html"]], "write_html() (in module cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.write_html"]], "append() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.append"]], "append() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.append"]], "append() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.append"]], "bracketed_link() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.bracketed_link"]], "cctbx.web.asu_gallery.jvx": [[210, "module-cctbx.web.asu_gallery.jvx"]], "extend() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.extend"]], "face (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.face"]], "faceset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.faceSet"]], "geometry (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.geometry"]], "head() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.head"]], "hide_points() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.hide_points"]], "html_loader() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.html_loader"]], "index() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.index"]], "jvx() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.geometry method)": [[210, "cctbx.web.asu_gallery.jvx.geometry.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.jvx"]], "jvx() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.jvx"]], "jvx_item_colors() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.jvx_item_colors"]], "line (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.line"]], "lineset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.lineSet"]], "make_point() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.make_point"]], "point (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.point"]], "pointset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.pointSet"]], "run() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.run"]], "size() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.size"]], "size() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.size"]], "size() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.size"]], "tail() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.tail"]], "cctbx.web.asu_gallery.web_links": [[211, "module-cctbx.web.asu_gallery.web_links"]], "cctbx.web.browse_settings": [[212, "module-cctbx.web.browse_settings"]], "interpret_form_data() (in module cctbx.web.browse_settings)": [[212, "cctbx.web.browse_settings.interpret_form_data"]], "run() (in module cctbx.web.browse_settings)": [[212, "cctbx.web.browse_settings.run"]], "formaterror": [[213, "cctbx.web.cgi_utils.FormatError"], [265, "iotbx.file_reader.FormatError"]], "base() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.base"]], "cctbx.web.cgi_utils": [[213, "module-cctbx.web.cgi_utils"]], "coordinates_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.coordinates_from_form"]], "empty (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.empty"]], "file() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.file"]], "inp_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.inp_from_form"]], "script() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.script"]], "server_info (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.server_info"]], "cctbx.web.change_basis": [[214, "module-cctbx.web.change_basis"]], "display_r() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_r"]], "display_rt() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_rt"]], "fmt_nums() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.fmt_nums"]], "interpret_form_data() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.interpret_form_data"]], "number_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.number_from_string"]], "nums_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.nums_from_string"]], "p_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.p_from_string"]], "raise_uninterpretable() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.raise_uninterpretable"]], "rt_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.rt_from_string"]], "run() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.run"]], "w_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.w_from_string"]], "xyz_from_string() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.xyz_from_string"]], "cctbx.web.change_hand": [[215, "module-cctbx.web.change_hand"]], "interpret_form_data() (in module cctbx.web.change_hand)": [[215, "cctbx.web.change_hand.interpret_form_data"]], "run() (in module cctbx.web.change_hand)": [[215, "cctbx.web.change_hand.run"]], "cctbx.web.change_setting": [[216, "module-cctbx.web.change_setting"]], "interpret_form_data() (in module cctbx.web.change_setting)": [[216, "cctbx.web.change_setting.interpret_form_data"]], "run() (in module cctbx.web.change_setting)": [[216, "cctbx.web.change_setting.run"]], "cctbx.web.dispatcher": [[217, "module-cctbx.web.dispatcher"]], "run() (in module cctbx.web.dispatcher)": [[217, "cctbx.web.dispatcher.run"]], "cctbx.web.emma": [[218, "module-cctbx.web.emma"]], "crystal_symmetry() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.crystal_symmetry"]], "get_next() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_next"]], "get_space_group_info() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_space_group_info"]], "get_unit_cell() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_unit_cell"]], "interpret_form_data() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_form_data"]], "interpret_generic_coordinate_line() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_generic_coordinate_line"]], "model_is_too_large() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.model_is_too_large"]], "pdb_file_to_emma_model() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.pdb_file_to_emma_model"]], "run() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.run"]], "run_implementation() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.run_implementation"]], "sdb_file_to_emma_model() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.sdb_file_to_emma_model"]], "web_to_models (class in cctbx.web.emma)": [[218, "cctbx.web.emma.web_to_models"]], "cctbx.web.explore_symmetry": [[219, "module-cctbx.web.explore_symmetry"]], "expand_shelx_latt() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.expand_shelx_latt"]], "interpret_form_data() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.interpret_form_data"]], "rt_mx_analysis() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.rt_mx_analysis"]], "rt_mx_analysis_header() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.rt_mx_analysis_header"]], "run() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.run"]], "show_group_generic() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.show_group_generic"]], "show_symbols() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.show_symbols"]], "str_ev() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.str_ev"]], "cctbx.web.frac_cart": [[220, "module-cctbx.web.frac_cart"]], "interpret_form_data() (in module cctbx.web.frac_cart)": [[220, "cctbx.web.frac_cart.interpret_form_data"]], "run() (in module cctbx.web.frac_cart)": [[220, "cctbx.web.frac_cart.run"]], "cctbx.web.io_utils": [[221, "module-cctbx.web.io_utils"]], "interpret_coordinate_line() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_coordinate_line"]], "interpret_skip_columns() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_skip_columns"]], "read_scatterer() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.read_scatterer"]], "show_input_symbol() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.show_input_symbol"]], "special_position_settings_from_inp() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.special_position_settings_from_inp"]], "structure_from_inp() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.structure_from_inp"]], "structure_from_inp_pdb() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.structure_from_inp_pdb"]], "cctbx.web.iotbx_cif_validate": [[222, "module-cctbx.web.iotbx_cif_validate"]], "interpret_form_data() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.interpret_form_data"]], "run() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.run"]], "run_implementation() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.run_implementation"]], "cctbx.web.lattice_symmetry": [[223, "module-cctbx.web.lattice_symmetry"]], "interpret_form_data() (in module cctbx.web.lattice_symmetry)": [[223, "cctbx.web.lattice_symmetry.interpret_form_data"]], "run() (in module cctbx.web.lattice_symmetry)": [[223, "cctbx.web.lattice_symmetry.run"]], "cctbx.web.libtbx_help": [[224, "module-cctbx.web.libtbx_help"]], "interpret_form_data() (in module cctbx.web.libtbx_help)": [[224, "cctbx.web.libtbx_help.interpret_form_data"]], "run() (in module cctbx.web.libtbx_help)": [[224, "cctbx.web.libtbx_help.run"]], "linkexploresymmetry() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.LinkExploreSymmetry"]], "cctbx.web.multiple_cell": [[225, "module-cctbx.web.multiple_cell"]], "escape() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.escape"]], "run() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.run"]], "cctbx.web.phase_o_phrenia": [[226, "module-cctbx.web.phase_o_phrenia"]], "inp_as_xray_structures() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.inp_as_xray_structures"]], "interpret_form_data() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.interpret_form_data"]], "run() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.run"]], "sdb_files_as_xray_structures() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.sdb_files_as_xray_structures"]], "cctbx.web.replay": [[227, "module-cctbx.web.replay"]], "empty (class in cctbx.web.replay)": [[227, "cctbx.web.replay.empty"]], "run() (in module cctbx.web.replay)": [[227, "cctbx.web.replay.run"]], "cctbx.web.shelx": [[228, "module-cctbx.web.shelx"]], "interpret_form_data() (in module cctbx.web.shelx)": [[228, "cctbx.web.shelx.interpret_form_data"]], "run() (in module cctbx.web.shelx)": [[228, "cctbx.web.shelx.run"]], "cctbx.web.structure_factors": [[229, "module-cctbx.web.structure_factors"]], "interpret_form_data() (in module cctbx.web.structure_factors)": [[229, "cctbx.web.structure_factors.interpret_form_data"]], "run() (in module cctbx.web.structure_factors)": [[229, "cctbx.web.structure_factors.run"]], "cctbx.web.structure_factors_pdb": [[230, "module-cctbx.web.structure_factors_pdb"]], "interpret_form_data() (in module cctbx.web.structure_factors_pdb)": [[230, "cctbx.web.structure_factors_pdb.interpret_form_data"]], "run() (in module cctbx.web.structure_factors_pdb)": [[230, "cctbx.web.structure_factors_pdb.run"]], "cctbx.web.wyckoff": [[231, "module-cctbx.web.wyckoff"]], "interpret_form_data() (in module cctbx.web.wyckoff)": [[231, "cctbx.web.wyckoff.interpret_form_data"]], "run() (in module cctbx.web.wyckoff)": [[231, "cctbx.web.wyckoff.run"]], "cctbx.xray": [[232, "module-cctbx.xray"]], "cctbx.xray.ext": [[233, "module-cctbx.xray.ext"]], "add_gradients() (in module cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.add_gradients"]], "apply_shifts() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.apply_shifts"]], "callback_after_step() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.callback_after_step"]], "cctbx.xray.minimization": [[234, "module-cctbx.xray.minimization"]], "compute_functional_and_gradients() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.compute_functional_and_gradients"]], "compute_target() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.compute_target"]], "functional() (cctbx.xray.minimization.occupancy_penalty_exp method)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp.functional"]], "gradient() (cctbx.xray.minimization.occupancy_penalty_exp method)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp.gradient"]], "lbfgs (class in cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.lbfgs"]], "occupancy_penalty_exp (class in cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp"]], "amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.amplitude"]], "any (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.any"]], "cctbx.xray.observation_types": [[235, "module-cctbx.xray.observation_types"]], "intensity (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.intensity"]], "reconstructed_amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.reconstructed_amplitude"]], "cctbx.xray.observations": [[236, "module-cctbx.xray.observations"]], "customized_copy() (in module cctbx.xray.observations)": [[236, "cctbx.xray.observations.customized_copy"]], "anomalous_scatterer_group (class in cctbx.xray.scatterer)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group"]], "cctbx.xray.scatterer": [[237, "module-cctbx.xray.scatterer"]], "copy_to_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.copy_to_scatterers_in_place"]], "extract_from_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.extract_from_scatterers_in_place"]], "labels_refine() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.labels_refine"]], "scatterer (class in cctbx.xray.scatterer)": [[237, "cctbx.xray.scatterer.scatterer"]], "select() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.select"]], "show_summary() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.show_summary"]], "add_scatterer() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterer"]], "add_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterers"]], "adjust_occupancy() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_occupancy"]], "adjust_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_u_iso"]], "all_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.all_selection"]], "apply_rigid_body_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift"]], "apply_rigid_body_shift_obj() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift_obj"]], "apply_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_shift"]], "apply_special_position_ops_d_target_d_site() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_special_position_ops_d_target_d_site"]], "apply_symmetry_sites() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_symmetry_sites"]], "apply_symmetry_u_stars() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_symmetry_u_stars"]], "as_cif_block() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_cif_block"]], "as_cif_simple() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_cif_simple"]], "as_emma_model() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_emma_model"]], "as_pdb_file() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_pdb_file"]], "as_py_code() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.as_py_code"]], "asu_mappings() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asu_mappings"]], "asymmetric_unit_in_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asymmetric_unit_in_p1"]], "atomic_weights() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.atomic_weights"]], "b_iso_min_max_mean() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_min_max_mean"]], "b_iso_or_b_equiv() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_or_b_equiv"]], "by_index_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.by_index_selection"]], "cctbx.xray.structure": [[238, "module-cctbx.xray.structure"]], "center_of_mass() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.center_of_mass"]], "change_basis() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.change_basis"]], "change_hand() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.change_hand"]], "closest_distances() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.closest_distances"]], "concatenate() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.concatenate"]], "concatenate_inplace() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.concatenate_inplace"]], "conservative_pair_proxies (class in cctbx.xray.structure)": [[238, "cctbx.xray.structure.conservative_pair_proxies"]], "conservative_pair_proxies() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.conservative_pair_proxies"]], "convert_to_anisotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_anisotropic"]], "convert_to_isotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_isotropic"]], "coordinate_degrees_of_freedom_counts() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.coordinate_degrees_of_freedom_counts"]], "crystal_density() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_density"]], "crystal_symmetry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_symmetry"]], "cubic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.cubic_unit_cell_around_centered_scatterers"]], "customized_copy() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.customized_copy"]], "deep_copy_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.deep_copy_scatterers"]], "difference_vectors_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.difference_vectors_cart"]], "discard_scattering_type_registry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.discard_scattering_type_registry"]], "distances() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.distances"]], "element_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.element_selection"]], "erase_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.erase_scatterers"]], "expand_to_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.expand_to_p1"]], "extract_u_cart_plus_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.extract_u_cart_plus_u_iso"]], "extract_u_iso_or_u_equiv() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.extract_u_iso_or_u_equiv"]], "f_000() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.f_000"]], "from_cif() (cctbx.xray.structure.structure class method)": [[238, "cctbx.xray.structure.structure.from_cif"]], "from_shelx() (cctbx.xray.structure.structure class method)": [[238, "cctbx.xray.structure.structure.from_shelx"]], "grads_and_curvs_target_simple() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.grads_and_curvs_target_simple"]], "guess_scattering_type_is_a_mixture_of_xray_and_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_is_a_mixture_of_xray_and_neutron"]], "guess_scattering_type_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_neutron"]], "hd_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.hd_selection"]], "intersection_of_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.intersection_of_scatterers"]], "is_positive_definite_u() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.is_positive_definite_u"]], "is_similar() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.is_similar"]], "make_scatterer_labels_shelx_compatible_in_place() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.make_scatterer_labels_shelx_compatible_in_place"]], "max_absolute() (cctbx.xray.structure.meaningful_site_cart_differences method)": [[238, "cctbx.xray.structure.meaningful_site_cart_differences.max_absolute"]], "max_distance() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.max_distance"]], "mean_distance() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.mean_distance"]], "mean_scattering_density() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.mean_scattering_density"]], "meaningful_site_cart_differences (class in cctbx.xray.structure)": 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"dxtbx.serialize.xds.to_xds.get_detector"]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_goniometer"]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_scan"]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_template"]], "imageset() (in module dxtbx.serialize.load)": [[258, "dxtbx.serialize.load.imageset"]], "to_crystal() (in module dxtbx.serialize.xds)": [[258, "dxtbx.serialize.xds.to_crystal"]], "to_imageset() (in module dxtbx.serialize.xds)": [[258, "dxtbx.serialize.xds.to_imageset"]], "to_xds (class in dxtbx.serialize.xds)": [[258, "dxtbx.serialize.xds.to_xds"]], "xds_detector_name() (in module dxtbx.serialize.xds)": [[258, "dxtbx.serialize.xds.xds_detector_name"]], "xparm_xds() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.xparm_xds"]], "add_column() (iotbx.cif.model.loop method)": [[264, 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(iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.copy"]], "copy() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.copy"]], "deepcopy() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.deepcopy"]], "deepcopy() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.deepcopy"]], "delete_row() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.delete_row"]], "error_count() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.error_count"]], "find_row() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.find_row"]], "get() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.get"]], "get_errors() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.get_errors"]], "iterrows() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.iterrows"]], "keys() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.keys"]], "keys() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.keys"]], "keys() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.keys"]], "loop (class in iotbx.cif.model)": [[264, "iotbx.cif.model.loop"]], "miller_arrays_as_cif_block (class in iotbx.cif)": [[264, "iotbx.cif.miller_arrays_as_cif_block"]], "model() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.model"]], "n_columns() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.n_columns"]], "n_rows() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.n_rows"]], "name() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.name"]], "order() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.order"]], "reader (class in iotbx.cif)": [[264, "iotbx.cif.reader"]], "save (class in iotbx.cif.model)": [[264, "iotbx.cif.model.save"]], "show() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.show"]], "show() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.show"]], "show() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.show"]], "show() (iotbx.cif.model.save method)": [[264, "iotbx.cif.model.save.show"]], "show_errors() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.show_errors"]], "size() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.size"]], "sort() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.sort"]], "sort() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.sort"]], "sort() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.sort"]], "update() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.update"]], "update_column() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.update_column"]], "validate() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.validate"]], "any_file() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file"]], "any_file_fast() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file_fast"]], "any_file_fast_input (class in iotbx.file_reader)": [[265, 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property)": [[265, "iotbx.file_reader.any_file_input.file_name"]], "file_object (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_object"]], "file_server (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_server"]], "file_type (iotbx.file_reader.any_file_input property)": [[265, "iotbx.file_reader.any_file_input.file_type"]], "find_closest_base_name() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.find_closest_base_name"]], "get_wildcard_string() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_string"]], "get_wildcard_strings() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_strings"]], "group_files (class in iotbx.file_reader)": [[265, "iotbx.file_reader.group_files"]], "guess_file_type() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.guess_file_type"]], "iotbx.file_reader": [[265, "module-iotbx.file_reader"]], "set_file_type() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.set_file_type"]], "show_summary() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.show_summary"]], "sort_by_file_type() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.sort_by_file_type"]], "splitext() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.splitext"]], "strip_shelx_format_extension() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.strip_shelx_format_extension"]], "try_all_types() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.try_all_types"]], "absolute_center_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.absolute_center_cart"]], "absolute_rt_info() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.absolute_rt_info"]], "add_crystal_symmetry_to_model_if_necessary() (iotbx.map_model_manager.map_model_manager method)": 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method)": [[266, "iotbx.map_model_manager.map_model_manager.add_model_by_id"]], "add_ncs_object() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.add_ncs_object"]], "add_to_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_to_info"]], "add_tuples_int() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.add_tuples_int"]], "apply_aniso_b_cart_to_f_array_info() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_aniso_b_cart_to_f_array_info"]], "apply_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_mask"]], "apply_mask_to_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_map"]], "apply_mask_to_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_maps"]], "apply_ncs_to_dv_results() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_ncs_to_dv_results"]], "apply_rt() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.apply_rt"]], "apply_spectral_scaling() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_spectral_scaling"]], "as_full_size_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.as_full_size_map"]], "as_map_model_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.as_map_model_manager"]], "as_map_model_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_map_model_manager"]], "as_map_model_manager() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.as_map_model_manager"]], "as_map_model_manager_with_resampled_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_map_model_manager_with_resampled_maps"]], "as_match_map_model_ncs() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.as_match_map_model_ncs"]], "binary_filter() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.binary_filter"]], "box_all_maps_around_density_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_density_and_shift_origin"]], "box_all_maps_around_mask_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_mask_and_shift_origin"]], "box_all_maps_around_model_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_model_and_shift_origin"]], "box_all_maps_around_unique_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_unique_and_shift_origin"]], "box_all_maps_with_bounds_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_with_bounds_and_shift_origin"]], "cart_to_grid_units() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cart_to_grid_units"]], "cc_to_other_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cc_to_other_map_manager"]], "check_model_and_set_to_match_map_if_necessary() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.check_model_and_set_to_match_map_if_necessary"]], "check_stop_file() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.check_stop_file"]], "choose_best_set() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.choose_best_set"]], "convert_tlso_group_info_to_lists() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.convert_tlso_group_info_to_lists"]], "counts() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.counts"]], "create_fine_spacing_array() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_fine_spacing_array"]], "create_map_manager_with_value_list() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_map_manager_with_value_list"]], "create_mask_around_atoms() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_atoms"]], "create_mask_around_atoms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_atoms"]], "create_mask_around_density() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_density"]], "create_mask_around_density() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_density"]], "create_mask_around_edges() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_edges"]], "create_mask_around_edges() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_edges"]], "create_mask_with_map_data() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_with_map_data"]], "create_masked_copies_of_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_masked_copies_of_maps"]], "create_spherical_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_spherical_mask"]], "crystal_symmetry() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.crystal_symmetry"]], "crystal_symmetry() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.crystal_symmetry"]], "customized_copy() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.customized_copy"]], "customized_copy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.customized_copy"]], "cutoff_values() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.cutoff_values"]], "deep_copy() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.deep_copy"]], "deep_copy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.deep_copy"]], "deep_copy() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.deep_copy"]], "delete_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.delete_mask"]], "density_at_model_sites() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.density_at_model_sites"]], "density_at_sites_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.density_at_sites_cart"]], "dummy_map_manager() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.dummy_map_manager"]], "duplicate_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.duplicate_id"]], "duplicate_map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.duplicate_map_manager"]], "expand_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.expand_mask"]], "experiment_type() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.experiment_type"]], "experiment_type() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.experiment_type"]], "external_origin_as_grid_units() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.external_origin_as_grid_units"]], "external_origin_is_compatible_with_gridding() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.external_origin_is_compatible_with_gridding"]], "external_sharpen() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.external_sharpen"]], "extract_all_maps_around_density() 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"iotbx.shelx.parsers.atom_parser.process_occupancies_depending_on_free_variable"]], "process_possible_constrained_occupancy() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.process_possible_constrained_occupancy"]], "process_possible_u_iso_constraints() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.process_possible_u_iso_constraints"]], "reader (class in iotbx.shelx.hklf)": [[271, "iotbx.shelx.hklf.reader"]], "residue_number (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.residue_number"]], "residue_number (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.residue_number"]], "residue_token (class in iotbx.shelx.tokens)": [[271, "iotbx.shelx.tokens.residue_token"]], "restraint_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.restraint_parser"]], "restraint_types (iotbx.shelx.parsers.restraint_parser attribute)": [[271, "iotbx.shelx.parsers.restraint_parser.restraint_types"]], "shelx_commands (iotbx.shelx.lexer.command_stream attribute)": [[271, "iotbx.shelx.lexer.command_stream.shelx_commands"]], "shelxd() (in module iotbx.shelx.write_ins)": [[271, "iotbx.shelx.write_ins.shelxd"]], "symm_space (iotbx.shelx.lexer.command_stream attribute)": [[271, "iotbx.shelx.lexer.command_stream.symm_space"]], "symmetry (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.symmetry"]], "variable_decoder (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.variable_decoder"]], "wavelength_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.wavelength_parser"]], "wavelengths() (iotbx.shelx.hklf.reader method)": [[271, "iotbx.shelx.hklf.reader.wavelengths"]], "as_miller_array() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.as_miller_array"]], "as_miller_arrays() (iotbx.xds.integrate_hkl.reader method)": [[272, "iotbx.xds.integrate_hkl.reader.as_miller_arrays"]], "as_miller_arrays() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.as_miller_arrays"]], "batch_as_miller_array() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.batch_as_miller_array"]], "column_index() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.column_index"]], "crystal_symmetry() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.crystal_symmetry"]], "find_version() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.find_version"]], "get_rhs() (in module iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.get_rhs"]], "iotbx.xds.integrate_hkl": [[272, "module-iotbx.xds.integrate_hkl"]], "iotbx.xds.read_ascii": [[272, "module-iotbx.xds.read_ascii"]], "iotbx.xds.spot_xds": [[272, "module-iotbx.xds.spot_xds"]], "iotbx.xds.xds_inp": [[272, "module-iotbx.xds.xds_inp"]], "iotbx.xds.xparm": [[272, "module-iotbx.xds.xparm"]], "is_integrate_hkl_file() (iotbx.xds.integrate_hkl.reader static method)": [[272, "iotbx.xds.integrate_hkl.reader.is_integrate_hkl_file"]], "is_xds_inp_file() (iotbx.xds.xds_inp.reader static method)": [[272, "iotbx.xds.xds_inp.reader.is_xds_inp_file"]], "is_xparm_file() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.is_xparm_file"]], "miller_set() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.miller_set"]], "parse_lines() (iotbx.xds.xds_inp.reader method)": [[272, "iotbx.xds.xds_inp.reader.parse_lines"]], "parse_version_1_tokens() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.parse_version_1_tokens"]], "parse_version_2_tokens() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.parse_version_2_tokens"]], "read_file() (iotbx.xds.integrate_hkl.reader method)": [[272, "iotbx.xds.integrate_hkl.reader.read_file"]], "read_file() (iotbx.xds.spot_xds.reader method)": [[272, "iotbx.xds.spot_xds.reader.read_file"]], "read_file() (iotbx.xds.xds_inp.reader method)": [[272, "iotbx.xds.xds_inp.reader.read_file"]], "read_file() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.read_file"]], "reader (class in iotbx.xds.integrate_hkl)": [[272, "iotbx.xds.integrate_hkl.reader"]], "reader (class in iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.reader"]], "reader (class in iotbx.xds.spot_xds)": [[272, "iotbx.xds.spot_xds.reader"]], "reader (class in iotbx.xds.xds_inp)": [[272, "iotbx.xds.xds_inp.reader"]], "reader (class in iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.reader"]], "show() (iotbx.xds.xparm.writer method)": [[272, "iotbx.xds.xparm.writer.show"]], "write() (in module iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.write"]], "write_file() (iotbx.xds.spot_xds.writer method)": [[272, "iotbx.xds.spot_xds.writer.write_file"]], "write_file() (iotbx.xds.xparm.writer method)": [[272, "iotbx.xds.xparm.writer.write_file"]], "writer (class in iotbx.xds.spot_xds)": [[272, "iotbx.xds.spot_xds.writer"]], "writer (class in iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.writer"]], "autotype (class in libtbx)": [[273, "libtbx.AutoType"]], "add_if_missing() (libtbx.group_args method)": [[273, "libtbx.group_args.add_if_missing"]], "adopt_init_args() (in module libtbx)": [[273, "libtbx.adopt_init_args"]], "adopt_optional_init_args() (in module libtbx)": [[273, "libtbx.adopt_optional_init_args"]], "copy() (libtbx.group_args method)": [[273, "libtbx.group_args.copy"]], "dict_with_default_0 (class in libtbx)": [[273, "libtbx.dict_with_default_0"]], "group_args (class in libtbx)": [[273, "libtbx.group_args"]], "libtbx": [[273, "module-libtbx"]], "merge() (libtbx.group_args method)": [[273, "libtbx.group_args.merge"]], "mutable (class in libtbx)": [[273, "libtbx.mutable"]], "slots_getstate_setstate (class in libtbx)": [[273, "libtbx.slots_getstate_setstate"]], "slots_getstate_setstate_default_initializer (class in libtbx)": [[273, "libtbx.slots_getstate_setstate_default_initializer"]], "unpicklable (class in libtbx)": [[273, "libtbx.unpicklable"]], "detect_problem() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.detect_problem"]], "enable_multiprocessing_if_possible() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.enable_multiprocessing_if_possible"]], "get_processes() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.get_processes"]], "parallel_map() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.parallel_map"]], "pool_map() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.pool_map"]], "programtemplate (class in libtbx.program_template)": [[275, "libtbx.program_template.ProgramTemplate"]], "__init__() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.__init__"]], "clean_up() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.clean_up"]], "custom_init() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.custom_init"]], "get_results() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.get_results"]], "run() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.run"]], "validate() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.validate"]], "dfc (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.DFC"]], "fc (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FC"]], "filled (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FILLED"]], "fo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FO"]], "mfo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.MFO"]], "anomalous (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous"]], "anomalous_residual (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous_residual"]], "create_target_functors() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.create_target_functors"]], "error() (mmtbx.map_names method)": [[276, "mmtbx.map_names.error"]], "f_obs_filled (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.f_obs_filled"]], "fmodel_neutron (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_neutron"]], "fmodel_neutron() (mmtbx.fmodels method)": [[276, "id0"]], "fmodel_xray (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_xray"]], "fmodel_xray() (mmtbx.fmodels method)": [[276, "id1"]], "fmodels (class in mmtbx)": [[276, "mmtbx.fmodels"]], "format() (mmtbx.map_names method)": [[276, "mmtbx.map_names.format"]], "k (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.k"]], "map_names (class in mmtbx)": [[276, "mmtbx.map_names"]], "ml_map (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.ml_map"]], "mmtbx": [[276, "module-mmtbx"]], "n (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.n"]], "neutron_refinement (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.neutron_refinement"]], "neutron_scattering_dict (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.neutron_scattering_dict"]], "phaser_sad_llg (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.phaser_sad_llg"]], "prepare_target_functors_for_minimization() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.prepare_target_functors_for_minimization"]], "pseudo_deep_copy() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.pseudo_deep_copy"]], "resolution_filter() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.resolution_filter"]], "show_comprehensive() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_comprehensive"]], "show_short() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_short"]], "show_targets() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.show_targets"]], "target_and_gradients() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_and_gradients"]], "target_functions_are_invariant_under_allowed_origin_shifts() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functions_are_invariant_under_allowed_origin_shifts"]], "target_functor_result_neutron() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functor_result_neutron"]], "target_functor_result_xray() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functor_result_xray"]], "update() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update"]], "update_all_scales() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update_all_scales"]], "update_xray_structure() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.update_xray_structure"]], "xray_scattering_dict (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.xray_scattering_dict"]], "align_model() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.align_model"]], "anneal() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.anneal"]], "apply_final() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.apply_final"]], "as_multi_model_hierarchy() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.as_multi_model_hierarchy"]], "atom_group_as_hierarchy() (in module mmtbx.building)": [[277, "mmtbx.building.atom_group_as_hierarchy"]], "atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_fofc_map_level"]], "atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_two_fofc_map_level"]], "atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_outside_density"]], "box_build_refine_base (class in mmtbx.building)": [[277, "mmtbx.building.box_build_refine_base"]], "cc_model_map() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.cc_model_map"]], "chain_id (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.chain_id"]], "conformation_scorer (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer"]], "correct_sequence() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.correct_sequence"]], "density_at_atom() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.density_at_atom"]], "ensembler (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.ensembler"]], "examine_model() (mmtbx.building.make_library.extract_related_models method)": [[277, "mmtbx.building.make_library.extract_related_models.examine_model"]], "extend_and_refine (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_and_refine"]], "extend_protein_model() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_protein_model"]], "extend_residue() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.extend_residue"]], "extract_and_superpose() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_and_superpose"]], "extract_iselection() (in module mmtbx.building)": [[277, "mmtbx.building.extract_iselection"]], "extract_peptide_fragments_by_sequence() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_peptide_fragments_by_sequence"]], "extract_related_models (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.extract_related_models"]], "fetch_similar_pdb_ids() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.fetch_similar_pdb_ids"]], "find_similar_chains() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.find_similar_chains"]], "fit_residue_in_box() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.fit_residue_in_box"]], "fraction_of_nearby_grid_points_above_cutoff() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.fraction_of_nearby_grid_points_above_cutoff"]], "generate_sidechain_clusters() (in module mmtbx.building)": [[277, "mmtbx.building.generate_sidechain_clusters"]], "geometry_minimization() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.geometry_minimization"]], "get_difference_maps() (in module mmtbx.building)": [[277, "mmtbx.building.get_difference_maps"]], "get_model_map_stats() (in module mmtbx.building)": [[277, "mmtbx.building.get_model_map_stats"]], "get_nearby_water_selection() (in module mmtbx.building)": [[277, "mmtbx.building.get_nearby_water_selection"]], "get_non_hydrogen_atom_indices() (in module mmtbx.building)": [[277, "mmtbx.building.get_non_hydrogen_atom_indices"]], "get_selected_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.get_selected_sites"]], "get_window_around_residue() (in module mmtbx.building)": [[277, "mmtbx.building.get_window_around_residue"]], "identity (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.identity"]], "is_stub_residue() (in module mmtbx.building)": [[277, "mmtbx.building.is_stub_residue"]], "iter_residue_groups() (in module mmtbx.building)": [[277, "mmtbx.building.iter_residue_groups"]], "join_hierarchies() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.join_hierarchies"]], "load_all_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_all_models_in_directory"]], "load_pdb_models() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_pdb_models"]], "load_related_models_from_pdb() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_from_pdb"]], "load_related_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_in_directory"]], "local_density_quality (class in mmtbx.building)": [[277, "mmtbx.building.local_density_quality"]], "max_fofc_value() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.max_fofc_value"]], "mean_density_at_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.mean_density_at_sites"]], "mmtbx.building": [[277, "module-mmtbx.building"]], "mmtbx.building.extend_sidechains": [[277, "module-mmtbx.building.extend_sidechains"]], "mmtbx.building.make_library": [[277, "module-mmtbx.building.make_library"]], "number_of_atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_below_fofc_map_level"]], "number_of_atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_below_two_fofc_map_level"]], "number_of_atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.number_of_atoms_outside_density"]], "only_residue() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.only_residue"]], "pdb_hierarchy (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.pdb_hierarchy"]], "prefilter (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.prefilter"]], "real_space_refine() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.real_space_refine"]], "realign() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.realign"]], "refit_residues() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.refit_residues"]], "related_chain (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.related_chain"]], "remove_sidechain_atoms() (in module mmtbx.building)": [[277, "mmtbx.building.remove_sidechain_atoms"]], "reprocess_pdb() (in module mmtbx.building)": [[277, "mmtbx.building.reprocess_pdb"]], "reset() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.reset"]], "residue_density_quality() (in module mmtbx.building)": [[277, "mmtbx.building.residue_density_quality"]], "residues_are_adjacent() (in module mmtbx.building)": [[277, "mmtbx.building.residues_are_adjacent"]], "restrain_atoms() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.restrain_atoms"]], "results() (mmtbx.building.make_library.extract_related_models method)": [[277, "mmtbx.building.make_library.extract_related_models.results"]], "run_real_space_annealing() (in module mmtbx.building)": [[277, "mmtbx.building.run_real_space_annealing"]], "selection_by_symmetry() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.selection_by_symmetry"]], "show_atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.show_atoms_outside_density"]], "show_chain_resseq_ranges() (in module mmtbx.building)": [[277, "mmtbx.building.show_chain_resseq_ranges"]], "source_info (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.source_info"]], "update() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.update"]], "update_coordinates() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_coordinates"]], "update_original_coordinates() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_original_coordinates"]], "update_sites_from_pdb_atoms() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.update_sites_from_pdb_atoms"]], "anisotropic_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.anisotropic_scaling"]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.apply_back_trace_of_overall_exp_scale_matrix"]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_back_trace_of_overall_exp_scale_matrix"]], "apply_overall_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_overall_scale"]], "b_cart() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.b_cart"]], "b_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.b_sols"]], "bulk_solvent_and_scales (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales"]], "bulk_solvent_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.bulk_solvent_scaling"]], "estimate_scale_k1() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.estimate_scale_k1"]], "format_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.format_scale_matrix"]], "format_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.format_scale_matrix"]], "get_k_total() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.get_k_total"]], "is_converged() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_converged"]], "is_flags_good() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_flags_good"]], "k_anisotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_anisotropic"]], "k_anisotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_anisotropic"]], "k_isotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_isotropic"]], "k_isotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_isotropic"]], "k_mask_grid_search() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_mask_grid_search"]], "k_masks() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_masks"]], "k_masks() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_masks"]], "k_sol_b_sol_b_cart_minimizer() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.k_sol_b_sol_b_cart_minimizer"]], "k_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_sols"]], "kb_range() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.kb_range"]], "ksol_bsol_result (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.ksol_bsol_result"]], "mmtbx.bulk_solvent": [[278, "module-mmtbx.bulk_solvent"]], "mmtbx.bulk_solvent.bulk_solvent_and_scaling": [[278, "module-mmtbx.bulk_solvent.bulk_solvent_and_scaling"]], "mmtbx.bulk_solvent.scaler": [[278, "module-mmtbx.bulk_solvent.scaler"]], "moving_average() (in module mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.moving_average"]], "overall_isotropic_kb_estimate() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.overall_isotropic_kb_estimate"]], "populate_bin_to_individual_k_mask_linear_interpolation() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.populate_bin_to_individual_k_mask_linear_interpolation"]], "r_all() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.r_all"]], "r_all() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_all"]], "r_factor() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.r_factor"]], "r_factor() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_factor"]], "r_work() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.r_work"]], "run (class in mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.run"]], "run_simple() (in module mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.run_simple"]], "set_k_isotropic_exp() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.set_k_isotropic_exp"]], "show() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.show"]], "smooth() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.smooth"]], "tmp (class in mmtbx.bulk_solvent.scaler)": [[278, "mmtbx.bulk_solvent.scaler.tmp"]], "try_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.try_scale"]], "u_star() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.u_star"]], "aligncablammeasures (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures"]], "capseudos() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.CApseudos"]], "copseudodihedrals() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.COpseudodihedrals"]], "findsimilarcablamregions (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions"]], "add_bond() (mmtbx.cablam.cablam_fingerprints.residue method)": [[279, "mmtbx.cablam.cablam_fingerprints.residue.add_bond"]], "add_probe_data() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.add_probe_data"]], "add_residue() (mmtbx.cablam.cablam_fingerprints.motif method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif.add_residue"]], "add_target_atom() (mmtbx.cablam.cablam_fingerprints.bond method)": [[279, "mmtbx.cablam.cablam_fingerprints.bond.add_target_atom"]], "add_to_instance() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.add_to_instance"]], "analyze_pdb() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb"]], "analyze_pdb_ca() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb_ca"]], "analyze_pdb_gui() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.analyze_pdb_gui"]], "assign_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.assign_sec_struc"]], "bond (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.bond"]], "build_superposition() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.build_superposition"]], "ca_measures() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.ca_measures"]], "cablam_align_wrapper() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.cablam_align_wrapper"]], "cablam_key() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.cablam_key"]], "cablam_measures() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.cablam_measures"]], "cablam_multicrit_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.cablam_multicrit_kin"]], "cablam_residues (class in mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.cablam_residues"]], "cablam_validation (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.cablam_validation"]], "check_for_motif() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.check_for_motif"]], "check_prolines() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.check_prolines"]], "check_protein() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.check_protein"]], "check_resname() (mmtbx.cablam.cablam_fingerprints.residue method)": [[279, "mmtbx.cablam.cablam_fingerprints.residue.check_resname"]], "condense_simple_aligned_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.condense_simple_aligned_regions"]], "consecutive() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.consecutive"]], "construct_linked_residues() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.construct_linked_residues"]], "cross() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.cross"]], "csv_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.csv_header"]], "csv_print() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.csv_print"]], "do_move() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.do_move"]], "dot() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.dot"]], "fail_cis_or_trans_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_cis_or_trans_check"]], "fail_forbidden_bond_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_forbidden_bond_check"]], "fail_index_match() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_index_match"]], "fail_required_bond_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_required_bond_check"]], "fail_residue_check() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fail_residue_check"]], "fails_cis_check() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.fails_cis_check"]], "fetch_ca_expectations() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_ca_expectations"]], "fetch_cis_trans_proline() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_cis_trans_proline"]], "fetch_fingerprints() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.fetch_fingerprints"]], "fetch_motifs() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_motifs"]], "fetch_peptide_expectations() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.fetch_peptide_expectations"]], "find_all_residue_stats() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_all_residue_stats"]], "find_ca_outliers() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_ca_outliers"]], "find_partial_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_partial_sec_struc"]], "find_peptide_outliers() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_peptide_outliers"]], "find_whole_sec_struc() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.find_whole_sec_struc"]], "firstalt() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.firstalt"]], "get_all_labels() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.get_all_labels"]], "get_chain_selection() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.get_chain_selection"]], "get_continuous_segments() (mmtbx.cablam.cablam_align.cablam_residues method)": [[279, "mmtbx.cablam.cablam_align.cablam_residues.get_continuous_segments"]], "get_measures() (mmtbx.cablam.cablam_align.findsimilarcablamregions method)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions.get_measures"]], "getatomxyz() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.getatomxyz"]], "give_ca_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_ca_kin"]], "give_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_kin"]], "give_points() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_points"]], "give_text() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.give_text"]], "has_all_measures() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.has_all_measures"]], "helix_or_sheet() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.helix_or_sheet"]], "helix_or_sheet_res() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.helix_or_sheet_res"]], "id_to_str() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.id_to_str"]], "id_with_resname() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.id_with_resname"]], "interpretation() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.interpretation"]], "is_complete() (mmtbx.cablam.cablam_fingerprints.motif_instance method)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance.is_complete"]], "kin_frame() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_frame"]], "kin_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_header"]], "kin_print() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print"]], "kin_print_by_instance() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_by_instance"]], "kin_print_by_instance_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_by_instance_header"]], "kin_print_probe() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe"]], "kin_print_probe_annote() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe_annote"]], "kin_print_probe_header() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.kin_print_probe_header"]], "linked_residue (class in mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.linked_residue"]], "make_pickle() (in module mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.make_pickle"]], "make_probe_data() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.make_probe_data"]], "mmtbx.cablam": [[279, "module-mmtbx.cablam"]], "mmtbx.cablam.cablam_align": [[279, "module-mmtbx.cablam.cablam_align"]], "mmtbx.cablam.cablam_fingerprints": [[279, "module-mmtbx.cablam.cablam_fingerprints"]], "mmtbx.cablam.cablam_math": [[279, "module-mmtbx.cablam.cablam_math"]], "mmtbx.cablam.cablam_res": [[279, "module-mmtbx.cablam.cablam_res"]], "mmtbx.cablam.cablam_training": [[279, "module-mmtbx.cablam.cablam_training"]], "mmtbx.cablam.cablam_validate": [[279, "module-mmtbx.cablam.cablam_validate"]], "motif (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.motif"]], "motif_chunk (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk"]], "motif_guess (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_guess"]], "motif_instance (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.motif_instance"]], "motif_value (class in mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.motif_value"]], "mp_id() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.mp_id"]], "not_enough_pdbs() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.not_enough_pdbs"]], "old_kin_print_probe_annote() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.old_kin_print_probe_annote"]], "omegacalc() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.omegacalc"]], "oneline() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.oneline"]], "oneline_header() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.oneline_header"]], "perpdist() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.perpdist"]], "perptersect() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.perptersect"]], "phipsi() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.phipsi"]], "print_aligned_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_aligned_regions"]], "print_cablam_markup_kin() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_cablam_markup_kin"]], "print_helix_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_helix_record"]], "print_helix_sheet_records() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_helix_sheet_records"]], "print_pdb_with_new_helix_sheet_records() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.print_pdb_with_new_helix_sheet_records"]], "print_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_record"]], "print_region() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_region"]], "print_sheet_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_sheet_record"]], "print_simple_similar_regions() (mmtbx.cablam.cablam_align.aligncablammeasures method)": [[279, "mmtbx.cablam.cablam_align.AlignCablamMeasures.print_simple_similar_regions"]], "print_threeten_record() (mmtbx.cablam.cablam_validate.motif_chunk method)": [[279, "mmtbx.cablam.cablam_validate.motif_chunk.print_threeten_record"]], "printtocsv() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.printtocsv"]], "printtokin() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.printtokin"]], "prune_alts() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.prune_alts"]], "prunerestype() (in module mmtbx.cablam.cablam_res)": [[279, "mmtbx.cablam.cablam_res.prunerestype"]], "removelinks() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.removelinks"]], "res_seq_by_instance() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.res_seq_by_instance"]], "residue (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.residue"]], "run() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.run"]], "run() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.run"]], "run() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.run"]], "seq_dist() (mmtbx.cablam.cablam_res.linked_residue method)": [[279, "mmtbx.cablam.cablam_res.linked_residue.seq_dist"]], "setup() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.setup"]], "simple_align_measures() (mmtbx.cablam.cablam_align.findsimilarcablamregions method)": [[279, "mmtbx.cablam.cablam_align.FindSimilarCablamRegions.simple_align_measures"]], "skipcheck() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.skipcheck"]], "stripb() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.stripB"]], "target_atom (class in mmtbx.cablam.cablam_fingerprints)": [[279, "mmtbx.cablam.cablam_fingerprints.target_atom"]], "taucalc() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.taucalc"]], "trim_motifs() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.trim_motifs"]], "usage() (in module mmtbx.cablam.cablam_align)": [[279, "mmtbx.cablam.cablam_align.usage"]], "usage() (in module mmtbx.cablam.cablam_training)": [[279, "mmtbx.cablam.cablam_training.usage"]], "usage() (in module mmtbx.cablam.cablam_validate)": [[279, "mmtbx.cablam.cablam_validate.usage"]], "veclen() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.veclen"]], "vectorize() (in module mmtbx.cablam.cablam_math)": [[279, "mmtbx.cablam.cablam_math.vectorize"]], "mmtbx.cablam.fingerprints": [[280, "module-mmtbx.cablam.fingerprints"]], "mmtbx.cablam.fingerprints.antiparallel_beta": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta"]], "mmtbx.cablam.fingerprints.antiparallel_beta_bridge": [[280, "module-mmtbx.cablam.fingerprints.antiparallel_beta_bridge"]], "mmtbx.cablam.fingerprints.how_to": [[280, "module-mmtbx.cablam.fingerprints.how_to"]], "mmtbx.cablam.fingerprints.parallel_beta": [[280, "module-mmtbx.cablam.fingerprints.parallel_beta"]], "mmtbx.cablam.fingerprints.regular_helix_definitions": [[280, "module-mmtbx.cablam.fingerprints.regular_helix_definitions"]], "empty (class in mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.empty"]], "find_data_dir() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.find_data_dir"]], "generate_chemical_components_codes() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.generate_chemical_components_codes"]], "get_alternative_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_alternative_name"]], "get_atom_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_names"]], "get_atom_type_symbol() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_type_symbol"]], "get_bond_pairs() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_bond_pairs"]], "get_cif_dictionary() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_dictionary"]], "get_cif_filename() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_filename"]], "get_field_simple() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_field_simple"]], "get_func() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_func"]], "get_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_group"]], "get_header() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_header"]], "get_hydrogen_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_hydrogen_names"]], "get_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_name"]], "get_restraints_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_restraints_group"]], "get_smiles() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_smiles"]], "get_type() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_type"]], "get_typed_field() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_typed_field"]], "is_code() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_code"]], "is_residue_specified() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_residue_specified"]], "mmtbx.chemical_components": [[281, "module-mmtbx.chemical_components"]], "mmtbx.chemical_components.cif_parser": [[281, "module-mmtbx.chemical_components.cif_parser"]], "run() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.run"]], "run2() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.run2"]], "smart_split_cif_line() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.smart_split_cif_line"]], "args (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.args"]], "check_files() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.check_files"]], "cif_file_names (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_file_names"]], "cif_objects (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_objects"]], "create_model_manager() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.create_model_manager"]], "crystal_symmetry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.crystal_symmetry"]], "f_obs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.f_obs"]], "fmodel (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.fmodel"]], "generate_master_phil_with_inputs() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generate_master_phil_with_inputs"]], "generic_simple_input_phil() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generic_simple_input_phil"]], "geometry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.geometry"]], "hl_coeffs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.hl_coeffs"]], "intensity_flag (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.intensity_flag"]], "load_and_validate_unmerged_data() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.load_and_validate_unmerged_data"]], "load_model_and_data (class in mmtbx.command_line)": [[282, "mmtbx.command_line.load_model_and_data"]], "log (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.log"]], "master_phil (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.master_phil"]], "miller_arrays (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.miller_arrays"]], "mmtbx.command_line": [[282, "module-mmtbx.command_line"]], "params (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.params"]], "pdb_file_names (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_file_names"]], "pdb_hierarchy (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_hierarchy"]], "pdb_inp (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.pdb_inp"]], "processed_pdb_file (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.processed_pdb_file"]], "r_free_flags (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.r_free_flags"]], "raw_data (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_data"]], "raw_flags (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_flags"]], "save_data_mtz() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.save_data_mtz"]], "sequence (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.sequence"]], "show_symmetry_error() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.show_symmetry_error"]], "start_log_file() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.start_log_file"]], "test_flag_value (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.test_flag_value"]], "unknown_residues_error_message (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unknown_residues_error_message"]], "unknown_residues_flag (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unknown_residues_flag"]], "unmerged_i_obs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.unmerged_i_obs"]], "validate_input_params() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.validate_input_params"]], "working_phil (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.working_phil"]], "xray_structure (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.xray_structure"]], "bond_angle_registry (class in mmtbx.conformation_dependent_library.bond_angle_registry)": [[283, "mmtbx.conformation_dependent_library.bond_angle_registry.bond_angle_registry"]], "convert_dict_to_excel() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_excel"]], "convert_dict_to_gnuplot() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_gnuplot"]], "convert_dict_to_kin2dcont() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_kin2Dcont"]], "convert_dict_to_scilab() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_scilab"]], "custom_cdl_dict (class in mmtbx.conformation_dependent_library.cdl_database)": [[283, "mmtbx.conformation_dependent_library.cdl_database.custom_cdl_dict"]], "generate_dna_rna_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_dna_rna_fragments"]], "generate_protein_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_fragments"]], "generate_protein_threes() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_threes"]], "generate_protein_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_tuples"]], "generate_residue_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_residue_tuples"]], "get_db_result() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_db_result"]], "get_grid_values() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_grid_values"]], "get_index() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_index"]], "get_managers() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_managers"]], "get_min_max_table() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_min_max_table"]], "get_rdl_database() (in module mmtbx.conformation_dependent_library.rdl_database)": [[283, "mmtbx.conformation_dependent_library.rdl_database.get_rdl_database"]], "get_restraint_values() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.get_restraint_values"]], "interpolate_2d() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_2d"]], "interpolate_at_point() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_at_point"]], "mmtbx.conformation_dependent_library": [[283, "module-mmtbx.conformation_dependent_library"]], "mmtbx.conformation_dependent_library.altloc_weighting": [[283, "module-mmtbx.conformation_dependent_library.altloc_weighting"]], "mmtbx.conformation_dependent_library.bond_angle_registry": [[283, "module-mmtbx.conformation_dependent_library.bond_angle_registry"]], "mmtbx.conformation_dependent_library.cdl_database": [[283, "module-mmtbx.conformation_dependent_library.cdl_database"]], "mmtbx.conformation_dependent_library.rdl_database": [[283, "module-mmtbx.conformation_dependent_library.rdl_database"]], "mmtbx.conformation_dependent_library.tst_cdl": [[283, "module-mmtbx.conformation_dependent_library.tst_cdl"]], "mmtbx.conformation_dependent_library.utils": [[283, "module-mmtbx.conformation_dependent_library.utils"]], "print_grid() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.print_grid"]], "restraints_show() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.restraints_show"]], "round_to_ten() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.round_to_ten"]], "run() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.run"]], "run() (in module mmtbx.conformation_dependent_library.altloc_weighting)": [[283, "mmtbx.conformation_dependent_library.altloc_weighting.run"]], "run() (in module mmtbx.conformation_dependent_library.cdl_database)": [[283, "mmtbx.conformation_dependent_library.cdl_database.run"]], "run() (in module mmtbx.conformation_dependent_library.rdl_database)": [[283, "mmtbx.conformation_dependent_library.rdl_database.run"]], "run() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.run"]], "run_apply() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.run_apply"]], "test_average() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_average"]], "test_cdl_lookup() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cdl_lookup"]], "test_cis_trans_peptide() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cis_trans_peptide"]], "test_phi_psi_key() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_phi_psi_key"]], "test_res_type() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_res_type"]], "test_threes_methods() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_threes_methods"]], "update_restraints() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.update_restraints"]], "update_restraints() (in module mmtbx.conformation_dependent_library.altloc_weighting)": [[283, "mmtbx.conformation_dependent_library.altloc_weighting.update_restraints"]], "adp_refinement() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.adp_refinement"]], "build_den_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_proxies"]], "build_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_restraints"]], "bulk_solvent_and_scale() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.bulk_solvent_and_scale"]], "check_den_pair_consistency() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.check_den_pair_consistency"]], "count_atoms_per_chain() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.count_atoms_per_chain"]], "den_restraints (class in mmtbx.den)": [[284, "mmtbx.den.den_restraints"]], "distance_squared() (in module mmtbx.den)": [[284, "mmtbx.den.distance_squared"]], "dump_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.dump_den_network"]], "exercise() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.exercise"]], "find_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.find_atom_pairs"]], "get_current_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_current_eq_distances"]], "get_den_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_den_atom_pairs"]], "get_n_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_n_proxies"]], "get_optimization_grid() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_optimization_grid"]], "get_selection_strings() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_selection_strings"]], "import_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.import_eq_distances"]], "load_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.load_den_network"]], "manager (class in mmtbx.den.refinement)": [[284, "mmtbx.den.refinement.manager"]], "minimize() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.minimize"]], "mmtbx.den": [[284, "module-mmtbx.den"]], "mmtbx.den.plot_weights": [[284, "module-mmtbx.den.plot_weights"]], "mmtbx.den.refinement": [[284, "module-mmtbx.den.refinement"]], "output_kinemage() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.output_kinemage"]], "plot_weights_pyplot() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.plot_weights_pyplot"]], "proxy_select() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.proxy_select"]], "remove_non_matching_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.remove_non_matching_pairs"]], "select_random_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.select_random_den_restraints"]], "show_den_opt_summary_cartesian() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.show_den_opt_summary_cartesian"]], "show_den_opt_summary_torsion() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.show_den_opt_summary_torsion"]], "show_den_summary() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.show_den_summary"]], "target_and_gradients() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.target_and_gradients"]], "try_den_weight_cartesian() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.try_den_weight_cartesian"]], "try_den_weight_torsion() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.try_den_weight_torsion"]], "update_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.update_eq_distances"]], "active_indices (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.active_indices"]], "add_cycle() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.add_cycle"]], "anisotropic_correction() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.anisotropic_correction"]], "calculate_solvent_mask() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.calculate_solvent_mask"]], "compute_map() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_map"]], "compute_map_coefficients() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_map_coefficients"]], "compute_phase_source() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_phase_source"]], "d_min (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.d_min"]], "density_modification (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.density_modification"]], "density_truncation() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.density_truncation"]], "dm_stats (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.dm_stats"]], "extract_loggraph() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.extract_loggraph"]], "f_obs_active (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.f_obs_active"]], "format_summary() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.format_summary"]], "get_cycle_stats() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_cycle_stats"]], "get_fom_for_plot() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_fom_for_plot"]], "get_stats() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.get_stats"]], "histogram() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.histogram"]], "hl_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.hl_coeffs_in_original_setting"]], "local_standard_deviation_map (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.local_standard_deviation_map"]], "map_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.map_coeffs_in_original_setting"]], "mask() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.mask"]], "matthews_analysis() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.matthews_analysis"]], "miller_array_in_original_setting() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.miller_array_in_original_setting"]], "mmtbx.density_modification": [[285, "module-mmtbx.density_modification"]], "ncs_averaging() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.ncs_averaging"]], "next_cycle() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.next_cycle"]], "radius (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.radius"]], "rms() (in module mmtbx.density_modification)": [[285, "mmtbx.density_modification.rms"]], "show_cycle_summary() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.show_cycle_summary"]], "solvent_adjust() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_adjust"]], "solvent_flattening() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flattening"]], "solvent_flipping() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flipping"]], "start_and_end_fom() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.start_and_end_fom"]], "alternate_conformations_as_multiple_models() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.alternate_conformations_as_multiple_models"]], "altloc (mmtbx.disorder.analyze_model.atom_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.altloc"]], "append_residue_group() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.append_residue_group"]], "atom_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy"]], "atom_groups() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.atom_groups"]], "atoms() (mmtbx.disorder.analyze_model.atom_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.atoms"]], "atoms_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy"]], "backrub_angle (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.backrub_angle"]], "backrub_residue (class in mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.backrub_residue"]], "carbonyl_oxygen_angle() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.carbonyl_oxygen_angle"]], "circ_len() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_len"]], "circ_mean() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_mean"]], "circ_stddev() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_stddev"]], "detect_sequence_disorder() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.detect_sequence_disorder"]], "disordered_segment (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.disordered_segment"]], "evaluate_backrub_pair_impl() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.evaluate_backrub_pair_impl"]], "extract_b() (mmtbx.disorder.analyze_model.atoms_proxy method)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy.extract_b"]], "extract_backrub_residue_groups() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.extract_backrub_residue_groups"]], "extract_occ() (mmtbx.disorder.analyze_model.atoms_proxy method)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy.extract_occ"]], "extract_validation_results() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.extract_validation_results"]], "find_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_backrubs"]], "find_ensemble_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_ensemble_backrubs"]], "find_peptide_flips() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.find_peptide_flips"]], "get_all_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_all_conformer_distances"]], "get_calphas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_calphas"]], "get_cbetas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_cbetas"]], "get_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_conformer_distances"]], "get_nconfs() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.get_nconfs"]], "get_previous_conformer() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_previous_conformer"]], "i_mod (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.i_mod"]], "icode (mmtbx.disorder.analyze_model.residue_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.icode"]], "id_str (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.id_str"]], "id_str() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.id_str"]], "is_joined_at_calpha() (in module mmtbx.disorder.analyze_model)": [[286, 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"mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_rmsd_between_conformers"]], "minimum_atom_group_occupancy() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.minimum_atom_group_occupancy"]], "mmtbx.disorder": [[286, "module-mmtbx.disorder"]], "mmtbx.disorder.analyze_model": [[286, "module-mmtbx.disorder.analyze_model"]], "mmtbx.disorder.backbone": [[286, "module-mmtbx.disorder.backbone"]], "n_cbeta_outliers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_cbeta_outliers"]], "n_confs() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_confs"]], "n_confs_max() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_confs_max"]], "n_outliers_of_type() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_outliers_of_type"]], "n_partial_splits() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_partial_splits"]], "n_residues() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_residues"]], "n_rotamer_changes() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.n_rotamer_changes"]], "only_amide_hydrogen_split() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.only_amide_hydrogen_split"]], "process_pdb_hierarchy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy"]], "process_residue_groups (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.process_residue_groups"]], "residue_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy"]], "resname (mmtbx.disorder.analyze_model.atom_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.resname"]], "resseq (mmtbx.disorder.analyze_model.residue_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.resseq"]], "rmsd (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.rmsd"]], "segments (mmtbx.disorder.analyze_model.process_pdb_hierarchy property)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.segments"]], "set_ensemble_b_factors_to_xyz_displacement() (in module mmtbx.disorder)": [[286, "mmtbx.disorder.set_ensemble_b_factors_to_xyz_displacement"]], "show() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.show"]], "show() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.show"]], "show() (mmtbx.disorder.analyze_model.process_residue_groups method)": [[286, "mmtbx.disorder.analyze_model.process_residue_groups.show"]], "show() (mmtbx.disorder.backbone.backrub_residue method)": [[286, "mmtbx.disorder.backbone.backrub_residue.show"]], "xyz (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.xyz"]], "accelerations() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.accelerations"]], "accelerations() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.accelerations"]], "cartesian_dynamics (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics"]], "center_of_mass_info() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.center_of_mass_info"]], "center_of_mass_info() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.center_of_mass_info"]], "compute_functional_and_gradients() (mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization method)": [[287, "mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization method)": [[287, "mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization.compute_functional_and_gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints.gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple.gradients"]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space.gradients"]], "gradients_calculator() (mmtbx.dynamics.simulated_annealing.run method)": [[287, "mmtbx.dynamics.simulated_annealing.run.gradients_calculator"]], "gradients_calculator_geometry_restraints (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints"]], "gradients_calculator_real_space_simple (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple"]], "gradients_calculator_reciprocal_space (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space"]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization"]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization"]], "interleaved_minimization() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.interleaved_minimization"]], "kinetic_energy_and_temperature (class in mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_and_temperature"]], "kinetic_energy_as_temperature() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_as_temperature"]], "manager() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.manager"]], "master_params() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.master_params"]], "mmtbx.dynamics": [[287, "module-mmtbx.dynamics"]], "mmtbx.dynamics.cartesian_dynamics": [[287, "module-mmtbx.dynamics.cartesian_dynamics"]], "mmtbx.dynamics.constants": [[287, "module-mmtbx.dynamics.constants"]], "mmtbx.dynamics.ensemble_cd": [[287, "module-mmtbx.dynamics.ensemble_cd"]], "mmtbx.dynamics.simulated_annealing": [[287, "module-mmtbx.dynamics.simulated_annealing"]], "print_detailed_dynamics_stats() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.print_detailed_dynamics_stats"]], "print_dynamics_stat() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.print_dynamics_stat"]], "random_velocities() (in module mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.random_velocities"]], "random_velocities() (in module mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.random_velocities"]], "run (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.run"]], "run (class in mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.run"]], "run_interleaved_minimization() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.run_interleaved_minimization"]], "set_velocities() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.set_velocities"]], "set_velocities() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.set_velocities"]], "show() (mmtbx.dynamics.simulated_annealing.run method)": [[287, "mmtbx.dynamics.simulated_annealing.run.show"]], "stop_global_motion() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.stop_global_motion"]], "stop_global_motion() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.stop_global_motion"]], "store_temperatures() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.store_temperatures"]], "temperature_as_kinetic_energy() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.temperature_as_kinetic_energy"]], "velocity_rescaling() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.velocity_rescaling"]], "velocity_rescaling() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.velocity_rescaling"]], "verlet_leapfrog_integration() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.verlet_leapfrog_integration"]], "verlet_leapfrog_integration() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.verlet_leapfrog_integration"]], "xray_grads() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.xray_grads"]], "mmtbx.f_model": [[288, "module-mmtbx.f_model"]], "mmtbx.f_model_info": [[288, "module-mmtbx.f_model_info"]], "asucontent (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ASUContent"]], "accessiblesurfaceareas (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas"]], "accessiblesurfaceresult (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceResult"]], "aggregator (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Aggregator"]], "alternate (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Alternate"]], "atom (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Atom"]], "atomdescriptor (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.AtomDescriptor"]], "case (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.Case"]], "clashcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCalculation"]], "clashcollection (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCollection"]], "clashcountcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCountCalculation"]], "clashpoint (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashPoint"]], "clashingpair (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashingPair"]], "compositecheckerbuilder (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.CompositeCheckerBuilder"]], "compound (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Compound"]], "description (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Description"]], "distancecalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.DistanceCalculation"]], "elementaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ElementAccumulator"]], "empty() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Empty"]], "greedymatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.GreedyMatch"]], "indexer (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Indexer"]], "inserter (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Inserter"]], "mcgregormatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.McGregorMatch"]], "model (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.Model"]], "molecule (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Molecule"]], "rascalmatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.RascalMatch"]], "reducingaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ReducingAccumulator"]], "separatecheckerbuilder (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder"]], "spheremodel (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModel"]], "spheremodelgroup (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModelGroup"]], "symmetryequivalent (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent"]], "accept() (mmtbx.geometry.altloc.description method)": [[289, "mmtbx.geometry.altloc.Description.accept"]], "add() (mmtbx.geometry.altloc.indexer method)": [[289, "mmtbx.geometry.altloc.Indexer.add"]], "add() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.add"]], "add() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.add"]], "add_atom() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_atom"]], "add_atoms_in() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.add_atoms_in"]], "add_bond() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_bond"]], "altid_for() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.altid_for"]], "altloc_averaged_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.altloc_averaged_calculation"]], "altloc_strategy_from_atom() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.altloc_strategy_from_atom"]], "append_neighbours() (mmtbx.geometry.asa.separatecheckerbuilder static method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.append_neighbours"]], "areas (mmtbx.geometry.asa.accessiblesurfaceareas property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas.areas"]], "asu_mapping_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.asu_mapping_for"]], "atom (mmtbx.geometry.clash.atomdescriptor property)": [[289, "mmtbx.geometry.clash.AtomDescriptor.atom"]], "atom_for (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atom_for"]], "atom_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.atom_group"]], "atom_pair() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.atom_pair"]], "atoms (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atoms"]], "atoms (mmtbx.geometry.topology.molecule property)": [[289, "mmtbx.geometry.topology.Molecule.atoms"]], "atoms() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.atoms"]], "bonds (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.bonds"]], "calculate() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.calculate"]], "calculate() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.calculate"]], "calculate_base_for_coordinates() (in module mmtbx.geometry.shared_types)": [[289, "mmtbx.geometry.shared_types.calculate_base_for_coordinates"]], "calculate_contents() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.calculate_contents"]], "chain (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.chain"]], "clashing_with() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.clashing_with"]], "composite_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.composite_distance_predicate"]], "composite_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.composite_predicate"]], "connected_segment_from() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segment_from"]], "connected_segments() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segments"]], "containment_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.containment_predicate"]], "coordinate_adaptor() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.coordinate_adaptor"]], "coordinate_of() (mmtbx.geometry.indexing.structure_indexer static method)": [[289, "mmtbx.geometry.indexing.structure_indexer.coordinate_of"]], "count() (mmtbx.geometry.clash.clashpoint method)": [[289, "mmtbx.geometry.clash.ClashPoint.count"]], "count() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.count"]], "count() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.count"]], "create() (mmtbx.geometry.clash.case class method)": [[289, "mmtbx.geometry.clash.Case.create"]], "create() (mmtbx.geometry.topology.compound class method)": [[289, "mmtbx.geometry.topology.Compound.create"]], "create_and_populate_indexer() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_and_populate_indexer"]], "create_description() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_description"]], "data_of() (mmtbx.geometry.indexing.structure_indexer static method)": [[289, "mmtbx.geometry.indexing.structure_indexer.data_of"]], "descriptor_for (mmtbx.geometry.topology.molecule property)": [[289, "mmtbx.geometry.topology.Molecule.descriptor_for"]], "descriptor_for() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.descriptor_for"]], "descriptors (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.descriptors"]], "descriptors() (mmtbx.geometry.clash.spheremodel method)": [[289, "mmtbx.geometry.clash.SphereModel.descriptors"]], "direct() (in module mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.direct"]], "distances_from() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.distances_from"]], "element_of() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.element_of"]], "elements() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.elements"]], "entities (mmtbx.geometry.altloc.aggregator property)": [[289, "mmtbx.geometry.altloc.Aggregator.entities"]], "exclude() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclude"]], "exclude_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.exclude_predicate"]], "exclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclusion"]], "filter() (in module mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.filter"]], "from_structure() (mmtbx.geometry.topology.compound class method)": [[289, "mmtbx.geometry.topology.Compound.from_structure"]], "frozenset() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.frozenset"]], "get_hash_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_hash_indexer_for"]], "get_linear_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_linear_indexer_for"]], "get_optimal_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_optimal_indexer_for"]], "get_voxelizer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_voxelizer_for"]], "group() (mmtbx.geometry.clash.spheremodelgroup method)": [[289, "mmtbx.geometry.clash.SphereModelGroup.group"]], "hash() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.hash"]], "hash_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.hash_indexer_for"]], "identity() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.identity"]], "identity_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.identity_predicate"]], "identity_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.identity_predicate"]], "include() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.include"]], "include_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.include_predicate"]], "inclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.inclusion"]], "interaction_counts_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_counts_with"]], "interaction_ranges_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_ranges_with"]], "interactions_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interactions_with"]], "is_self_clash() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.is_self_clash"]], "length() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.length"]], "length() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.length"]], "length() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.length"]], "linear_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.linear_indexer_for"]], "mmtbx.geometry": [[289, "module-mmtbx.geometry"]], "mmtbx.geometry.altloc": [[289, "module-mmtbx.geometry.altloc"]], "mmtbx.geometry.asa": [[289, "module-mmtbx.geometry.asa"]], "mmtbx.geometry.clash": [[289, "module-mmtbx.geometry.clash"]], "mmtbx.geometry.indexing": [[289, "module-mmtbx.geometry.indexing"]], "mmtbx.geometry.shared_types": [[289, "module-mmtbx.geometry.shared_types"]], "mmtbx.geometry.sphere_surface_sampling": [[289, "module-mmtbx.geometry.sphere_surface_sampling"]], "mmtbx.geometry.topology": [[289, "module-mmtbx.geometry.topology"]], "molecule (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.molecule"]], "overlap_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.overlap_predicate"]], "overlap_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.overlap_predicate"]], "pairs() (mmtbx.geometry.clash.clashcollection method)": [[289, "mmtbx.geometry.clash.ClashCollection.pairs"]], "pairs() (mmtbx.geometry.clash.clashpoint method)": [[289, "mmtbx.geometry.clash.ClashPoint.pairs"]], "points (mmtbx.geometry.asa.accessiblesurfaceareas property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas.points"]], "process_altloc() (mmtbx.geometry.altloc.aggregator method)": [[289, "mmtbx.geometry.altloc.Aggregator.process_altloc"]], "process_altloc() (mmtbx.geometry.altloc.inserter method)": [[289, "mmtbx.geometry.altloc.Inserter.process_altloc"]], "process_altloc() (mmtbx.geometry.asa.separatecheckerbuilder method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.process_altloc"]], "process_regular() (mmtbx.geometry.altloc.aggregator method)": [[289, "mmtbx.geometry.altloc.Aggregator.process_regular"]], "process_regular() (mmtbx.geometry.altloc.inserter method)": [[289, "mmtbx.geometry.altloc.Inserter.process_regular"]], "process_regular() (mmtbx.geometry.asa.separatecheckerbuilder method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.process_regular"]], "radius_adaptor() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.radius_adaptor"]], "radius_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.radius_for"]], "remapped() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.remapped"]], "remapped() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.remapped"]], "remapped() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.remapped"]], "residue_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.residue_group"]], "root (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.root"]], "simple_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.simple_distance_predicate"]], "simple_surface_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.simple_surface_calculation"]], "size() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.size"]], "sphere_model_group_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.sphere_model_group_for"]], "structure_indexer (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.structure_indexer"]], "subset() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.subset"]], "surface (mmtbx.geometry.asa.accessiblesurfaceresult property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceResult.surface"]], "to_xray_structure() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.to_xray_structure"]], "voxelizer() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.voxelizer"]], "add_coordinate_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.add_coordinate_restraints"]], "append_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley8k_proxies"]], "append_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley_proxies"]], "append_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_oldfield_proxies"]], "append_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_phi_psi_2_proxies"]], "exclude_outliers_from_reference_restraints_selection() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.exclude_outliers_from_reference_restraints_selection"]], "extract_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.extract_proxies"]], "generate_torsion_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.generate_torsion_restraints"]], "get_c_beta_torsion_proxies() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_c_beta_torsion_proxies"]], "get_cb_target_angle_pair() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_cb_target_angle_pair"]], "get_n_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley8k_proxies"]], "get_n_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley_proxies"]], "get_n_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_oldfield_proxies"]], "get_n_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_phi_psi_2_proxies"]], "get_n_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_proxies"]], "get_selection_to_sites_map() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.get_selection_to_sites_map"]], "is_proxy_present() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.is_proxy_present"]], "is_schrodinger_installed() (in module mmtbx.geometry_restraints.external)": [[290, "mmtbx.geometry_restraints.external.is_schrodinger_installed"]], "load_emsley8k_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_emsley8k_tables"]], "load_phi_psi_2_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_phi_psi_2_tables"]], "load_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_tables"]], "mmtbx.geometry_restraints": [[290, "module-mmtbx.geometry_restraints"]], "mmtbx.geometry_restraints.c_beta": [[290, "module-mmtbx.geometry_restraints.c_beta"]], "mmtbx.geometry_restraints.external": [[290, "module-mmtbx.geometry_restraints.external"]], "mmtbx.geometry_restraints.ramachandran": [[290, "module-mmtbx.geometry_restraints.ramachandran"]], "mmtbx.geometry_restraints.reference": [[290, "module-mmtbx.geometry_restraints.reference"]], "proxy_select() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.proxy_select"]], "ramachandran_manager (class in mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager"]], "ramachandran_plot_data (class in mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data"]], "select_good() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.select_good"]], "show_sorted() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.show_sorted"]], "split_array() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.split_array"]], "target_and_gradients() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.target_and_gradients"]], "update_phi_psi_targets() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.update_phi_psi_targets"]], "update_phi_psi_targets_on_init() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.update_phi_psi_targets_on_init"]], "add_arg_like_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_arg_like_h"]], "add_ca_ha1_and_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_and_ha2"]], "add_ca_ha1_or_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_or_ha2"]], "add_hhh() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_hhh"]], "add_ring_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ring_h"]], "all_master_params() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.all_master_params"]], "assert_water_is_consistent() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.assert_water_is_consistent"]], "atom_as_str() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_as_str"]], "atom_scat() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_scat"]], "build_dod_and_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_dod_and_od"]], "build_water_hydrogens_from_map() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map"]], "build_water_hydrogens_from_map2() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map2"]], "choose_h_for_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.choose_h_for_water"]], "count_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.count_rotatable"]], "distances_to_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.distances_to_peaks"]], "extract_hoh_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.extract_hoh_peaks"]], "find_hydrogen_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.find_hydrogen_peaks"]], "fit_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.fit_rotatable"]], "fit_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.fit_water"]], "get_pdb_oxygen() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.get_pdb_oxygen"]], "h_peak (class in mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.h_peak"]], "insert_atom_into_model() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.insert_atom_into_model"]], "len_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.len_peaks"]], "make_peak_dict() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.make_peak_dict"]], "map_peak_filter() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.map_peak_filter"]], "match_dod() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_dod"]], "match_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_od"]], "mmtbx.hydrogens": [[291, "module-mmtbx.hydrogens"]], "mmtbx.hydrogens.build_hydrogens": [[291, "module-mmtbx.hydrogens.build_hydrogens"]], "mmtbx.hydrogens.find": [[291, "module-mmtbx.hydrogens.find"]], "obs_map() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.obs_map"]], "one_water_correlation() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.one_water_correlation"]], "print_atom() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_atom"]], "print_scat() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_scat"]], "print_scats() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.print_scats"]], "regularize_model() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.regularize_model"]], "remove_zero_occupancy() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.remove_zero_occupancy"]], "rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.rotatable"]], "run() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.run"]], "run() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.run"]], "run_fit_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.run_fit_rotatable"]], "scatterers_info() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.scatterers_info"]], "select_one_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.select_one_water"]], "shortcut() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.shortcut"]], "water_and_peaks (class in mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_and_peaks"]], "water_bond_angle() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_bond_angle"]], "water_map_correlations() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.water_map_correlations"]], "write_atoms() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.write_atoms"]], "add_lone_pairs_for_peptyde_o() (in module mmtbx.ias)": [[292, "mmtbx.ias.add_lone_pairs_for_peptyde_o"]], "all_bonds() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.all_bonds"]], "atom (class in mmtbx.ias)": [[292, "mmtbx.ias.atom"]], "bond_density (class in mmtbx.ias)": [[292, "mmtbx.ias.bond_density"]], "check_at_bond_vector() (in module mmtbx.ias)": [[292, "mmtbx.ias.check_at_bond_vector"]], "deep_copy() (mmtbx.ias.ias method)": [[292, "mmtbx.ias.ias.deep_copy"]], "extract_ias (class in mmtbx.ias)": [[292, "mmtbx.ias.extract_ias"]], "find_peak() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.find_peak"]], "find_peak_at_bond (class in mmtbx.ias)": [[292, "mmtbx.ias.find_peak_at_bond"]], "get_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.get_ias_selection"]], "ias (class in mmtbx.ias)": [[292, "mmtbx.ias.ias"]], "ias_counters (class in mmtbx.ias)": [[292, "mmtbx.ias.ias_counters"]], "ias_position_at_lone_pairs() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_position_at_lone_pairs"]], "ias_site_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_site_position"]], "iass_as_xray_structure() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.iass_as_xray_structure"]], "manager (class in mmtbx.ias)": [[292, "mmtbx.ias.manager"]], "mmtbx.ias": [[292, "module-mmtbx.ias"]], "set_ias_name_and_predicted_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_ias_name_and_predicted_position"]], "set_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.set_ias_selection"]], "set_peaks() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_peaks"]], "set_status() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_status"]], "set_status() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.set_status"]], "setup_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.setup_ias_selection"]], "show() (mmtbx.ias.ias_counters method)": [[292, "mmtbx.ias.ias_counters.show"]], "write_pdb_file() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.write_pdb_file"]], "atom_type_flags (class in mmtbx.ions)": [[293, "mmtbx.ions.atom_type_flags"]], "bad_coord_atom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_atom"]], "bad_coord_residue (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_residue"]], "bad_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_geom"]], "bad_halide (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_halide"]], "bad_valence (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_valence"]], "bad_vectors (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_vectors"]], "calculate_valence() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valence"]], "calculate_valences() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valences"]], "charge_as_int() (mmtbx.ions.metal_parameters method)": [[293, "mmtbx.ions.metal_parameters.charge_as_int"]], "check_supported() (in module mmtbx.ions)": [[293, "mmtbx.ions.check_supported"]], "close_contact (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.close_contact"]], "coord_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.coord_geom"]], "flag_names_and_labels (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.flag_names_and_labels"]], "get_charge() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charge"]], "get_charges() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charges"]], "get_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_element"]], "get_flag_captions() (mmtbx.ions.atom_type_flags method)": [[293, "mmtbx.ions.atom_type_flags.get_flag_captions"]], "get_metal_parameters() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_metal_parameters"]], "get_valence_params() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_valence_params"]], "high_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_anom"]], "high_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_b_iso"]], "high_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fdp"]], "high_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fofc"]], "high_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_occ"]], "high_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_two_fofc"]], "is_supported_donor() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_donor"]], "is_supported_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_element"]], "like_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.like_coord"]], "low_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_anom"]], "low_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_b_iso"]], "low_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fdp"]], "low_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fofc"]], "low_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_occ"]], "low_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_two_fofc"]], "metal_parameters (class in mmtbx.ions)": [[293, "mmtbx.ions.metal_parameters"]], "missing_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.missing_geom"]], "mmtbx.ions": [[293, "module-mmtbx.ions"]], "name (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.name"]], "parameter_server (class in mmtbx.ions)": [[293, "mmtbx.ions.parameter_server"]], "params (mmtbx.ions.parameter_server attribute)": [[293, "id0"], [293, "mmtbx.ions.parameter_server.params"]], "scattering_type() (mmtbx.ions.metal_parameters method)": [[293, "mmtbx.ions.metal_parameters.scattering_type"]], "show() (mmtbx.ions.atom_type_flags method)": [[293, "mmtbx.ions.atom_type_flags.show"]], "too_few_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_few_coord"]], "too_few_non_waters (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_few_non_waters"]], "too_many_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.too_many_coord"]], "very_bad_valence (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.very_bad_valence"]], "clean_up_ions() (in module mmtbx.ions.build)": [[294, "mmtbx.ions.build.clean_up_ions"]], "find_and_build_ions() (in module mmtbx.ions.build)": [[294, "mmtbx.ions.build.find_and_build_ions"]], "mmtbx.ions.build": [[294, "module-mmtbx.ions.build"]], "chemicalenvironment (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.ChemicalEnvironment"]], "scatteringenvironment (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.ScatteringEnvironment"]], "altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.altloc"]], "anom_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id6"], [295, "mmtbx.ions.environment.ScatteringEnvironment.anom_density"]], "atom (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id0"], [295, "mmtbx.ions.environment.ChemicalEnvironment.atom"]], "atom (mmtbx.ions.environment.atom_contact attribute)": [[295, "id15"], [295, "mmtbx.ions.environment.atom_contact.atom"]], "atom_contact (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.atom_contact"]], "atom_i_seq() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_i_seq"]], "atom_id_no_altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_id_no_altloc"]], "atom_name() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_name"]], "b_iso (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id7"], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_iso"]], "b_mean_hoh (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id8"], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_mean_hoh"]], "charge (mmtbx.ions.environment.atom_contact attribute)": [[295, "id16"], [295, "mmtbx.ions.environment.atom_contact.charge"]], "chemistry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id1"], [295, "mmtbx.ions.environment.ChemicalEnvironment.chemistry"]], "contacts (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id2"], [295, "mmtbx.ions.environment.ChemicalEnvironment.contacts"]], "contacts_no_alts (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id3"], [295, "mmtbx.ions.environment.ChemicalEnvironment.contacts_no_alts"]], "d_min (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id9"], [295, "mmtbx.ions.environment.ScatteringEnvironment.d_min"]], "distance() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance"]], "distance_from() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance_from"]], "element (mmtbx.ions.environment.atom_contact attribute)": [[295, "id17"], [295, "mmtbx.ions.environment.atom_contact.element"]], "find_nearby_atoms() (in module mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.find_nearby_atoms"]], "fo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id10"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fo_density"]], "fofc_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofc_density"]], "fofo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofo_density"]], "fp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id11"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fp"]], "fpp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id12"], [295, "mmtbx.ions.environment.ScatteringEnvironment.fpp"]], "geometry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id4"], [295, "mmtbx.ions.environment.ChemicalEnvironment.geometry"]], "get_valence() (mmtbx.ions.environment.chemicalenvironment method)": [[295, "mmtbx.ions.environment.ChemicalEnvironment.get_valence"]], "id_str() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.id_str"]], "is_carboxy_terminus (mmtbx.ions.environment.atom_contact attribute)": [[295, "mmtbx.ions.environment.atom_contact.is_carboxy_terminus"]], "mmtbx.ions.environment": [[295, "module-mmtbx.ions.environment"]], "occ (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id13"], [295, "mmtbx.ions.environment.ScatteringEnvironment.occ"]], "occ (mmtbx.ions.environment.atom_contact property)": [[295, "mmtbx.ions.environment.atom_contact.occ"]], "pai (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id14"], [295, "mmtbx.ions.environment.ScatteringEnvironment.pai"]], "resname() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.resname"]], "rt_mx (mmtbx.ions.environment.atom_contact attribute)": [[295, "id18"], [295, "mmtbx.ions.environment.atom_contact.rt_mx"]], "site_cart (mmtbx.ions.environment.atom_contact attribute)": [[295, "id19"], [295, "mmtbx.ions.environment.atom_contact.site_cart"]], "vector (mmtbx.ions.environment.atom_contact attribute)": [[295, "id20"], [295, "mmtbx.ions.environment.atom_contact.vector"]], "wavelengeth (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.wavelengeth"]], "wavelength (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.wavelength"]], "find_coordination_geometry() (in module mmtbx.ions.geometry)": [[296, "mmtbx.ions.geometry.find_coordination_geometry"]], "mmtbx.ions.geometry": [[296, "module-mmtbx.ions.geometry"]], "is_favorable_halide_environment() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_favorable_halide_environment"]], "is_negatively_charged_oxygen() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_negatively_charged_oxygen"]], "mmtbx.ions.halides": [[297, "module-mmtbx.ions.halides"]], "anom_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.ANOM_PEAK"]], "atomproperties (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.AtomProperties"]], "bad_coord_atom (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_ATOM"]], "bad_coord_residue (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_RESIDUE"]], "bad_fpp (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_FPP"]], "bad_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_GEOMETRY"]], "bad_halide (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_HALIDE"]], "bad_valences (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VALENCES"]], "bad_vectors (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VECTORS"]], "close_contact (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.CLOSE_CONTACT"]], "coording_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.COORDING_GEOMETRY"]], "fofc_hole (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_HOLE"]], "fofc_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_PEAK"]], "high_2fofc (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_2FOFC"]], "high_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_B"]], "high_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_OCC"]], "like_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LIKE_COORD"]], "low_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_B"]], "low_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_OCC"]], "no_2fofc_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_2FOFC_PEAK"]], "no_anom_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_ANOM_PEAK"]], "no_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.NO_GEOMETRY"]], "too_few_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_FEW_COORD"]], "too_few_non_waters (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_FEW_NON_WATERS"]], "too_many_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.TOO_MANY_COORD"]], "very_bad_valences (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.VERY_BAD_VALENCES"]], "altloc (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.altloc"]], "analyze_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_substructure"]], "analyze_water() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_water"]], "analyze_waters() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_waters"]], "atom_selection (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.atom_selection"]], "atom_weight() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.atom_weight"]], "b_iso (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.b_iso"]], "chain_id (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.chain_id"]], "check_fpp_ratio() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_fpp_ratio"]], "check_ion_environment() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_ion_environment"]], "chem_env (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.chem_env"]], "create_manager() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.create_manager"]], "element (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.element"]], "error_strs (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.error_strs"]], "find_anomalous_scatterers() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.find_anomalous_scatterers"]], "find_nearby_atoms() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.find_nearby_atoms"]], "get_atom_type() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.get_atom_type"]], "get_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_b_iso"]], "get_fp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fp"]], "get_fpp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fpp"]], "get_initial_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_initial_b_iso"]], "get_map() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map"]], "get_map_gaussian_fit() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_gaussian_fit"]], "get_map_sphere_variance() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_sphere_variance"]], "get_strict_valence_flag() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_strict_valence_flag"]], "guess_b_iso_real() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_b_iso_real"]], "guess_molecular_weight() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_molecular_weight"]], "has_compatible_ligands() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.has_compatible_ligands"]], "icode (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.icode"]], "identity() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.identity"]], "ion_master_phil() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_master_phil"]], "ion_result (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_result"]], "is_compatible_anomalous_scattering() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_anomalous_scattering"]], "is_compatible_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_site"]], "is_correctly_identified() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_correctly_identified"]], "looks_like_halide_ion() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.looks_like_halide_ion"]], "looks_like_nucleotide_phosphate_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.looks_like_nucleotide_phosphate_site"]], "manager (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.manager"]], "map_stats() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.map_stats"]], "mmtbx.ions.identify": [[298, "module-mmtbx.ions.identify"]], "model_id (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.model_id"]], "name (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.name"]], "number_of_atoms_within_radius() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_atoms_within_radius"]], "number_of_backbone_oxygens() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_backbone_oxygens"]], "number_of_favored_ligand_residues() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.number_of_favored_ligand_residues"]], "occupancy (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.occupancy"]], "outlier (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.outlier"]], "principal_axes_of_inertia() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.principal_axes_of_inertia"]], "refine_anomalous_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.refine_anomalous_substructure"]], "resname (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.resname"]], "resseq (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.resseq"]], "scatter_env (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.scatter_env"]], "score (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.score"]], "segid (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.segid"]], "show() (mmtbx.ions.identify.ion_result method)": [[298, "mmtbx.ions.identify.ion_result.show"]], "show_brief() (mmtbx.ions.identify.ion_result method)": [[298, "mmtbx.ions.identify.ion_result.show_brief"]], "show_current_scattering_statistics() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.show_current_scattering_statistics"]], "show_ion_results() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.show_ion_results"]], "show_properties() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.show_properties"]], "show_summary() (mmtbx.ions.identify.water_result method)": [[298, "mmtbx.ions.identify.water_result.show_summary"]], "symop (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.symop"]], "update_maps() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.update_maps"]], "update_structure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.update_structure"]], "validate_ion() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.validate_ion"]], "validate_ions() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.validate_ions"]], "water_result (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.water_result"]], "water_selection() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.water_selection"]], "xyz (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.xyz"]], "analyze_water() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_water"]], "analyze_waters() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_waters"]], "atom_info_str (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id0"], [299, "mmtbx.ions.svm.svm_prediction.atom_info_str"]], "atom_types (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id1"], [299, "mmtbx.ions.svm.svm_prediction.atom_types"]], "final_choice (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id2"], [299, "mmtbx.ions.svm.svm_prediction.final_choice"]], "i_seq (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id3"], [299, "mmtbx.ions.svm.svm_prediction.i_seq"]], "ion_anomalous_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_anomalous_vector"]], "ion_class() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_class"]], "ion_electron_density_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_electron_density_vector"]], "ion_geometry_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_geometry_vector"]], "ion_model_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_model_vector"]], "ion_nearby_atoms_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_nearby_atoms_vector"]], "ion_valence_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_valence_vector"]], "ion_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_vector"]], "manager (class in mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.manager"]], "map_stats (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id4"], [299, "mmtbx.ions.svm.svm_prediction.map_stats"]], "mmtbx.ions.svm": [[299, "module-mmtbx.ions.svm"]], "pdb_id_str (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id5"], [299, "mmtbx.ions.svm.svm_prediction.pdb_id_str"]], "predict_ion() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.predict_ion"]], "scores (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id6"], [299, "mmtbx.ions.svm.svm_prediction.scores"]], "show() (mmtbx.ions.svm.svm_prediction method)": [[299, "mmtbx.ions.svm.svm_prediction.show"]], "show_brief() (mmtbx.ions.svm.svm_prediction method)": [[299, "mmtbx.ions.svm.svm_prediction.show_brief"]], "svm_prediction (class in mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.svm_prediction"]], "dump_sites() (in module mmtbx.ions.svm.dump_sites)": [[300, "mmtbx.ions.svm.dump_sites.dump_sites"]], "mmtbx.ions.svm.dump_sites": [[300, "module-mmtbx.ions.svm.dump_sites"]], "filter_svm_outputs() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.filter_svm_outputs"]], "iterate_sites() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.iterate_sites"]], "mmtbx.ions.svm.utils": [[301, "module-mmtbx.ions.svm.utils"]], "scale_to() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.scale_to"]], "anonymize_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.anonymize_ions"]], "collect_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.collect_ions"]], "compare_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.compare_ions"]], "count_coordinating_residues() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.count_coordinating_residues"]], "fit_gaussian() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.fit_gaussian"]], "mmtbx.ions.utils": [[302, "module-mmtbx.ions.utils"]], "sort_atoms_permutation() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.sort_atoms_permutation"]], "add_fan() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_fan"]], "add_spring() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_spring"]], "angle_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.angle_outlier_as_kinemage"]], "bond_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.bond_outlier_as_kinemage"]], "build_name_hash() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.build_name_hash"]], "cbeta_dev() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.cbeta_dev"]], "chiral_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.chiral_outlier_as_kinemage"]], "export_molprobity_result_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.export_molprobity_result_as_kinemage"]], "get_altid_controls() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_altid_controls"]], "get_angle_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_angle_outliers"]], "get_bond_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_bond_outliers"]], "get_chain_color() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_chain_color"]], "get_default_header() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_default_header"]], "get_footer() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_footer"]], "get_ions() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_ions"]], "get_kin_lots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_kin_lots"]], "get_master_phil() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_master_phil"]], "get_residue_bonds() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_residue_bonds"]], "kin_vec() (in module mmtbx.kinemage)": [[303, "mmtbx.kinemage.kin_vec"]], "make_multikin() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_multikin"]], "make_probe_dots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_probe_dots"]], "midpoint() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.midpoint"]], "mmtbx.kinemage": [[303, "module-mmtbx.kinemage"]], "mmtbx.kinemage.validation": [[303, "module-mmtbx.kinemage.validation"]], "pperp_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.pperp_outliers"]], "rama_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.rama_outliers"]], "rotamer_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.rotamer_outliers"]], "run() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.run"]], "usage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.usage"]], "condition_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_"]], "condition_name() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_name"]], "condition_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.condition_number_"]], "get_condition() (mmtbx.ligands.xtal_screens.server method)": [[304, "mmtbx.ligands.xtal_screens.server.get_condition"]], "ligands() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands"]], "ligands_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands_"]], "mmtbx.ligands": [[304, "module-mmtbx.ligands"]], "mmtbx.ligands.xtal_screens": [[304, "module-mmtbx.ligands.xtal_screens"]], "ph() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.pH"]], "ph_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.pH_"]], "screen_name_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.screen_name_"]], "screen_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.screen_number_"]], "server (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.server"]], "solution (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.solution"]], "tube_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.tube_number_"]], "well_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.well_number_"]], "add_box() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.add_box"]], "amplitudes() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.amplitudes"]], "apply_new_sites_to_hierarchies() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_hierarchies"]], "apply_new_sites_to_xray_structure() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_xray_structure"]], "as_p1_map() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.as_p1_map"]], "asu_map_from_fmodel() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.asu_map_from_fmodel"]], "atom_iselection() (mmtbx.maps.write_xplor_map_file method)": [[305, "mmtbx.maps.write_xplor_map_file.atom_iselection"]], "b_factor_sharpening_by_map_kurtosis_maximization() (in module mmtbx.maps)": [[305, "mmtbx.maps.b_factor_sharpening_by_map_kurtosis_maximization"]], "box_around_selection() (mmtbx.maps.write_xplor_map_file method)": [[305, "mmtbx.maps.write_xplor_map_file.box_around_selection"]], "box_iterator() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.box_iterator"]], "boxes (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.boxes"]], "cast_map_coeff_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.cast_map_coeff_params"]], "ccp4_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.ccp4_map"]], "combine_maps() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.combine_maps"]], "combine_with() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.combine_with"]], "common_frame_of_reference (class in mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.common_frame_of_reference"]], "compute_f_calc() (in module mmtbx.maps)": [[305, "mmtbx.maps.compute_f_calc"]], "compute_fo_minus_fo_map (class in mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map"]], "compute_map_and_combine() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.compute_map_and_combine"]], "compute_map_coefficients (class in mmtbx.maps)": [[305, "mmtbx.maps.compute_map_coefficients"]], "compute_original_map() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.compute_original_map"]], "compute_xplor_maps() (in module mmtbx.maps)": [[305, "mmtbx.maps.compute_xplor_maps"]], "convert_to_non_anomalous() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.convert_to_non_anomalous"]], "counter (class in mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.counter"]], "create_fmodel() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.create_fmodel"]], "create_map_from_pdb_and_mtz() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.create_map_from_pdb_and_mtz"]], "create_omit_regions() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.create_omit_regions"]], "decode_resolve_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.decode_resolve_map_coeffs"]], "exercise() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.exercise"]], "extract_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.extract_map_coeffs"]], "extract_phenix_refine_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.extract_phenix_refine_map_coeffs"]], "fast_maps_from_hkl_file (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file"]], "finish_job() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.finish_job"]], "fo_minus_fo_master_params() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.fo_minus_fo_master_params"]], "format_map_coeffs_for_resolve() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.format_map_coeffs_for_resolve"]], "frac_max (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.frac_max"]], "frac_min (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.frac_min"]], "generate_p1_box() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.generate_p1_box"]], "generate_water_omit_map (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.generate_water_omit_map"]], "get_anomalous_map() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_anomalous_map"]], "get_default_map_coefficients_phil() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_default_map_coefficients_phil"]], "get_inverse_matrix() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.get_inverse_matrix"]], "get_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.get_map"]], "get_map() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.get_map"]], "get_map_coeff_labels() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeff_labels"]], "get_map_coeffs_for_build() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeffs_for_build"]], "get_maps_from_fmodel() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_maps_from_fmodel"]], "get_maps_from_fmodel() (mmtbx.maps.utils.fast_maps_from_hkl_file method)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file.get_maps_from_fmodel"]], "get_p1_map_unscaled() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.get_p1_map_unscaled"]], "good_atoms_selection() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.good_atoms_selection"]], "grid_max() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.grid_max"]], "inner_loop() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.inner_loop"]], "inverse_transform_hierarchy() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.inverse_transform_hierarchy"]], "join_selections() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.join_selections"]], "kick_fmodel() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_fmodel"]], "kick_map_coeffs() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_map_coeffs"]], "launcher (class in mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.launcher"]], "low_volume_density_elimination() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.low_volume_density_elimination"]], "map_and_map_coeff_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_and_map_coeff_master_params"]], "map_coefficients() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.map_coefficients"]], "map_coefficients_from_fmodel() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_coefficients_from_fmodel"]], "map_coeffs_from_map() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.map_coeffs_from_map"]], "map_coeffs_from_mtz_file() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.map_coeffs_from_mtz_file"]], "map_coeffs_list (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.map_coeffs_list"]], "map_coeffs_mtz_label_manager (class in mmtbx.maps)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager"]], "maps_including_io_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.maps_including_IO_master_params"]], "mask_grid() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.mask_grid"]], "mmtbx.maps": [[305, "module-mmtbx.maps"]], "mmtbx.maps.composite_omit_map": [[305, "module-mmtbx.maps.composite_omit_map"]], "mmtbx.maps.fem": [[305, "module-mmtbx.maps.fem"]], "mmtbx.maps.fobs_minus_fobs_map": [[305, "module-mmtbx.maps.fobs_minus_fobs_map"]], "mmtbx.maps.kick": [[305, "module-mmtbx.maps.kick"]], "mmtbx.maps.superpose": [[305, "module-mmtbx.maps.superpose"]], "mmtbx.maps.utils": [[305, "module-mmtbx.maps.utils"]], "n_atoms (mmtbx.maps.composite_omit_map.omit_box property)": [[305, "mmtbx.maps.composite_omit_map.omit_box.n_atoms"]], "n_atoms (mmtbx.maps.composite_omit_map.omit_regions property)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.n_atoms"]], "n_boxes (mmtbx.maps.composite_omit_map.omit_regions property)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.n_boxes"]], "noise_filtered_map_coefficients() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.noise_filtered_map_coefficients"]], "omit_box (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_box"]], "omit_box() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.omit_box"]], "omit_region_results (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results"]], "omit_regions (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.omit_regions"]], "outer_loop() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.outer_loop"]], "phases() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.phases"]], "prepare_f_obs_and_flags() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.prepare_f_obs_and_flags"]], "r_free (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.r_free"]], "r_work (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.r_work"]], "random_weight_averaged_map_coefficients() (mmtbx.maps.kick.weighted_average method)": [[305, "mmtbx.maps.kick.weighted_average.random_weight_averaged_map_coefficients"]], "randomize_completeness() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_completeness"]], "randomize_completeness2() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_completeness2"]], "randomize_struture_factors() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_struture_factors"]], "remove_common_isotropic_adp() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.remove_common_isotropic_adp"]], "resolve_filter_map() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.resolve_filter_map"]], "result_as_sf() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.result_as_sf"]], "run (class in mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.run"]], "run (class in mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.run"]], "run (class in mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.run"]], "run() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.run"]], "run() (mmtbx.maps.fobs_minus_fobs_map.launcher method)": [[305, "mmtbx.maps.fobs_minus_fobs_map.launcher.run"]], "run() (mmtbx.maps.superpose.transform_maps method)": [[305, "mmtbx.maps.superpose.transform_maps.run"]], "run() (mmtbx.maps.utils.fast_maps_from_hkl_file method)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file.run"]], "selection (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.selection"]], "selection (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.selection"]], "serial (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.serial"]], "serial (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.serial"]], "serial (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.serial"]], "show() (mmtbx.maps.composite_omit_map.omit_box method)": [[305, "mmtbx.maps.composite_omit_map.omit_box.show"]], "show() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.show"]], "show() (mmtbx.maps.fem.counter method)": [[305, "mmtbx.maps.fem.counter.show"]], "to_asu_map() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.to_asu_map"]], "transform_map_by_lsq_fit() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.transform_map_by_lsq_fit"]], "transform_maps (class in mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.transform_maps"]], "truncate_with_roots() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.truncate_with_roots"]], "validate_params() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.validate_params"]], "weighted_average (class in mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.weighted_average"]], "write_map_coeffs() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_map_coeffs"]], "write_map_coeffs() (mmtbx.maps.utils.generate_water_omit_map method)": [[305, "mmtbx.maps.utils.generate_water_omit_map.write_map_coeffs"]], "write_map_file() (mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map method)": [[305, "mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map.write_map_file"]], "write_mc() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.write_mc"]], "write_mtz_file() (mmtbx.maps.compute_map_coefficients method)": [[305, "mmtbx.maps.compute_map_coefficients.write_mtz_file"]], "write_output_files() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.write_output_files"]], "write_pdb_file() (mmtbx.maps.utils.generate_water_omit_map method)": [[305, "mmtbx.maps.utils.generate_water_omit_map.write_pdb_file"]], "write_xplor_map() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_xplor_map"]], "write_xplor_map_file (class in mmtbx.maps)": [[305, "mmtbx.maps.write_xplor_map_file"]], "write_xplor_map_file() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.write_xplor_map_file"]], "zero_below_threshold() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.zero_below_threshold"]], "asu_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.asu_mask"]], "bulk_solvent (class in mmtbx.masks)": [[306, "mmtbx.masks.bulk_solvent"]], "bulk_solvent_mask() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.bulk_solvent_mask"]], "compute_f_mask() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.compute_f_mask"]], "deep_copy() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.deep_copy"]], "manager (class in mmtbx.masks)": [[306, "mmtbx.masks.manager"]], "mask_as_xplor_map() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.mask_as_xplor_map"]], "mask_data_whole_uc() (mmtbx.masks.asu_mask method)": [[306, "mmtbx.masks.asu_mask.mask_data_whole_uc"]], "mask_from_xray_structure (class in mmtbx.masks)": [[306, "mmtbx.masks.mask_from_xray_structure"]], "mmtbx.masks": [[306, "module-mmtbx.masks"]], "select() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.select"]], "shell_f_masks() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks"]], "shell_f_masks_twin() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks_twin"]], "show_summary() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.show_summary"]], "smooth_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.smooth_mask"]], "structure_factors() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.structure_factors"]], "subtract_non_uniform_solvent_region_in_place() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.subtract_non_uniform_solvent_region_in_place"]], "alpha_beta (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta"]], "alpha_beta() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.alpha_beta"]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta"]], "alpha_beta_calc (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc"]], "alpha_beta_est_manager (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager"]], "alpha_beta_for_each_reflection() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta_for_each_reflection"]], "distribution_as_array() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_array"]], "distribution_as_xplor_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_xplor_file"]], "f_ordered_solvent() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.f_ordered_solvent"]], "fcalc_from_distribution() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.fcalc_from_distribution"]], "figures_of_merit_() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.figures_of_merit_"]], "fo_fc_alpha_over_eps_beta() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fo_fc_alpha_over_eps_beta"]], "fom() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fom"]], "form_factor() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.form_factor"]], "form_factor() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.form_factor"]], "map_of_coeff_scaled() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.map_of_coeff_scaled"]], "max_number_of_shells() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.max_number_of_shells"]], "mmtbx.max_lik": [[307, "module-mmtbx.max_lik"]], "mmtbx.max_lik.max_like_non_uniform": [[307, "module-mmtbx.max_lik.max_like_non_uniform"]], "mmtbx.max_lik.maxlik": [[307, "module-mmtbx.max_lik.maxlik"]], "ordered_solvent_distribution (class in mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution"]], "phase_error() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.phase_error"]], "print_all_reflections_in_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.print_all_reflections_in_file"]], "sigma_miss() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.sigma_miss"]], "smooth() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.smooth"]], "monomerlibraryservererror": [[308, "mmtbx.monomer_library.server.MonomerLibraryServerError"]], "residuelinkclass (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass"]], "active_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.active_atoms"]], "ad_hoc_single_atom_residue (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ad_hoc_single_atom_residue"]], "add_angle_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_angle_proxies"]], "add_angle_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_angle_proxies"]], "add_bond_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_bond_proxies"]], "add_bond_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_bond_proxies"]], "add_chirality_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_chirality_proxies"]], "add_chirality_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_chirality_proxies"]], "add_dihedral_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_dihedral_proxies"]], "add_dihedral_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_dihedral_proxies"]], "add_parallelity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_parallelity_proxies"]], "add_parallelity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_parallelity_proxies"]], "add_planarity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_planarity_proxies"]], "add_planarity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_planarity_proxies"]], "adjust_class() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.adjust_class"]], "all_associated_i_seqs() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.all_associated_i_seqs"]], "all_atoms_are_in_main_conf() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.all_atoms_are_in_main_conf"]], "angle_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.angle_counters"]], "angle_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.angle_list"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.apply_change_in_place"]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.apply_change_in_place"]], "apply_chem_mod_list() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.apply_chem_mod_list"]], "apply_glyco_link_using_proxies_and_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.apply_glyco_link_using_proxies_and_atoms"]], "apply_mod() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.apply_mod"]], "apply_mod() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.apply_mod"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_atom.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.as_chem_comp"]], "as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.as_chem_comp"]], "as_cif() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.as_cif"]], "as_cif_block() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.as_cif_block"]], "as_cif_loop() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.as_cif_loop"]], "as_geometry_restraints_motif() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.as_geometry_restraints_motif"]], "as_geometry_restraints_motif_manipulation() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.as_geometry_restraints_motif_manipulation"]], "as_geometry_restraints_motif_manipulation() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.as_geometry_restraints_motif_manipulation"]], "assign() (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate method)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.assign"]], "assign_charge() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_charge"]], "assign_directly() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_directly"]], "assign_from_monomer_mapping() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_from_monomer_mapping"]], "atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_by_id"]], "atom_dict() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_dict"]], "atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond.atom_ids"]], "atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tor.atom_ids"]], "atom_ids() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_ids"]], "atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_list"]], "atom_name_interpretation (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_name_interpretation"]], "atom_names_given (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_given"]], "atom_names_mappings (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_mappings"]], "atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.atom_selection"]], "bond_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.bond_counters"]], "bond_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.bond_list"]], "build_all_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies"]], "build_angle_start_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_angle_start_by_tor_id"]], "build_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_chain_proxies"]], "build_conformation_dependent_angle_proxies() (in module mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.build_conformation_dependent_angle_proxies"]], "build_i_q_packed_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_i_q_packed_by_tor_id"]], "build_rotamer_tor_atom_ids_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_rotamer_tor_atom_ids_by_tor_id"]], "chainid (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chainid"]], "change_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.change_atom_in_place"]], "check_all_classes() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.check_all_classes"]], "check_comp() (in module mmtbx.monomer_library.cif_triage)": [[308, "mmtbx.monomer_library.cif_triage.check_comp"]], "check_for_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_for_acid"]], "check_for_peptide_links() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.check_for_peptide_links"]], "check_valence() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence"]], "check_valence_and_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence_and_acid"]], "chem_comp (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp"]], "chem_comp (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chem_comp"]], "chem_comp_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_angle"]], "chem_comp_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_atom"]], "chem_comp_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond"]], "chem_comp_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_chir"]], "chem_comp_deriv (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_deriv"]], "chem_comp_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_plane_atom"]], "chem_comp_rotamer_info (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_rotamer_info"]], "chem_comp_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym"]], "chem_comp_synonym_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym_atom"]], "chem_comp_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tor"]], "chem_comp_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tree"]], "chem_link (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link"]], "chem_link_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_angle"]], "chem_link_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_bond"]], "chem_link_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_chir"]], "chem_link_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_plane"]], "chem_link_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_tor"]], "chem_mod (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod"]], "chem_mod_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle"]], "chem_mod_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_atom"]], "chem_mod_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond"]], "chem_mod_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir"]], "chem_mod_ids (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chem_mod_ids"]], "chem_mod_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom"]], "chem_mod_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor"]], "chem_mod_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree"]], "chem_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_plane"]], "chir_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chir_list"]], "chirality_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chirality_counters"]], "cif_keywords() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.cif_keywords"]], "cif_object (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.cif_object"]], "cif_output_holder (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.cif_output_holder"]], "clash_guard() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.clash_guard"]], "classification (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.classification"]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.classification"]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.classification"]], "comp_comp_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id"]], "conf_altloc (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.conf_altloc"]], "conf_altloc (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.conf_altloc"]], "conformation_dependent_restraints (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints"]], "conformer_i_seq (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq"]], "construct_geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.construct_geometry_restraints_manager"]], "convert() (mmtbx.monomer_library.pdb_interpretation.conformer_i_seq method)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq.convert"]], "convert_all() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_all"]], "convert_all() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_all"]], "convert_ccp4_tor_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_ccp4_tor_list"]], "convert_comp_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_comp_list"]], "convert_comp_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_list"]], "convert_comp_synonym_atom_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_synonym_atom_list"]], "convert_comp_synonym_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_comp_synonym_list"]], "convert_deriv_list_dict() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_deriv_list_dict"]], "convert_lib_atom() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_atom"]], "convert_lib_synonym() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_synonym"]], "convert_lib_vdw() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_vdw"]], "convert_link_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_link_list"]], "convert_link_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_link_list"]], "convert_list_block() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_list_block"]], "convert_mod_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_mod_list"]], "convert_mod_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_mod_list"]], "correct_hydrogen_geometries() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.correct_hydrogen_geometries"]], "counters (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.counters"]], "create_disulfides() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_disulfides"]], "create_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_link"]], "delete_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.delete_atom_in_place"]], "delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.delta"]], "dihedral_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.dihedral_counters"]], "discard_conflicting_pdb_element_column() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.discard_conflicting_pdb_element_column"]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.discard_tables"]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.discard_tables"]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.duplicate_atoms"]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.duplicate_atoms"]], "empty (class in mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.empty"]], "ener_lib (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.ener_lib"]], "ener_lib_as_nonbonded_params() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ener_lib_as_nonbonded_params"]], "energy_lib_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_atom"]], "energy_lib_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_synonym"]], "energy_lib_vdw (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_vdw"]], "epsilon (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.epsilon"]], "esd_as_weight() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.esd_as_weight"]], "evaluate (class in mmtbx.monomer_library.rna_sugar_pucker_analysis)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate"]], "evaluate_registry_process_result() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.evaluate_registry_process_result"]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.expected_atoms"]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.expected_atoms"]], "extract_bonds_to_omit() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.extract_bonds_to_omit"]], "extract_secondary_structure() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.extract_secondary_structure"]], "extract_xray_structure() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.extract_xray_structure"]], "fatal_problems_message() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.fatal_problems_message"]], "fatal_problems_report() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.fatal_problems_report"]], "find_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.find_mon_lib_file"]], "flush_log() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.flush_log"]], "format_exception_message() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.format_exception_message"]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.generate_atoms_from_atom_groups"]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.generate_atoms_from_atom_groups"]], "generate_loop_data() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.generate_loop_data"]], "generic_metal_run() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.generic_metal_run"]], "geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.geometry_restraints_manager"]], "geometry_restraints_proxy_registries (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries"]], "geostd_list_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.geostd_list_cif"]], "get_c1_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_C1_carbon"]], "get_alpha_beta() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_alpha_beta"]], "get_angle() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_angle"]], "get_angle() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_angle"]], "get_angles_from_included_bonds() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_angles_from_included_bonds"]], "get_anomeric_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_carbon"]], "get_anomeric_hydrogen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_hydrogen"]], "get_any_linking_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_any_linking_carbon"]], "get_bad_hydrogen_i_seqs() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.get_bad_hydrogen_i_seqs"]], "get_basepair_target_distance() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_basepair_target_distance"]], "get_bond() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_bond"]], "get_bond() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_bond"]], "get_bond() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_bond"]], "get_bonded() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded"]], "get_bonded_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded_from_atom_groups"]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_bonds_and_angles"]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_bonds_and_angles"]], "get_chir_volume_ideal() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_chir_volume_ideal"]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_volume_ideal"]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_volume_ideal"]], "get_chiral_i_seqs() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_chiral_i_seqs"]], "get_chiral_sign() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_chiral_sign"]], "get_chiral_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_chiral_volume"]], "get_classes() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_classes"]], "get_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_classification"]], "get_code() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_code"]], "get_comp_comp_id_and_atom_name_interpretation() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_and_atom_name_interpretation"]], "get_comp_comp_id_direct() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_direct"]], "get_comp_comp_id_mod() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_mod"]], "get_default_bondlength() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_default_bondlength"]], "get_distance2() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_distance2"]], "get_distance2() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_distance2"]], "get_glyco_link_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_glyco_link_atoms"]], "get_hand() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_hand"]], "get_isomer() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_isomer"]], "get_lib_link() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link"]], "get_lib_link_peptide() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link_peptide"]], "get_link_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon"]], "get_link_carbon_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon_on_distance"]], "get_link_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen"]], "get_link_oxygen_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen_on_distance"]], "get_link_phi_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_phi_carbon"]], "get_planes() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_planes"]], "get_planes() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_planes"]], "get_planes() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.get_planes"]], "get_restraints_loading_flags() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_restraints_loading_flags"]], "get_ring_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_carbon"]], "get_ring_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen"]], "get_ring_oxygen_substitute() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen_substitute"]], "get_rows() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.get_rows"]], "get_unknown_atoms() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.get_unknown_atoms"]], "get_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_volume"]], "glyco_link_class (class in mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class"]], "group_planes() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.group_planes"]], "hydrogen_deuterium_aliases() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.hydrogen_deuterium_aliases"]], "i_atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.i_atom_by_id"]], "i_conformer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.i_conformer"]], "id_dict (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.id_dict"]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.ignored_atoms"]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.ignored_atoms"]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.incomplete_info"]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.incomplete_info"]], "initialize_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.initialize_tables"]], "involves_broken_bonds() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.involves_broken_bonds"]], "involves_special_positions() (mmtbx.monomer_library.pdb_interpretation.special_position_dict method)": [[308, "mmtbx.monomer_library.pdb_interpretation.special_position_dict.involves_special_positions"]], "is_2p (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p"]], "is_2p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_delta"]], "is_2p_o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_o3p_distance_c1p_outbound_line"]], "is_2p_p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_p_distance_c1p_outbound_line"]], "is_3p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_3p_delta"]], "is_atom_group_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_group_pair_linked"]], "is_atom_metal_coordinated() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_metal_coordinated"]], "is_atom_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked"]], "is_atom_pair_linked_tuple() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked_tuple"]], "is_correct() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.is_correct"]], "is_delta_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_delta_outlier"]], "is_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_dna"]], "is_epsilon_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_epsilon_outlier"]], "is_first_conformer_in_chain (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_first_conformer_in_chain"]], "is_glyco_amino_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_amino_bond"]], "is_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_bond"]], "is_match() (mmtbx.monomer_library.pdb_interpretation.link_match_one method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one.is_match"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.is_matching_mod_for"]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.is_matching_mod_for"]], "is_n_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_n_glyco_bond"]], "is_o_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_o_glyco_bond"]], "is_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_peptide"]], "is_proper_match() (mmtbx.monomer_library.pdb_interpretation.link_match method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match.is_proper_match"]], "is_rna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna"]], "is_rna2p (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna2p"]], "is_rna_dna (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna_dna"]], "is_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna_dna"]], "is_same_model_as_before() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.is_same_model_as_before"]], "is_standard_glyco_link() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.is_standard_glyco_link"]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_terminus"]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_terminus"]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_unusual"]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_unusual"]], "is_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_water"]], "iselection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.iselection"]], "iselection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.iselection"]], "iter_until_loop() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.iter_until_loop"]], "labels() (mmtbx.monomer_library.pdb_interpretation.source_info_server method)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server.labels"]], "lib_link (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.lib_link"]], "link_link_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.link_link_id"]], "link_match (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match"]], "link_match_one (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one"]], "linking_mixins (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.linking_mixins"]], "load_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.load_mon_lib_file"]], "lookup() (mmtbx.monomer_library.conformation_dependent_restraints.pgd_server method)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server.lookup"]], "looped_data (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.looped_data"]], "looped_ids() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.looped_ids"]], "merge_and_overwrite_cifs() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.merge_and_overwrite_cifs"]], "missing_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.missing_hydrogen_atoms"]], "missing_non_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.missing_non_hydrogen_atoms"]], "mmtbx.monomer_library": [[308, "module-mmtbx.monomer_library"]], "mmtbx.monomer_library.bondlength_defaults": [[308, "module-mmtbx.monomer_library.bondlength_defaults"]], "mmtbx.monomer_library.cif_triage": [[308, "module-mmtbx.monomer_library.cif_triage"]], "mmtbx.monomer_library.cif_types": [[308, "module-mmtbx.monomer_library.cif_types"]], "mmtbx.monomer_library.conformation_dependent_restraints": [[308, "module-mmtbx.monomer_library.conformation_dependent_restraints"]], "mmtbx.monomer_library.conv_v2_v3": [[308, "module-mmtbx.monomer_library.conv_v2_v3"]], "mmtbx.monomer_library.correct_hydrogen_geometries": [[308, "module-mmtbx.monomer_library.correct_hydrogen_geometries"]], "mmtbx.monomer_library.glyco_chiral_values": [[308, "module-mmtbx.monomer_library.glyco_chiral_values"]], "mmtbx.monomer_library.glyco_utils": [[308, "module-mmtbx.monomer_library.glyco_utils"]], "mmtbx.monomer_library.hydrogen_restrictions": [[308, "module-mmtbx.monomer_library.hydrogen_restrictions"]], "mmtbx.monomer_library.idealized_aa": [[308, "module-mmtbx.monomer_library.idealized_aa"]], "mmtbx.monomer_library.linking_mixins": [[308, "module-mmtbx.monomer_library.linking_mixins"]], "mmtbx.monomer_library.linking_setup": [[308, "module-mmtbx.monomer_library.linking_setup"]], "mmtbx.monomer_library.linking_utils": [[308, "module-mmtbx.monomer_library.linking_utils"]], "mmtbx.monomer_library.pdb_interpretation": [[308, "module-mmtbx.monomer_library.pdb_interpretation"]], "mmtbx.monomer_library.rna_sugar_pucker_analysis": [[308, "module-mmtbx.monomer_library.rna_sugar_pucker_analysis"]], "mmtbx.monomer_library.rotamer_utils": [[308, "module-mmtbx.monomer_library.rotamer_utils"]], "mmtbx.monomer_library.server": [[308, "module-mmtbx.monomer_library.server"]], "mod_mod_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id"]], "mon_lib_cif_loader (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_cif_loader"]], "mon_lib_ener_lib_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_ener_lib_cif"]], "mon_lib_list_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.mon_lib_list_cif"]], "mon_lib_names (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.mon_lib_names"]], "mon_lib_srv (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.mon_lib_srv"]], "monomer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.monomer"]], "monomer_atom_dict (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.monomer_atom_dict"]], "monomer_mapping (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping"]], "monomer_mapping_summary (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary"]], "n_expected_atoms() (mmtbx.monomer_library.pdb_interpretation.source_info_server method)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server.n_expected_atoms"]], "n_unknown_type_symbols() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.n_unknown_type_symbols"]], "new_if_defined() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.new_if_defined"]], "next() (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator.next"]], "next() (mmtbx.monomer_library.server.trivial_html_tag_filter method)": [[308, "mmtbx.monomer_library.server.trivial_html_tag_filter.next"]], "non_hydrogen_atoms() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.non_hydrogen_atoms"]], "nonbonded_energy_type_registry (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.nonbonded_energy_type_registry"]], "normalize_atom_ids_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalize_atom_ids_in_place"]], "normalized_angle_list() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_angle_list"]], "normalized_bond_list() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.normalized_bond_list"]], "normalized_bond_list() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_bond_list"]], "normalized_rna_dna (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.normalized_rna_dna"]], "o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.o3p_distance_c1p_outbound_line"]], "o3p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.o3p_perp_xyz"]], "p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.p_distance_c1p_outbound_line"]], "p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.p_perp_xyz"]], "parallelity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.parallelity_counters"]], "pdb_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_atoms"]], "pdb_residue (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_residue"]], "pdb_residue_id_str (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.pdb_residue_id_str"]], "pgd_server (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server"]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection"]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.phil_atom_selection"]], "phil_atom_selection_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection_multiple"]], "phil_atom_selections_as_i_seqs() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs"]], "phil_atom_selections_as_i_seqs_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs_multiple"]], "planarity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.planarity_counters"]], "plane_atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.plane_atom_list"]], "possible_cyclic_peptide() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.possible_cyclic_peptide"]], "print_apply() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.print_apply"]], "print_dict() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.print_dict"]], "print_filtered_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.print_filtered_cif"]], "process (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.process"]], "process_apply_cif_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_apply_cif_link"]], "process_apply_cif_modification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_apply_cif_modification"]], "process_atom_groups_for_linking_single_link() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.process_atom_groups_for_linking_single_link"]], "process_cif() (mmtbx.monomer_library.server.process_cif_mixin method)": [[308, "mmtbx.monomer_library.server.process_cif_mixin.process_cif"]], "process_cif_mixin (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.process_cif_mixin"]], "process_cif_object() (mmtbx.monomer_library.server.process_cif_mixin method)": [[308, "mmtbx.monomer_library.server.process_cif_mixin.process_cif_object"]], "process_custom_links() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_links"]], "process_custom_nonbonded_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_nonbonded_exclusions"]], "process_custom_nonbonded_symmetry_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_custom_nonbonded_symmetry_exclusions"]], "process_geometry_restraints_edits() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits"]], "process_geometry_restraints_edits_angle() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_angle"]], "process_geometry_restraints_edits_bond() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_bond"]], "process_geometry_restraints_edits_dihedral() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_dihedral"]], "process_geometry_restraints_edits_parallelity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_parallelity"]], "process_geometry_restraints_edits_planarity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_edits_planarity"]], "process_geometry_restraints_remove() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_remove"]], "process_geometry_restraints_scale() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_geometry_restraints_scale"]], "process_geostd_rna_dna() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.process_geostd_rna_dna"]], "process_hydrogen_bonds() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.process_hydrogen_bonds"]], "process_nonbonded_for_links() (mmtbx.monomer_library.linking_mixins.linking_mixins method)": [[308, "mmtbx.monomer_library.linking_mixins.linking_mixins.process_nonbonded_for_links"]], "read_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.read_cif"]], "remove_link() (mmtbx.monomer_library.linking_mixins.residuelinkclass method)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass.remove_link"]], "rename_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_angle"]], "rename_atom() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_atom"]], "rename_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_bond"]], "rename_chir() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_chir"]], "rename_generic() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_generic"]], "rename_link_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_angle"]], "rename_link_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_bond"]], "rename_link_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_tor"]], "rename_plan() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_plan"]], "rename_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tor"]], "rename_tree() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tree"]], "report() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.report"]], "report() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report"]], "report_unknown_message() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report_unknown_message"]], "reset() (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator.reset"]], "residue_altloc() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_altloc"]], "residue_dict() (in module mmtbx.monomer_library.idealized_aa)": [[308, "mmtbx.monomer_library.idealized_aa.residue_dict"]], "residue_id_str() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.residue_id_str"]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_name"]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.residue_name"]], "resolve_unexpected() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.resolve_unexpected"]], "rotamer_info() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_info"]], "rotamer_info_master_phil() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_info_master_phil"]], "rotamer_info_phil_str_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_info_phil_str_list"]], "rotamer_iterator (class in mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator"]], "rotamer_iterator() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.rotamer_iterator"]], "rotamer_iterator() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.rotamer_iterator"]], "run() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.run"]], "run() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.run"]], "run() (in module mmtbx.monomer_library.hydrogen_restrictions)": [[308, "mmtbx.monomer_library.hydrogen_restrictions.run"]], "run() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.run"]], "scattering_type_registry (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.scattering_type_registry"]], "search_for_ncs() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.search_for_ncs"]], "sel_backbone() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_backbone"]], "sel_backbone() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_backbone"]], "sel_backbone_or_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_backbone_or_sidechain"]], "sel_backbone_or_sidechain() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_backbone_or_sidechain"]], "sel_classification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_classification"]], "sel_classification() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_classification"]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_phosphate"]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_phosphate"]], "sel_residues_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_residues_within"]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_ribose"]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_ribose"]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_sidechain"]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_sidechain"]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_within"]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_within"]], "selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.selection"]], "selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.selection"]], "selection_manager (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager"]], "server (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.server"]], "set_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.set_classification"]], "show() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.show"]], "show() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show"]], "show() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.show"]], "show_loop() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.show_loop"]], "show_loop_data() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show_loop_data"]], "show_loop_header() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.show_loop_header"]], "show_residue_groups() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.show_residue_groups"]], "site_symmetry_table() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.site_symmetry_table"]], "sites_cart_exact() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sites_cart_exact"]], "skip_if_non_linking() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.skip_if_non_linking"]], "source_info (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.source_info"]], "source_info_server (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server"]], "special_position_dict (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.special_position_dict"]], "sulfur_class() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.sulfur_class"]], "summary() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.summary"]], "summary() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.summary"]], "tardy_model() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.tardy_model"]], "test_for_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_peptide"]], "test_for_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_rna_dna"]], "test_for_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_water"]], "tor_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.tor_list"]], "trans_field() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.trans_field"]], "trivial_html_tag_filter (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.trivial_html_tag_filter"]], "type_symbol_registry_base (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base"]], "unexpected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.unexpected_atoms"]], "unexpected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.unexpected_atoms"]], "update() (mmtbx.monomer_library.pdb_interpretation.cif_output_holder method)": [[308, "mmtbx.monomer_library.pdb_interpretation.cif_output_holder.update"]], "update_internals_due_to_coordinates_change() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.update_internals_due_to_coordinates_change"]], "update_restraints() (mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints method)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints.update_restraints"]], "update_skip_if_longer() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.update_skip_if_longer"]], "validate_geometry_edits_params() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.validate_geometry_edits_params"]], "xray_structure() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.xray_structure"]], "chains_info (class in mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.Chains_info"]], "abs() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.abs"]], "add_cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_cc"]], "add_cc_list() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_cc_list"]], "add_chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_chain_residue_id"]], "add_identity_op() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_identity_op"]], "add_identity_op() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_identity_op"]], "add_note() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_note"]], "add_operator() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.add_operator"]], "add_residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_residues_in_common_list"]], "add_rmsd_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_rmsd_list"]], "add_source_info() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_source_info"]], "adjust_magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.adjust_magnification"]], "adjust_magnification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.adjust_magnification"]], "apply_cob_to_vector() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.apply_cob_to_vector"]], "apply_ligand_ncs (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs"]], "apply_ncs_to_sites() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.apply_ncs_to_sites"]], "apply_transforms() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.apply_transforms"]], "as_ncs_spec_string() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.as_ncs_spec_string"]], "cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.cc"]], "centers() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.centers"]], "chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.chain_residue_id"]], "change_of_basis() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.change_of_basis"]], "combine_ligands_and_hierarchy() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.combine_ligands_and_hierarchy"]], "compute_transform_grad() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.compute_transform_grad"]], "coordinate_offset() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.coordinate_offset"]], "copy_rot_trans() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_rot_trans"]], "copy_vector_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_vector_list"]], "crystal_symmetry_to_ncs() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.crystal_symmetry_to_ncs"]], "deep_copy() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.deep_copy"]], "deep_copy() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy"]], "deep_copy_ops_to_keep() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy_ops_to_keep"]], "deep_copy_order() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.deep_copy_order"]], "delete_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.delete_inv"]], "display_all() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.display_all"]], "display_summary() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.display_summary"]], "distance_from_center() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.distance_from_center"]], "euler_frac_to_rot_trans() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.euler_frac_to_rot_trans"]], "extend_helix_operators() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.extend_helix_operators"]], "extend_helix_operators() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.extend_helix_operators"]], "extract_ligand_residues() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.extract_ligand_residues"]], "extract_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.extract_point_group_symmetry"]], "find_ncs_in_hierarchy() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.find_ncs_in_hierarchy"]], "flip_atoms_in_ncs_groups() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.flip_atoms_in_ncs_groups"]], "format_all_for_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_biomt"]], "format_all_for_group_specification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_group_specification"]], "format_all_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_phenix_refine"]], "format_all_for_resolve() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_resolve"]], "format_for_biomt() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_biomt"]], "format_for_phenix_refine() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_phenix_refine"]], "format_for_resolve() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_resolve"]], "format_group_specification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_group_specification"]], "format_phil_for_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_ncs"]], "format_phil_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_phenix_refine"]], "generate_ncs_ops() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.generate_ncs_ops"]], "get_1_char_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_char_after_key"]], "get_1_value_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_value_after_key"]], "get_3_values_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_3_values_after_key"]], "get_bool_selection_to_keep() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_bool_selection_to_keep"]], "get_c_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_c_symmetry"]], "get_chain_xyz() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chain_xyz"]], "get_chains_info() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chains_info"]], "get_copy_master_selections_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_copy_master_selections_from_match_dict"]], "get_d_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_d_symmetry"]], "get_final_maps_and_cc (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.get_final_maps_and_cc"]], "get_forwards_reverse_helix() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_forwards_reverse_helix"]], "get_helical_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_helical_symmetry"]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_helix_parameters"]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_parameters"]], "get_helix_theta() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_theta"]], "get_helix_z_translation() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_z_translation"]], "get_info_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_info_from_match_dict"]], "get_inverses() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_inverses"]], "get_list_of_best_ncs_copy_map_correlation() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_list_of_best_ncs_copy_map_correlation"]], "get_match_rmsd() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_match_rmsd"]], "get_matching_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_matching_atoms"]], "get_ncs_from_text() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_ncs_from_text"]], "get_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_ncs_name"]], "get_new_fcalc_map() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_new_fcalc_map"]], "get_new_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_new_group"]], "get_order_dict() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_order_dict"]], "get_preliminary_ncs_groups() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_preliminary_ncs_groups"]], "get_refine_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_refine_selection"]], "get_res_range_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_res_range_after_key"]], "get_rot_y() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_y"]], "get_rot_z() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_z"]], "get_sites_cc() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_sites_cc"]], "get_theta_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_theta_along_z"]], "get_trans_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_trans_along_z"]], "get_weight() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_weight"]], "group_operators (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.group_operators"]], "helix_rt_forwards() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_forwards"]], "helix_rt_reverse() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_reverse"]], "identity_op_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.identity_op_id"]], "identity_op_id_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.identity_op_id_in_first_group"]], "import_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.import_ncs_group"]], "init_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_ncs_group"]], "init_oper() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_oper"]], "invert_matrices() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.invert_matrices"]], "invert_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.invert_matrices"]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_helical_along_z"]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_helical_along_z"]], "is_identity() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_identity"]], "is_in_range() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_in_range"]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_point_group_symmetry"]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_point_group_symmetry"]], "is_same_transform() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_same_transform"]], "is_similar_ncs_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_similar_ncs_group"]], "is_similar_ncs_object() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_similar_ncs_object"]], "magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.magnification"]], "make_flips_if_necessary_torsion() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.make_flips_if_necessary_torsion"]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.map_inside_unit_cell"]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.map_inside_unit_cell"]], "max_operators() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.max_operators"]], "mmtbx.ncs": [[309, "module-mmtbx.ncs"]], "mmtbx.ncs.ligands": [[309, "module-mmtbx.ncs.ligands"]], "mmtbx.ncs.ncs": [[309, "module-mmtbx.ncs.ncs"]], "mmtbx.ncs.ncs_search": [[309, "module-mmtbx.ncs.ncs_search"]], "mmtbx.ncs.ncs_utils": [[309, "module-mmtbx.ncs.ncs_utils"]], "mmtbx_res_alignment() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.mmtbx_res_alignment"]], "my_get_rot_trans() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.my_get_rot_trans"]], "my_selection() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.my_selection"]], "n_ligands (mmtbx.ncs.ligands.apply_ligand_ncs property)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.n_ligands"]], "n_ncs_oper() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.n_ncs_oper"]], "ncs (class in mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs"]], "ncs_domain_pdb() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.ncs_domain_pdb"]], "ncs_from_import() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_import"]], "ncs_from_pdb_input_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_pdb_input_BIOMT"]], "ncs_group (class in mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs_group"]], "ncs_grouping_and_group_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.ncs_grouping_and_group_dict"]], "ncs_groups() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_groups"]], "ncs_oper_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_oper_in_first_group"]], "ncs_read() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_read"]], "note() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.note"]], "offset_inside_cell() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.offset_inside_cell"]], "offset_inside_zero_one() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.offset_inside_zero_one"]], "oper_adds_offset() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.oper_adds_offset"]], "overall_cc() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_cc"]], "overall_note() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_note"]], "overall_rmsd() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_rmsd"]], "print_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.print_list"]], "read_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.read_ncs"]], "remove_clashing_atoms() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.remove_clashing_atoms"]], "remove_extra() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_extra"]], "remove_far_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.remove_far_atoms"]], "remove_items_from_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.remove_items_from_selection"]], "remove_ncs_not_consistent_with_space_group_number() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_ncs_not_consistent_with_space_group_number"]], "remove_quotes_from_chain_id() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_quotes_from_chain_id"]], "remove_single_quotes() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_single_quotes"]], "resid_str() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.resid_str"]], "residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.residues_in_common_list"]], "rmsd_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rmsd_list"]], "rota_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rota_matrices"]], "rota_matrices_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rota_matrices_inv"]], "rotate_about_y() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_about_y"]], "rotate_about_z() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_about_z"]], "rotate_matrices() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.rotate_matrices"]], "rotate_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rotate_matrices"]], "rotation_to_angles() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.rotation_to_angles"]], "rotations_translations_forward_euler() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.rotations_translations_forward_euler"]], "round() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.round"]], "sample_operators (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.sample_operators"]], "save_existing_group_info() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_existing_group_info"]], "save_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_ncs_group"]], "save_oper() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.save_oper"]], "search_ncs_relations() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.search_ncs_relations"]], "select_first_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_group"]], "select_first_ncs_operator() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_operator"]], "selected_positions() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.selected_positions"]], "set_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_ncs_name"]], "set_shift_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_shift_cart"]], "set_unit_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_unit_ncs"]], "setup_maps() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.setup_maps"]], "shake_transformations() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.shake_transformations"]], "shift_back_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.shift_back_cart"]], "shift_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.shift_cart"]], "shortcut_1() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.shortcut_1"]], "show_summary() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.show_summary"]], "show_summary() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.show_summary"]], "sort_by_z_translation() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.sort_by_z_translation"]], "sort_by_z_translation() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.sort_by_z_translation"]], "source_of_ncs_info() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.source_of_ncs_info"]], "translations_orth() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.translations_orth"]], "translations_orth_inv() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.translations_orth_inv"]], "value() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.value"]], "write_maps() (mmtbx.ncs.ligands.apply_ligand_ncs method)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.write_maps"]], "write_maps() (mmtbx.ncs.ligands.get_final_maps_and_cc method)": [[309, "mmtbx.ncs.ligands.get_final_maps_and_cc.write_maps"]], "write_pdb() (mmtbx.ncs.ligands.apply_ligand_ncs method)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs.write_pdb"]], "xyz_distance() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.xyz_distance"]], "get_results() (mmtbx.pdbtools.modify method)": [[310, "mmtbx.pdbtools.modify.get_results"]], "master_params() (in module mmtbx.pdbtools)": [[310, "mmtbx.pdbtools.master_params"]], "mmtbx.pdbtools": [[310, "module-mmtbx.pdbtools"]], "modify (class in mmtbx.pdbtools)": [[310, "mmtbx.pdbtools.modify"]], "apply_default_filter() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.apply_default_filter"]], "blue_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.blue_color_model"]], "color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.color_model"]], "convert_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.convert_histogram_data"]], "convert_to_histogram() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.convert_to_histogram"]], "draw() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw"]], "draw_box() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_box"]], "draw_dashed_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_dashed_line"]], "draw_labels() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_labels"]], "draw_solid_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_solid_line"]], "filter_and_convert() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.filter_and_convert"]], "format_value() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.format_value"]], "get_absolute_label_position() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_absolute_label_position"]], "get_basic_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_basic_histogram_data"]], "get_bin_color() (mmtbx.polygon.output.blue_color_model method)": [[311, "mmtbx.polygon.output.blue_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.grayscale_color_model method)": [[311, "mmtbx.polygon.output.grayscale_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.rainbow_color_model method)": [[311, "mmtbx.polygon.output.rainbow_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.red_color_model method)": [[311, "mmtbx.polygon.output.red_color_model.get_bin_color"]], "get_bin_color() (mmtbx.polygon.output.rmb_color_model method)": [[311, "mmtbx.polygon.output.rmb_color_model.get_bin_color"]], "get_color_key() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.get_color_key"]], "get_histogram_colors() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_histogram_colors"]], "get_line_segments() (mmtbx.polygon.output.polygon_layout method)": [[311, "mmtbx.polygon.output.polygon_layout.get_line_segments"]], "get_polygon_intersection() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_polygon_intersection"]], "get_statistics_percentiles() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.get_statistics_percentiles"]], "get_stats_and_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_stats_and_histogram_data"]], "grayscale_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.grayscale_color_model"]], "histogram_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.histogram_layout"]], "hsv2rgb() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.hsv2rgb"]], "load_db() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.load_db"]], "mmtbx.polygon": [[311, "module-mmtbx.polygon"]], "mmtbx.polygon.output": [[311, "module-mmtbx.polygon.output"]], "original_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.original_color_model"]], "polygon() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.polygon"]], "polygon_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.polygon_layout"]], "rainbow_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.rainbow_color_model"]], "ratio_cutoffs (mmtbx.polygon.output.renderer attribute)": [[311, "mmtbx.polygon.output.renderer.ratio_cutoffs"]], "red_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.red_color_model"]], "renderer (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.renderer"]], "resize() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.resize"]], "rmb_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.rmb_color_model"]], "select_dict() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.select_dict"]], "set_color_model() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.set_color_model"]], "set_colors() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.set_colors"]], "show_histogram() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.show_histogram"]], "around_atom (class in mmtbx.real_space)": [[312, "mmtbx.real_space.around_atom"]], "data() (mmtbx.real_space.around_atom method)": [[312, "mmtbx.real_space.around_atom.data"]], "data() (mmtbx.real_space.sampled_model_density method)": [[312, "mmtbx.real_space.sampled_model_density.data"]], "distances() (mmtbx.real_space.around_atom method)": [[312, "mmtbx.real_space.around_atom.distances"]], "mmtbx.real_space": [[312, "module-mmtbx.real_space"]], "sampled_model_density (class in mmtbx.real_space)": [[312, "mmtbx.real_space.sampled_model_density"]], "write_as_xplor_map() (mmtbx.real_space.sampled_model_density method)": [[312, "mmtbx.real_space.sampled_model_density.write_as_xplor_map"]], "action() (in module mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.action"]], "add() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.add"]], "add() (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator.add"]], "add_occupancy_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.add_occupancy_selection"]], "add_rotamer_restraints() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.add_rotamer_restraints"]], "annealing_callback (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.annealing_callback"]], "apply_shifts() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.apply_shifts"]], "apply_shifts() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.apply_shifts"]], "apply_transformation() (in module mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.apply_transformation"]], "apply_transformation() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.apply_transformation"]], "apply_transformation_() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.apply_transformation_"]], "as_ave (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.as_ave"]], "assemble_constraint_groups_3d() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.assemble_constraint_groups_3d"]], "average_sites_cart() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.average_sites_cart"]], "bs_ave (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.bs_ave"]], "ca() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.ca"]], "call_back() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.call_back"]], "callback_after_step() (mmtbx.refinement.geometry_minimization.lbfgs method)": [[313, "mmtbx.refinement.geometry_minimization.lbfgs.callback_after_step"]], "callback_after_step() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.callback_after_step"]], "check_all() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.check_all"]], "collect() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.collect"]], "collect() (mmtbx.refinement.monitors method)": [[313, "mmtbx.refinement.monitors.collect"]], "collect() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.collect"]], "compute_functional_and_gradients() (mmtbx.refinement.anomalous_scatterer_groups.minimizer method)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.compute_functional_and_gradients"]], "compute_target() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.compute_target"]], "coordinate_shifts (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts"]], "count_occupancies() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.count_occupancies"]], "crystal_symmetry() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.crystal_symmetry"]], "d_e_pot_d_sites() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.d_e_pot_d_sites"]], "d_target_d_f_calc_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.d_target_d_f_calc_work"]], "d_target_d_f_model_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.d_target_d_f_model_work"]], "d_target_d_site_cart() (mmtbx.refinement.targets.target_result_mixin method)": [[313, "mmtbx.refinement.targets.target_result_mixin.d_target_d_site_cart"]], "data_target_and_grads() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space.data_target_and_grads"]], "data_target_and_grads() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.data_target_and_grads"]], "deep_copy() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.deep_copy"]], "dump_statistics() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.dump_statistics"]], "e_pot() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.e_pot"]], "evaluate_after_end() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.evaluate_after_end"]], "evaluate_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model"]], "evaluate_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.evaluate_model"]], "expand (class in mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand"]], "expand_angle_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_angle_proxies"]], "expand_bond_params_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_bond_params_table"]], "expand_dihedral_or_chirality_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_dihedral_or_chirality_proxies"]], "expand_model_or_conformer_indices() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_model_or_conformer_indices"]], "expand_nonbonded_types() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_nonbonded_types"]], "expand_pair_sym_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_pair_sym_table"]], "expand_planarity_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_planarity_proxies"]], "expand_site_symmetry_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_site_symmetry_table"]], "extract_partial_occupancy_selections() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.extract_partial_occupancy_selections"]], "finalize() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.finalize"]], "find_anomalous_scatterer_groups() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.find_anomalous_scatterer_groups"]], "finite_difference_test() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.finite_difference_test"]], "finite_difference_test() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.finite_difference_test"]], "format_stats_for_phenix_gui() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.format_stats_for_phenix_gui"]], "get_best_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.get_best_model"]], "get_restraints_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_restraints_tg"]], "get_shifts() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.get_shifts"]], "get_single_atom_selection_string() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.get_single_atom_selection_string"]], "get_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_tg"]], "gradients_wrt_atomic_parameters() (mmtbx.refinement.targets.target_result_mixin method)": [[313, "mmtbx.refinement.targets.target_result_mixin.gradients_wrt_atomic_parameters"]], "gradients_wrt_par() (mmtbx.refinement.group.target_and_grads method)": [[313, "mmtbx.refinement.group.target_and_grads.gradients_wrt_par"]], "gradients_wrt_r() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_r"]], "gradients_wrt_t() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_t"]], "grads_asu_to_one_ncs() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_asu_to_one_ncs"]], "grads_one_ncs_to_asu() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_one_ncs_to_asu"]], "group_minimizer (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.group_minimizer"]], "inflate() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.inflate"]], "is_bool() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_bool"]], "is_size_t() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_size_t"]], "lbfgs (class in mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.lbfgs"]], "lbfgs (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.lbfgs"]], "lbfgs (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs"]], "list_3d_as_bool_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.list_3d_as_bool_selection"]], "ls_ff_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_ff_weights"]], "ls_sigma_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_sigma_weights"]], "macro_cycle_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.macro_cycle_header"]], "make_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_header"]], "make_sub_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_sub_header"]], "manager (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.manager"]], "manager (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.manager"]], "manager (class in mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.manager"]], "manager (class in mmtbx.refinement.refinement_flags)": [[313, "mmtbx.refinement.refinement_flags.manager"]], "manager (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.manager"]], "min_max_mean() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.min_max_mean"]], "minimize() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.minimize"]], "minimize_wrapper_for_ramachandran() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.minimize_wrapper_for_ramachandran"]], "minimizer (class in mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer"]], "minimizer (class in mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.minimizer"]], "mmtbx.refinement": [[313, "module-mmtbx.refinement"]], "mmtbx.refinement.adp_refinement": [[313, "module-mmtbx.refinement.adp_refinement"]], "mmtbx.refinement.anomalous_scatterer_groups": [[313, "module-mmtbx.refinement.anomalous_scatterer_groups"]], "mmtbx.refinement.geometry_minimization": [[313, "module-mmtbx.refinement.geometry_minimization"]], "mmtbx.refinement.group": [[313, "module-mmtbx.refinement.group"]], "mmtbx.refinement.inspect_tardy_trajectory": [[313, "module-mmtbx.refinement.inspect_tardy_trajectory"]], "mmtbx.refinement.minimization": [[313, "module-mmtbx.refinement.minimization"]], "mmtbx.refinement.minimization_ncs_constraints": [[313, "module-mmtbx.refinement.minimization_ncs_constraints"]], "mmtbx.refinement.occupancies": [[313, "module-mmtbx.refinement.occupancies"]], "mmtbx.refinement.orca": [[313, "module-mmtbx.refinement.orca"]], "mmtbx.refinement.print_statistics": [[313, "module-mmtbx.refinement.print_statistics"]], "mmtbx.refinement.refinement_flags": [[313, "module-mmtbx.refinement.refinement_flags"]], "mmtbx.refinement.rigid_body": [[313, "module-mmtbx.refinement.rigid_body"]], "mmtbx.refinement.select_best_starting_model": [[313, "module-mmtbx.refinement.select_best_starting_model"]], "mmtbx.refinement.tardy": [[313, "module-mmtbx.refinement.tardy"]], "mmtbx.refinement.targets": [[313, "module-mmtbx.refinement.targets"]], "mmtbx.refinement.weights_params": [[313, "module-mmtbx.refinement.weights_params"]], "monitor (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.monitor"]], "monitors (class in mmtbx.refinement)": [[313, "mmtbx.refinement.monitors"]], "neutron_flag (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.neutron_flag"]], "neutron_line() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.neutron_line"]], "occupancy_regroupping() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.occupancy_regroupping"]], "occupancy_selections() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.occupancy_selections"]], "pack() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.pack"]], "pack() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.pack"]], "pack() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.pack"]], "pack_gradients() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.pack_gradients"]], "pack_unpack() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.pack_unpack"]], "phaser_sad_target_functor (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor"]], "potential_object (class in mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.potential_object"]], "prepare_for_minimization() (mmtbx.refinement.targets.phaser_sad_target_functor method)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor.prepare_for_minimization"]], "prepare_for_minimization() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.prepare_for_minimization"]], "r_free (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_free"]], "r_free() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.r_free"]], "r_free_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_free_start"]], "r_frees (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.r_frees"]], "r_work (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_work"]], "r_work() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.r_work"]], "r_work_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.r_work_start"]], "r_works (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.r_works"]], "refinable_params_one_ncs_to_asu() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.refinable_params_one_ncs_to_asu"]], "refine_adp (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.refine_adp"]], "refine_anomalous_substructure() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.refine_anomalous_substructure"]], "refinement_monitor (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor"]], "requires_experimental_phases() (mmtbx.refinement.targets.target_attributes method)": [[313, "mmtbx.refinement.targets.target_attributes.requires_experimental_phases"]], "restraints_target_and_grads() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.restraints_target_and_grads"]], "rigid_body_minimizer (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer"]], "rigid_body_shift_accumulator (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator"]], "rigid_groups_from_pdb_chains() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.rigid_groups_from_pdb_chains"]], "rmsd_calculation() (mmtbx.refinement.orca.expand method)": [[313, "mmtbx.refinement.orca.expand.rmsd_calculation"]], "rmsd_calculator() (mmtbx.refinement.orca.expand method)": [[313, "mmtbx.refinement.orca.expand.rmsd_calculator"]], "rotation() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.rotation"]], "run() (in module mmtbx.refinement.inspect_tardy_trajectory)": [[313, "mmtbx.refinement.inspect_tardy_trajectory.run"]], "run() (in module mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.run"]], "run2 (class in mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.run2"]], "run_constrained (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.run_constrained"]], "run_lbfgs() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.run_lbfgs"]], "save_best_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.save_best_model"]], "save_pdb_file() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.save_pdb_file"]], "save_updated_data() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.save_updated_data"]], "score() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.score"]], "select() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.select"]], "select() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select"]], "select_detached() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select_detached"]], "select_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.select_model"]], "set_refinable_parameters() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.set_refinable_parameters"]], "show() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.show"]], "show() (mmtbx.refinement.adp_refinement.weight_result method)": [[313, "mmtbx.refinement.adp_refinement.weight_result.show"]], "show() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.show"]], "show() (mmtbx.refinement.group.manager method)": [[313, "mmtbx.refinement.group.manager.show"]], "show() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.show"]], "show() (mmtbx.refinement.occupancies.manager method)": [[313, "mmtbx.refinement.occupancies.manager.show"]], "show() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.show"]], "show() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.show"]], "show() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.show"]], "show() (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator.show"]], "show() (mmtbx.refinement.select_best_starting_model.evaluate_model method)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.show"]], "show() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.show"]], "show_current_r_factors_summary() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.show_current_r_factors_summary"]], "show_helper() (mmtbx.refinement.occupancies.manager method)": [[313, "mmtbx.refinement.occupancies.manager.show_helper"]], "show_process_info() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_process_info"]], "show_rigid_body_rotations_and_translations() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_rigid_body_rotations_and_translations"]], "show_times() (in module mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.show_times"]], "show_times() (in module mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.show_times"]], "show_times() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_times"]], "space_group_info() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.space_group_info"]], "sphere_similarity_restraints (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.sphere_similarity_restraints"]], "split_resolution_range() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.split_resolution_range"]], "stats_table (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.stats_table"]], "steps (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.steps"]], "strip_model() (in module mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.strip_model"]], "success() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.success"]], "szs() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.szs"]], "target() (mmtbx.refinement.group.target_and_grads method)": [[313, "mmtbx.refinement.group.target_and_grads.target"]], "target() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.target"]], "target_and_gradients() (mmtbx.refinement.group.sphere_similarity_restraints method)": [[313, "mmtbx.refinement.group.sphere_similarity_restraints.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space.target_and_gradients"]], "target_and_gradients() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space.target_and_gradients"]], "target_and_grads (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.target_and_grads"]], "target_and_grads (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.target_and_grads"]], "target_attributes (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_attributes"]], "target_function_and_grads_geometry_minimization (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization"]], "target_function_and_grads_real_space (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space"]], "target_function_and_grads_reciprocal_space (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space"]], "target_function_is_invariant_under_allowed_origin_shifts() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.target_function_is_invariant_under_allowed_origin_shifts"]], "target_functor (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_functor"]], "target_memory() (mmtbx.refinement.targets.phaser_sad_target_functor method)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor.target_memory"]], "target_per_reflection() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_per_reflection"]], "target_result (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_result"]], "target_result_mixin (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.target_result_mixin"]], "target_test() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_test"]], "target_work() (mmtbx.refinement.targets.target_result method)": [[313, "mmtbx.refinement.targets.target_result.target_work"]], "trajectory_output (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.trajectory_output"]], "translation() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.translation"]], "try_weight() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.try_weight"]], "ucf() (in module mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.ucf"]], "unpack() (mmtbx.refinement.anomalous_scatterer_groups.minimizer method)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.minimizer.unpack"]], "unpack_x() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.unpack_x"]], "unpack_x() (mmtbx.refinement.occupancies.minimizer method)": [[313, "mmtbx.refinement.occupancies.minimizer.unpack_x"]], "unpack_x() (mmtbx.refinement.rigid_body.rigid_body_minimizer method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_minimizer.unpack_x"]], "update_cdl_restraints() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.update_cdl_restraints"]], "update_xray_structure() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.update_xray_structure"]], "updaterdl() (mmtbx.refinement.geometry_minimization.run2 method)": [[313, "mmtbx.refinement.geometry_minimization.run2.updaterdl"]], "validate() (mmtbx.refinement.targets.target_attributes method)": [[313, "mmtbx.refinement.targets.target_attributes.validate"]], "weight_result (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.weight_result"]], "xray_line() (mmtbx.refinement.minimization.monitor method)": [[313, "mmtbx.refinement.minimization.monitor.xray_line"]], "xray_structure (mmtbx.refinement.select_best_starting_model.evaluate_model attribute)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model.xray_structure"]], "bin_generator_equal_range() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_range"]], "bin_generator_equal_size() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_size"]], "bivariate_histogram() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bivariate_histogram"]], "closest_to_mean() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.closest_to_mean"]], "dist2() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.dist2"]], "ensemble_mean_geometry_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_mean_geometry_stats"]], "ensemble_mean_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.ensemble_mean_hierarchy"]], "ensemble_reduction() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_reduction"]], "ensemble_rmsf_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_rmsf_stats"]], "get_centroid_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_centroid_hierarchy"]], "get_rmsf_b_factor_per_residue_per_atom() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_rmsf_B_factor_per_residue_per_atom"]], "get_selected_hierarchys() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, 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method)": [[315, "mmtbx.refinement.real_space.structure_monitor.assert_pdb_hierarchy_xray_structure_sync"]], "backrub_move() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.backrub_move"]], "box_refinement_manager (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager"]], "check_sites_match() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.check_sites_match"]], "cluster (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.cluster"]], "common_map_values() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.common_map_values"]], "compute_functional_and_gradients() (mmtbx.refinement.real_space.rigid_body.refine method)": [[315, "mmtbx.refinement.real_space.rigid_body.refine.compute_functional_and_gradients"]], "compute_map() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.compute_map"]], "compute_target() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.compute_target"]], "compute_target() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.compute_target"]], "compute_target() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.compute_target"]], "count_outliers() (mmtbx.refinement.real_space.fit_residues.run method)": [[315, "mmtbx.refinement.real_space.fit_residues.run.count_outliers"]], "d_e_pot_d_sites() (mmtbx.refinement.real_space.rigid_body.refine method)": [[315, "mmtbx.refinement.real_space.rigid_body.refine.d_e_pot_d_sites"]], "diff_map (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map"]], "easy (class in mmtbx.refinement.real_space.individual_sites)": [[315, 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mmtbx.refinement.real_space.fit_residues)": [[315, "mmtbx.refinement.real_space.fit_residues.fix_outliers"]], "flatten() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.flatten"]], "flatten() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.flatten"]], "format_info_string() (mmtbx.refinement.real_space.residue_monitor method)": [[315, "mmtbx.refinement.real_space.residue_monitor.format_info_string"]], "generate_angles_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.generate_angles_nested"]], "get_nonbonded_bumpers() (mmtbx.refinement.real_space.fit_residues.run method)": [[315, "mmtbx.refinement.real_space.fit_residues.run.get_nonbonded_bumpers"]], "get_radii() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radii"]], "get_radius() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radius"]], "get_rotamer_iterator() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.get_rotamer_iterator"]], "get_rotamer_iterator() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_rotamer_iterator"]], "get_target_value() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_target_value"]], "get_vector_flat() (mmtbx.refinement.real_space.cluster method)": [[315, "mmtbx.refinement.real_space.cluster.get_vector_flat"]], "grid_sample_around_c_n_axis() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.grid_sample_around_c_n_axis"]], "initialize() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.initialize"]], "initialize() (mmtbx.refinement.real_space.structure_monitor method)": [[315, 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(class in mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.refine_mz"]], "refinery (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery"]], "reset() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.reset"]], "reset() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.reset"]], "reset() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.reset"]], "residue_monitor (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.residue_monitor"]], "rmsds() (mmtbx.refinement.real_space.individual_sites.refinery method)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery.rmsds"]], "rmsds() (mmtbx.refinement.real_space.individual_sites.simple method)": [[315, "mmtbx.refinement.real_space.individual_sites.simple.rmsds"]], "rsr_model (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.rsr_model"]], "run (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.run"]], "run (class in mmtbx.refinement.real_space.fit_residues)": [[315, "mmtbx.refinement.real_space.fit_residues.run"]], "run (class in mmtbx.refinement.real_space.weight)": [[315, "mmtbx.refinement.real_space.weight.run"]], "run() (in module mmtbx.refinement.real_space.fit_water)": [[315, "mmtbx.refinement.real_space.fit_water.run"]], "run_with_minimization (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization"]], "score (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score"]], "score2 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score2"]], "score3 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score3"]], "score4 (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.score4"]], "sel_all() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_all"]], "sel_outliers() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers"]], "sel_outliers_and_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_and_poormap"]], "sel_outliers_or_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_or_poormap"]], "sel_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_poormap"]], "selection_around_to_negate() (in module mmtbx.refinement.real_space)": [[315, 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"torsion_search_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.torsion_search_nested"]], "tune_up (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.tune_up"]], "update() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.update"]], "update() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.update"]], "update() (mmtbx.refinement.real_space.score2 method)": [[315, "mmtbx.refinement.real_space.score2.update"]], "update() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.update"]], "update() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.update"]], "update() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.update"]], "update_statistics() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.update_statistics"]], "update_target_map() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager.update_target_map"]], "update_xray_structure() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager.update_xray_structure"]], "ndimtable (class in mmtbx.rotamer.n_dim_table)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable"]], "namedrot (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.NamedRot"]], "propertyfile (class in mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.PropertyFile"]], "ramachandraneval (class in mmtbx.rotamer.ramachandran_eval)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval"]], "rotamereval (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval"]], "rotamerid (class in mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID"]], "sidechainangles (class in mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles"]], "aatables (mmtbx.rotamer.rotamer_eval.rotamereval attribute)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.aaTables"]], "anglesforaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForAA"]], "anglesforrot (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForRot"]], "atomsforangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsForAngle"]], "atomsmovewithangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsMoveWithAngle"]], "bin2index() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index"]], "bin2index_limit() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index_limit"]], "centerof() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.centerOf"]], "check_table_name() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.check_table_name"]], "chi_angles() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.chi_angles"]], "chisperaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.chisPerAA"]], "clampinclusive() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.clampInclusive"]], "collect_residue_torsion_angles() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.collect_residue_torsion_angles"]], "collect_sidechain_chi_angles() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.collect_sidechain_chi_angles"]], "contains() (mmtbx.rotamer.rotamer_eval.namedrot method)": [[316, "mmtbx.rotamer.rotamer_eval.NamedRot.contains"]], "createfromtext() (mmtbx.rotamer.n_dim_table.ndimtable static method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.createFromText"]], "draw_plot() (mmtbx.rotamer.graphics.rotarama_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin.draw_plot"]], "draw_ramachandran_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_ramachandran_plot"]], "draw_rotamer_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_rotamer_plot"]], "eval_residue_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_residue_completeness"]], "eval_sidechain_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_sidechain_completeness"]], "evaluate() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate"]], "evaluate() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate"]], "evaluate_residue() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue"]], "evaluate_residue_2() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue_2"]], "evaluate_sites() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate_sites"]], "exercise() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.exercise"]], "extent (mmtbx.rotamer.graphics.ramachandran_plot_mixin attribute)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin.extent"]], "extent (mmtbx.rotamer.graphics.rotarama_plot_mixin attribute)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin.extent"]], "extract_chi_atoms() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.extract_chi_atoms"]], "find_rotarama_data_dir() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.find_rotarama_data_dir"]], "find_source_dir() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.find_source_dir"]], "find_source_dir() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.find_source_dir"]], "format_ramachandran_plot_title() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.format_ramachandran_plot_title"]], "frequencies_from_rotamer (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.frequencies_from_rotamer"]], "get_atom_dict() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.get_atom_dict"]], "get_omega_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_omega_atoms"]], "get_phi_psi_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_phi_psi_atoms"]], "get_phi_psi_indices() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_phi_psi_indices"]], "get_residue_ramachandran_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_ramachandran_data"]], "get_residue_rotamer_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_rotamer_data"]], "get_rotamer_angles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_angles"]], "get_rotamer_expectation_frequencies() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_expectation_frequencies"]], "get_rotamers() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamers"]], "identify() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.identify"]], "improper_cnab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_cnab_from_atoms"]], "improper_ncab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_ncab_from_atoms"]], "is_cis_peptide() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.is_cis_peptide"]], "iterator() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.iterator"]], "makeatomdict() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.makeAtomDict"]], "measureangle() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureAngle"]], "measurechiangles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureChiAngles"]], "mmtbx.rotamer": [[316, "module-mmtbx.rotamer"]], "mmtbx.rotamer.graphics": [[316, "module-mmtbx.rotamer.graphics"]], "mmtbx.rotamer.n_dim_table": [[316, "module-mmtbx.rotamer.n_dim_table"]], "mmtbx.rotamer.ramachandran_eval": [[316, "module-mmtbx.rotamer.ramachandran_eval"]], "mmtbx.rotamer.rotamer_eval": [[316, "module-mmtbx.rotamer.rotamer_eval"]], "mmtbx.rotamer.sidechain_angles": [[316, "module-mmtbx.rotamer.sidechain_angles"]], "mon_lib_query() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.mon_lib_query"]], "names (mmtbx.rotamer.rotamer_eval.rotamerid attribute)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.names"]], "nearest_rotamer_sites_cart() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.nearest_rotamer_sites_cart"]], "omega_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.omega_from_atoms"]], "open_rotarama_dlite() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.open_rotarama_dlite"]], "phi_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_atoms"]], "phi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_sites"]], "phi_psi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_psi_from_sites"]], "process() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.process"]], "process() (mmtbx.rotamer.sidechain_angles.propertyfile method)": [[316, "mmtbx.rotamer.sidechain_angles.PropertyFile.process"]], "psi_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.psi_from_atoms"]], "psi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.psi_from_sites"]], "ramachandran_plot (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot"]], "ramachandran_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin"]], "resatomstochi (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.resAtomsToChi"]], "rotamer_plot (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotamer_plot"]], "rotamer_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotamer_plot_mixin"]], "rotamersforaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.rotamersForAA"]], "rotarama_plot_mixin (class in mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin"]], "setvalueat() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.setValueAt"]], "set_labels() (mmtbx.rotamer.graphics.ramachandran_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin.set_labels"]], "set_labels() (mmtbx.rotamer.graphics.rotamer_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotamer_plot_mixin.set_labels"]], "valueat() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.valueAt"]], "whereis() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.whereIs"]], "wrap_chis() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.wrap_chis"]], "wrap_sym() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.wrap_sym"]], "wrapbin() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.wrapbin"]], "mmtbx.rsr": [[317, "module-mmtbx.rsr"]], "absence_type() (mmtbx.scaling.absences.conditions_for_operator method)": [[318, "mmtbx.scaling.absences.conditions_for_operator.absence_type"]], "absences (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.absences"]], "absences_list (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.absences_list"]], "acentric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_e_sq_minus_one_library"]], "acentric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_f_ratio_library"]], "acentric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.acentric_i_ratio_library"]], "add_wavelength_info() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.add_wavelength_info"]], "alpha_beta() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.alpha_beta"]], "alpha_beta() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.alpha_beta"]], "analyse() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.analyse"]], "analyze_absences (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.analyze_absences"]], "analyze_aniso_correction() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.analyze_aniso_correction"]], "analyze_intensity_statistics() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.analyze_intensity_statistics"]], "analyze_measurability (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_measurability"]], "analyze_resolution_limits (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits"]], "aniso_b_min (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_min"]], "aniso_b_ratio (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_ratio"]], "aniso_range_of_b (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_range_of_b"]], "aniso_ratio_p_value() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.aniso_ratio_p_value"]], "anisotropic_correction() (in module mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.anisotropic_correction"]], "ano_scaling (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.ano_scaling"]], "anomalous (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.anomalous"]], "apply_scale_to_original_data() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.apply_scale_to_original_data"]], "average_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver.average_all"]], "axis_type (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.axis_type"]], "basic_analyses (class in mmtbx.scaling.basic_analyses)": [[318, "mmtbx.scaling.basic_analyses.basic_analyses"]], "basic_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.basic_wilson_outliers"]], "beamstop_shadow_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.beamstop_shadow_outliers"]], "britton_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.britton_frac"]], "britton_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.britton_test"]], "calc_correlation() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.calc_correlation"]], "cc_one_half_outer (mmtbx.scaling.xtriage.merging_statistics property)": [[318, "mmtbx.scaling.xtriage.merging_statistics.cc_one_half_outer"]], "centric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_e_sq_minus_one_library"]], "centric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_f_ratio_library"]], "centric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.centric_i_ratio_library"]], "change_symmetry() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.change_symmetry"]], "check() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check"]], "check_condition() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_condition"]], "check_conditions() (mmtbx.scaling.absences.analyze_absences method)": [[318, "mmtbx.scaling.absences.analyze_absences.check_conditions"]], "check_for_pathological_input_data() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.check_for_pathological_input_data"]], "check_mask() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_mask"]], "closest_rational() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.closest_rational"]], "cns_fa_driver (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver"]], "combined_scaling (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling"]], "comparator() (mmtbx.scaling.absences.sgi_iterator method)": [[318, "mmtbx.scaling.absences.sgi_iterator.comparator"]], "completeness_enforcement (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.completeness_enforcement"]], "component (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.component"]], "compute_coefs() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_coefs"]], "compute_coefs() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_coefs"]], "compute_determinant() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_determinant"]], "compute_determinant() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_determinant"]], "compute_fa_values() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.compute_fa_values"]], "compute_fa_values() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.compute_fa_values"]], "compute_functional() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_functional"]], "compute_functional_and_gradients() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.compute_functional_and_gradients"]], "compute_gradient() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient"]], "compute_gradient_fd() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient_fd"]], "compute_maha_l() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.compute_maha_l"]], "compute_ratios() (mmtbx.scaling.twin_analyses.wilson_moments method)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.compute_ratios"]], "condition() (mmtbx.scaling.absences.conditions_for_operator method)": [[318, "mmtbx.scaling.absences.conditions_for_operator.condition"]], "conditions_for_operator (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.conditions_for_operator"]], "correlation_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses"]], "curve() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.curve"]], "data_analysis (class in mmtbx.scaling)": [[318, "mmtbx.scaling.data_analysis"]], "data_as_flex_arrays() (mmtbx.scaling.relative_wilson.summary method)": [[318, "mmtbx.scaling.relative_wilson.summary.data_as_flex_arrays"]], "data_strength_and_completeness (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness"]], "data_summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.data_summary"]], "default_2wmad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_2wmad"]], "default_3wmad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_3wmad"]], "default_rip() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_rip"]], "default_sad() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_sad"]], "default_sir() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_sir"]], "default_siras() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.default_siras"]], "delta (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.delta"]], "delta_f_prime_f_double_prime_ratio (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.delta_f_prime_f_double_prime_ratio"]], "delta_generator (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.delta_generator"]], "delta_le_page (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_le_page"]], "delta_le_page() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_le_page"]], "delta_lebedev (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_lebedev"]], "delta_lebedev() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_lebedev"]], "delta_santoro (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.delta_santoro"]], "delta_santoro() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.delta_santoro"]], "density_calculator (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.density_calculator"]], "detect_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers"]], "detect_outliers_rms() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_rms"]], "detect_outliers_sigma() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_sigma"]], "detect_outliers_solve() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_solve"]], "detect_pseudo_translations (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations"]], "eobs_and_ecalc_miller_array_normalizers() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.eobs_and_ecalc_miller_array_normalizers"]], "estimate_d_min() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.estimate_d_min"]], "exercise() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.exercise"]], "exercise() (in module mmtbx.scaling.thorough_outlier_test)": [[318, "mmtbx.scaling.thorough_outlier_test.exercise"]], "expected_intensity (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.expected_intensity"]], "extreme_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.extreme_wilson_outliers"]], "f_double_prime_ratio (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio"]], "find_maximum() (mmtbx.scaling.twin_analyses.correlation_analyses method)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses.find_maximum"]], "finish_job() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.finish_job"]], "flush() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.flush"]], "fom() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.fom"]], "fom() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.fom"]], "format_it() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.format_it"]], "fraction_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.fraction_outliers"]], "functional() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.functional"]], "gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein.gamma"]], "gamma_nucleic (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_nucleic"]], "gamma_protein (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein"]], "get_alpha() (mmtbx.scaling.twin_analyses.britton_test method)": [[318, "mmtbx.scaling.twin_analyses.britton_test.get_alpha"]], "get_completeness() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_completeness"]], "get_data_file() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_data_file"]], "get_log_p_solc() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.get_log_p_solc"]], "get_merging_statistics() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_merging_statistics"]], "get_r_value_total() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.get_r_value_total"]], "get_relative_wilson() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_relative_wilson"]], "get_twin_laws() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.get_twin_laws"]], "get_z_scores() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.get_z_scores"]], "gradients() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.gradients"]], "guesstimate() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.guesstimate"]], "guesstimate_mod_hkl() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.guesstimate_mod_hkl"]], "gui_output (mmtbx.scaling.loggraph_output attribute)": [[318, "mmtbx.scaling.loggraph_output.gui_output"]], "gui_output (mmtbx.scaling.xtriage_output attribute)": [[318, "mmtbx.scaling.xtriage_output.gui_output"]], "h (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.h"]], "h_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.h_frac"]], "h_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.h_test"]], "halton_x() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.halton_x"]], "has_abnormal_intensity_statistics() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_abnormal_intensity_statistics"]], "has_higher_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_higher_symmetry"]], "has_pseudo_translational_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_pseudo_translational_symmetry"]], "has_twinning() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_twinning"]], "hessian() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian"]], "hessian_transform() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian_transform"]], "high_resolution_for_twin_tests() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.high_resolution_for_twin_tests"]], "i_over_sigma_outer_shell (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.i_over_sigma_outer_shell"]], "i_over_sigma_outer_shell() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.i_over_sigma_outer_shell"]], "i_sigi_completeness_stats (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.i_sigi_completeness_stats"]], "ice_ring_checker (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.ice_ring_checker"]], "is_centric() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.is_centric"]], "is_elliptically_truncated() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.is_elliptically_truncated"]], "is_twinned() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.is_twinned"]], "iso_b_wilson (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.iso_b_wilson"]], "kernel_normalisation (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.kernel_normalisation"]], "l_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.l_test"]], "l_test_mean_l (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l"]], "l_test_mean_l_squared (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l_squared"]], "launcher (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.launcher"]], "likelihood() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.likelihood"]], "list() (mmtbx.scaling.absences.sgi_iterator method)": [[318, "mmtbx.scaling.absences.sgi_iterator.list"]], "local_lsq_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_lsq_scaling"]], "local_moment_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_moment_scaling"]], "local_nikonov_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_nikonov_scaling"]], "local_scaling_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver"]], "log_binned_completeness (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.log_binned_completeness"]], "log_p() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.log_p"]], "loggraph_output (class in mmtbx.scaling)": [[318, "mmtbx.scaling.loggraph_output"]], "low_d_cut (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.low_d_cut"]], "ls_rel_scale_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.ls_rel_scale_driver"]], "macromolecule_fraction() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.macromolecule_fraction"]], "make_big_header() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.make_big_header"]], "make_log_beam_stop() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_beam_stop"]], "make_log_model() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_model"]], "make_log_wilson() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_wilson"]], "make_pg_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_pg_r_table"]], "make_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_r_table"]], "make_sym_op_table() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.make_sym_op_table"]], "massage_data (class in mmtbx.scaling.massage_twin_detwin_data)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data"]], "matthews_n_copies() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.matthews_n_copies"]], "matthews_rupp (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.matthews_rupp"]], "max_d_min_delta() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.max_d_min_delta"]], "max_estimated_twin_fraction (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.max_estimated_twin_fraction"]], "max_twin_fraction() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.max_twin_fraction"]], "merge_data_and_guess_space_groups() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.merge_data_and_guess_space_groups"]], "merging_statistics (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.merging_statistics"]], "ml_aniso_absolute_scaling (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling"]], "ml_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.ml_frac"]], "ml_iso_absolute_scaling (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling"]], "ml_murray_rust (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust"]], "ml_murray_rust_with_ncs (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs"]], "mmtbx.scaling": [[318, "module-mmtbx.scaling"]], "mmtbx.scaling.absence_likelihood": [[318, "module-mmtbx.scaling.absence_likelihood"]], "mmtbx.scaling.absences": [[318, "module-mmtbx.scaling.absences"]], "mmtbx.scaling.absolute_scaling": [[318, "module-mmtbx.scaling.absolute_scaling"]], "mmtbx.scaling.basic_analyses": [[318, "module-mmtbx.scaling.basic_analyses"]], "mmtbx.scaling.data_statistics": [[318, "module-mmtbx.scaling.data_statistics"]], "mmtbx.scaling.fa_estimation": [[318, "module-mmtbx.scaling.fa_estimation"]], "mmtbx.scaling.fest": [[318, "module-mmtbx.scaling.fest"]], "mmtbx.scaling.make_param": [[318, "module-mmtbx.scaling.make_param"]], "mmtbx.scaling.massage_twin_detwin_data": [[318, "module-mmtbx.scaling.massage_twin_detwin_data"]], "mmtbx.scaling.matthews": [[318, "module-mmtbx.scaling.matthews"]], "mmtbx.scaling.outlier_plots": [[318, "module-mmtbx.scaling.outlier_plots"]], "mmtbx.scaling.outlier_rejection": [[318, "module-mmtbx.scaling.outlier_rejection"]], "mmtbx.scaling.pair_analyses": [[318, "module-mmtbx.scaling.pair_analyses"]], "mmtbx.scaling.pre_scale": [[318, "module-mmtbx.scaling.pre_scale"]], "mmtbx.scaling.random_omit": [[318, "module-mmtbx.scaling.random_omit"]], "mmtbx.scaling.relative_scaling": [[318, "module-mmtbx.scaling.relative_scaling"]], "mmtbx.scaling.relative_wilson": [[318, "module-mmtbx.scaling.relative_wilson"]], "mmtbx.scaling.remove_outliers": [[318, "module-mmtbx.scaling.remove_outliers"]], "mmtbx.scaling.rip_scale": [[318, "module-mmtbx.scaling.rip_scale"]], "mmtbx.scaling.sad_scale": [[318, "module-mmtbx.scaling.sad_scale"]], "mmtbx.scaling.sigmaa_estimation": [[318, "module-mmtbx.scaling.sigmaa_estimation"]], "mmtbx.scaling.sir_scale": [[318, "module-mmtbx.scaling.sir_scale"]], "mmtbx.scaling.siras_scale": [[318, "module-mmtbx.scaling.siras_scale"]], "mmtbx.scaling.ta_alpha_beta_calc": [[318, "module-mmtbx.scaling.ta_alpha_beta_calc"]], "mmtbx.scaling.thorough_outlier_test": [[318, "module-mmtbx.scaling.thorough_outlier_test"]], "mmtbx.scaling.twin_analyses": [[318, "module-mmtbx.scaling.twin_analyses"]], "mmtbx.scaling.twmad_scale": [[318, "module-mmtbx.scaling.twmad_scale"]], "mmtbx.scaling.xtriage": [[318, "module-mmtbx.scaling.xtriage"]], "model_based_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.model_based_outliers"]], "modify_weights() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.modify_weights"]], "mum_dad (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.mum_dad"]], "mum_dad (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.mum_dad"]], "n_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.n_outliers"]], "n_outliers() (mmtbx.scaling.relative_wilson.summary method)": [[318, "mmtbx.scaling.relative_wilson.summary.n_outliers"]], "n_problems (mmtbx.scaling.xtriage.summary property)": [[318, "mmtbx.scaling.xtriage.summary.n_problems"]], "n_z_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.n_z_test"]], "naive_fa_estimation (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.naive_fa_estimation"]], "new_format (mmtbx.scaling.xtriage.xtriage_analyses attribute)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.new_format"]], "new_format (mmtbx.scaling.xtriage.xtriage_summary attribute)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.new_format"]], "newline() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.newline"]], "newline() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.newline"]], "newline() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.newline"]], "normalise_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method)": [[318, "mmtbx.scaling.fa_estimation.cns_fa_driver.normalise_all"]], "nucleic() (mmtbx.scaling.matthews.component class method)": [[318, "mmtbx.scaling.matthews.component.nucleic"]], "number_of_wilson_outliers (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.number_of_wilson_outliers"]], "number_table() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.number_table"]], "obliquity (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.obliquity"]], "operator (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.operator"]], "original_intensities_flag() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.original_intensities_flag"]], "out (mmtbx.scaling.printed_output attribute)": [[318, "mmtbx.scaling.printed_output.out"]], "outlier_manager (class in mmtbx.scaling.outlier_rejection)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager"]], "outlier_rejection (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection"]], "overall_i_sig_i (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.overall_i_sig_i"]], "p_solc_calc() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.p_solc_calc"]], "p_solc_calc() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.p_solc_calc"]], "p_value() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.p_value"]], "p_vm_calculator (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.p_vm_calculator"]], "pack() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.pack"]], "pack() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.pack"]], "patterson_verdict (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.patterson_verdict"]], "patterson_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.patterson_verdict"]], "perform_least_squares_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_least_squares_scaling"]], "perform_local_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_local_scaling"]], "perform_outlier_rejection() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_outlier_rejection"]], "phase_errors() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.phase_errors"]], "phase_errors() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.phase_errors"]], "phil_lego (class in mmtbx.scaling.make_param)": [[318, "mmtbx.scaling.make_param.phil_lego"]], "plotit() (in module mmtbx.scaling.outlier_plots)": [[318, "mmtbx.scaling.outlier_plots.plotit"]], "possible_outliers (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.possible_outliers"]], "pre_scaler (class in mmtbx.scaling.pre_scale)": [[318, "mmtbx.scaling.pre_scale.pre_scaler"]], "print_banner() (in module mmtbx.scaling.fest)": [[318, "mmtbx.scaling.fest.print_banner"]], "print_banner() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.print_banner"]], "print_help() (in module mmtbx.scaling.remove_outliers)": [[318, "mmtbx.scaling.remove_outliers.print_help"]], "print_help() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.print_help"]], "printed_output (class in mmtbx.scaling)": [[318, 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"mmtbx.scaling.random_omit.random_omit_data"]], "refinery (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.refinery"]], "reindexing (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.reindexing"]], "relative_wilson (class in mmtbx.scaling.relative_wilson)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson"]], "remove_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.remove_outliers"]], "remove_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.remove_outliers"]], "resolution_cut() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.resolution_cut"]], "resolution_dependent_r_values() (mmtbx.scaling.twin_analyses.r_values method)": [[318, "mmtbx.scaling.twin_analyses.r_values.resolution_dependent_r_values"]], "resolution_limit_of_anomalous_signal() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.resolution_limit_of_anomalous_signal"]], "return_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data.return_data"]], "return_point_groups() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.return_point_groups"]], "run() (in module mmtbx.scaling.fest)": [[318, "mmtbx.scaling.fest.run"]], "run() (in module mmtbx.scaling.make_param)": [[318, "mmtbx.scaling.make_param.run"]], "run() (in module mmtbx.scaling.outlier_plots)": [[318, "mmtbx.scaling.outlier_plots.run"]], "run() (in module mmtbx.scaling.remove_outliers)": [[318, "mmtbx.scaling.remove_outliers.run"]], "run() (in module mmtbx.scaling.rip_scale)": [[318, "mmtbx.scaling.rip_scale.run"]], "run() (in module mmtbx.scaling.sad_scale)": [[318, "mmtbx.scaling.sad_scale.run"]], "run() (in module mmtbx.scaling.sir_scale)": [[318, "mmtbx.scaling.sir_scale.run"]], "run() (in module mmtbx.scaling.siras_scale)": [[318, "mmtbx.scaling.siras_scale.run"]], "run() (in module mmtbx.scaling.thorough_outlier_test)": [[318, "mmtbx.scaling.thorough_outlier_test.run"]], "run() (in module mmtbx.scaling.twmad_scale)": [[318, "mmtbx.scaling.twmad_scale.run"]], "run() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.run"]], "run() (mmtbx.scaling.xtriage.launcher method)": [[318, "mmtbx.scaling.xtriage.launcher.run"]], "run_call_back() (in module mmtbx.scaling.thorough_outlier_test)": [[318, "mmtbx.scaling.thorough_outlier_test.run_call_back"]], "scat_data() (mmtbx.scaling.absolute_scaling.scattering_information method)": [[318, "mmtbx.scaling.absolute_scaling.scattering_information.scat_data"]], "scattering_information (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.scattering_information"]], "score_isigi() (mmtbx.scaling.absences.analyze_absences method)": [[318, "mmtbx.scaling.absences.analyze_absences.score_isigi"]], "select_and_transform() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.select_and_transform"]], "set_sigma_ratio() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.set_sigma_ratio"]], "set_sigma_ratio() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.set_sigma_ratio"]], "sgi_iterator (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.sgi_iterator"]], "show() (mmtbx.scaling.absences.absences_list method)": [[318, "mmtbx.scaling.absences.absences_list.show"]], "show() (mmtbx.scaling.data_analysis method)": [[318, "mmtbx.scaling.data_analysis.show"]], "show() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.show"]], "show() (mmtbx.scaling.relative_scaling.ls_rel_scale_driver method)": [[318, "mmtbx.scaling.relative_scaling.ls_rel_scale_driver.show"]], "show() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.show"]], "show() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.show"]], "show() (mmtbx.scaling.xtriage_analysis method)": [[318, "mmtbx.scaling.xtriage_analysis.show"]], "show() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show"]], "show_big_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_big_header"]], "show_big_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_big_header"]], "show_big_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_big_header"]], "show_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_header"]], "show_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_header"]], "show_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_header"]], "show_lines() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_lines"]], "show_lines() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_lines"]], "show_lines() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_lines"]], "show_paragraph_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_paragraph_header"]], "show_paragraph_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_paragraph_header"]], "show_paragraph_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_paragraph_header"]], "show_plot() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_plot"]], "show_plot() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_plot"]], "show_plot() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_plot"]], "show_plots_row() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_plots_row"]], "show_plots_row() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_plots_row"]], "show_plots_row() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_plots_row"]], "show_preformatted_text() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_preformatted_text"]], "show_preformatted_text() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_preformatted_text"]], "show_preformatted_text() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_preformatted_text"]], "show_short() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.show_short"]], "show_short() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.show_short"]], "show_sub_header() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_sub_header"]], "show_sub_header() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_sub_header"]], "show_sub_header() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_sub_header"]], "show_summary() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.show_summary"]], "show_table() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_table"]], "show_table() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_table"]], "show_table() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_table"]], "show_text() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_text"]], "show_text() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_text"]], "show_text() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_text"]], "show_text_columns() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_text_columns"]], "show_text_columns() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_text_columns"]], "show_text_columns() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_text_columns"]], "show_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.show_verdict"]], "show_worrisome_shells() (mmtbx.scaling.data_statistics.wilson_scaling method)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling.show_worrisome_shells"]], "sigma_gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein.sigma_gamma"]], "sigmaa() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.sigmaa"]], "sigmaa() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.sigmaa"]], "sigmaa_estimator (class in mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator"]], "sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.sigmaa_estimation)": [[318, 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"mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate"]], "singh_ramasheshan_fa_estimate (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate"]], "solc() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.solc"]], "solvent_fraction() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.solvent_fraction"]], "std() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.std"]], "strain_tensor() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.strain_tensor"]], "string_it() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.string_it"]], "suggest_likely_candidates() (mmtbx.scaling.absences.protein_space_group_choices method)": [[318, "mmtbx.scaling.absences.protein_space_group_choices.suggest_likely_candidates"]], "suggest_new_space_groups() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.suggest_new_space_groups"]], "summarize_issues() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.anomalous method)": [[318, "mmtbx.scaling.data_statistics.anomalous.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.ice_ring_checker method)": [[318, "mmtbx.scaling.data_statistics.ice_ring_checker.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.summarize_issues"]], "summarize_issues() (mmtbx.scaling.data_statistics.wilson_scaling method)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling.summarize_issues"]], "summarize_issues() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.data_summary method)": [[318, "mmtbx.scaling.xtriage.data_summary.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.merging_statistics method)": [[318, "mmtbx.scaling.xtriage.merging_statistics.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.summarize_issues"]], "summarize_issues() (mmtbx.scaling.xtriage_analysis method)": [[318, "mmtbx.scaling.xtriage_analysis.summarize_issues"]], "summary (class in mmtbx.scaling.relative_wilson)": [[318, "mmtbx.scaling.relative_wilson.summary"]], "summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.summary"]], "summary() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.summary"]], "symmetry_issues (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues"]], "t (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.t"]], "ta_alpha_beta_calc (class in mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc"]], "table (mmtbx.scaling.twin_analyses.britton_test property)": [[318, "mmtbx.scaling.twin_analyses.britton_test.table"]], "table (mmtbx.scaling.twin_analyses.h_test property)": [[318, "mmtbx.scaling.twin_analyses.h_test.table"]], "table (mmtbx.scaling.twin_analyses.l_test property)": [[318, "mmtbx.scaling.twin_analyses.l_test.table"]], "table (mmtbx.scaling.twin_analyses.ml_murray_rust property)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust.table"]], "table (mmtbx.scaling.twin_analyses.n_z_test property)": [[318, "mmtbx.scaling.twin_analyses.n_z_test.table"]], "target() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.target"]], "tau (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.tau"]], "test() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.test"]], "test() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.test"]], "twin_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses"]], "twin_analyses_brief() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses_brief"]], "twin_law (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law"]], "twin_law_dependent_twin_tests (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests"]], "twin_law_quality (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality"]], "twin_laws (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_laws"]], "twin_results_interpretation (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation"]], "twin_type (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.twin_type"]], "twmad_fa_driver (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.twmad_fa_driver"]], "type (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.type"]], "u (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.u"]], "unpack() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.unpack"]], "unpack() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.unpack"]], "validate_params() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.validate_params"]], "vm() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.vm"]], "vm() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.vm"]], "vm_prop_table() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.vm_prop_table"]], "warn() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.warn"]], "warn() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.warn"]], "warn() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.warn"]], "weighted_cc() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.weighted_cc"]], "wilson_moments (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments"]], "wilson_normalised_intensities (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.wilson_normalised_intensities"]], "wilson_scaling (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling"]], "write() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.write"]], "write() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.write"]], "write() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.write"]], "write_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data.write_data"]], "write_datasets() (mmtbx.scaling.random_omit.random_omit_data method)": [[318, "mmtbx.scaling.random_omit.random_omit_data.write_datasets"]], "xtriage_analyses (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses"]], "xtriage_analysis (class in mmtbx.scaling)": [[318, "mmtbx.scaling.xtriage_analysis"]], "xtriage_output (class in mmtbx.scaling)": [[318, "mmtbx.scaling.xtriage_output"]], "xtriage_summary (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.xtriage_summary"]], "apply_phil_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.apply_phil_str"]], "as_pdb_records() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_pdb_records"]], "as_phil_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.as_phil_str"]], "as_restraint_group_phil() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_restraint_group_phil"]], "as_restraint_groups() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.as_restraint_groups"]], "base_pair_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selection"]], "base_pair_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selections"]], "beta_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selection"]], "beta_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selections"]], "build_selections() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.build_selections"]], "calculate_structure_content() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.calculate_structure_content"]], "contiguous_ss_selections() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.contiguous_ss_selections"]], "create_all_new_restraints() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_all_new_restraints"]], "create_helix_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_helix_hydrogen_bond_proxies"]], "create_protein_hbond_proxies() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_protein_hbond_proxies"]], "create_sheet_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_sheet_hydrogen_bond_proxies"]], "find_approximate_helices() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_approximate_helices"]], "find_automatically() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_automatically"]], "find_base_pairs() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_base_pairs"]], "find_helices_simple (class in mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple"]], "find_sec_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_sec_str"]], "get_default_ss_params() (mmtbx.secondary_structure.manager static method)": [[319, "mmtbx.secondary_structure.manager.get_default_ss_params"]], "get_helix_types() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_helix_types"]], "get_ksdssp_exe_path() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.get_ksdssp_exe_path"]], "get_residue_name_from_selection() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.get_residue_name_from_selection"]], "get_simple_bonds() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_simple_bonds"]], "helix_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selection"]], "helix_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selections"]], "hydrogen_bond_from_selection_pair() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.hydrogen_bond_from_selection_pair"]], "initialize() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.initialize"]], "is_approximately_helical() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.is_approximately_helical"]], "manager (class in mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.manager"]], "mmtbx.secondary_structure": [[319, "module-mmtbx.secondary_structure"]], "mmtbx.secondary_structure.proteins": [[319, "module-mmtbx.secondary_structure.proteins"]], "mmtbx.secondary_structure.utils": [[319, "module-mmtbx.secondary_structure.utils"]], "process_break() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.process_break"]], "push_back() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.push_back"]], "records_for_pdb_file() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.records_for_pdb_file"]], "run() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.run"]], "run_ksdssp() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.run_ksdssp"]], "run_ksdssp_direct() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.run_ksdssp_direct"]], "sec_str_from_phil() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.sec_str_from_phil"]], "show() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.show"]], "show_summary() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.show_summary"]], "mmtbx.secondary_structure.build": [[320, "module-mmtbx.secondary_structure.build"]], "add() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.add"]], "add_new_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.add_new_solvent"]], "compare_peaks_with_positions() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.compare_peaks_with_positions"]], "find_peaks() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.find_peaks"]], "is_water_last() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.is_water_last"]], "manager (class in mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager"]], "manager (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.manager"]], "maps (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.maps"]], "master_params() (in module mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.master_params"]], "master_params() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.master_params"]], "mmtbx.solvent": [[321, "module-mmtbx.solvent"]], "mmtbx.solvent.ensemble_ordered_solvent": [[321, "module-mmtbx.solvent.ensemble_ordered_solvent"]], "mmtbx.solvent.ordered_solvent": [[321, "module-mmtbx.solvent.ordered_solvent"]], "move_solvent_to_the_end_of_atom_list() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.move_solvent_to_the_end_of_atom_list"]], "msg_accumulator (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator"]], "randomize_new_velocities() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.randomize_new_velocities"]], "randomize_velocity() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.randomize_velocity"]], "refine_adp() (mmtbx.solvent.ordered_solvent.manager method)": [[321, "mmtbx.solvent.ordered_solvent.manager.refine_adp"]], "refine_occupancies() (mmtbx.solvent.ordered_solvent.manager method)": [[321, "mmtbx.solvent.ordered_solvent.manager.refine_occupancies"]], "remove_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.remove_solvent"]], "reset_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.reset_solvent"]], "score_atom() (mmtbx.solvent.ordered_solvent.maps method)": [[321, "mmtbx.solvent.ordered_solvent.maps.score_atom"]], "set_prefix() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.set_prefix"]], "show() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.show"]], "show() (mmtbx.solvent.ordered_solvent.msg_accumulator method)": [[321, "mmtbx.solvent.ordered_solvent.msg_accumulator.show"]], "as_cif_block() (mmtbx.tls.tools.tls_groups method)": [[322, "mmtbx.tls.tools.tls_groups.as_cif_block"]], "check_u_cart() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.check_u_cart"]], "combine_tls_and_u_local() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.combine_tls_and_u_local"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_from_uaniso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uaniso_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_from_uiso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uiso_minimizer.compute_functional_and_gradients"]], "compute_functional_and_gradients() (mmtbx.tls.tools.tls_xray_target_minimizer method)": [[322, "mmtbx.tls.tools.tls_xray_target_minimizer.compute_functional_and_gradients"]], "ensemble_generator (class in mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.ensemble_generator"]], "extract_tls_from_pdb() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.extract_tls_from_pdb"]], "finite_differences_grads_of_xray_target_wrt_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.finite_differences_grads_of_xray_target_wrt_tls"]], "formula_49() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.formula_49"]], "generate_tlsos() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.generate_tlsos"]], "get_axes_and_atoms_i_seqs() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.get_axes_and_atoms_i_seqs"]], "get_u_cart() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.get_u_cart"]], "make_tlso_compatible_with_u_positive_definite() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.make_tlso_compatible_with_u_positive_definite"]], "mmtbx.tls": [[322, "module-mmtbx.tls"]], "mmtbx.tls.command_line": [[322, "module-mmtbx.tls.command_line"]], "mmtbx.tls.ladp": [[322, "module-mmtbx.tls.ladp"]], "mmtbx.tls.tls_as_xyz": [[322, "module-mmtbx.tls.tls_as_xyz"]], "mmtbx.tls.tools": [[322, "module-mmtbx.tls.tools"]], "pack() (mmtbx.tls.tools.tls_from_uaniso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uaniso_minimizer.pack"]], "pack() (mmtbx.tls.tools.tls_from_uiso_minimizer method)": [[322, "mmtbx.tls.tools.tls_from_uiso_minimizer.pack"]], "pack() (mmtbx.tls.tools.tls_xray_target_minimizer method)": [[322, "mmtbx.tls.tools.tls_xray_target_minimizer.pack"]], "print_step() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.print_step"]], "remark_3_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.remark_3_tls"]], "run() (in module mmtbx.tls.command_line)": [[322, "mmtbx.tls.command_line.run"]], "run() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.run"]], "select() (mmtbx.tls.tools.tls_groups method)": [[322, "mmtbx.tls.tools.tls_groups.select"]], "set_ladp() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.set_ladp"]], "show_times() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_times"]], "show_tls (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_tls"]], "show_tls_one_group (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_tls_one_group"]], "split_u() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.split_u"]], "step_i__compute_delta_l_r_dp() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.step_i__compute_delta_L_r_dp"]], "step_i__get_dxdydz() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.step_i__get_dxdydz"]], "tls_from_pdb_inp() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_pdb_inp"]], "tls_from_u_cart() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_u_cart"]], "tls_from_uaniso_minimizer (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_uaniso_minimizer"]], "tls_from_uanisos() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_uanisos"]], "tls_from_uiso_minimizer (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_uiso_minimizer"]], "tls_group (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_group"]], "tls_groups (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_groups"]], "tls_refinement (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_refinement"]], "tls_xray_grads (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_xray_grads"]], "tls_xray_target_minimizer (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_xray_target_minimizer"]], "u_cart_from_ensemble() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.u_cart_from_ensemble"]], "u_cart_from_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.u_cart_from_tls"]], "u_tls_vs_u_ens (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.u_tls_vs_u_ens"]], "unpack_x() (mmtbx.tls.tools.tls_from_uaniso_minimizer method)": [[322, 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"mmtbx.validation.rna_validate.rna_angle.atom_selection"]], "atom_selection (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atom_selection"]], "atom_selection (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.atom_selection"]], "atom_selection (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.atom_selection"]], "atom_selection (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.atom_selection"]], "atom_selection (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.atom_selection"]], "atom_selection_string() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.atom_selection_string"]], "atom_selection_string() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.atom_selection_string"]], "atoms (class in mmtbx.validation)": [[326, "mmtbx.validation.atoms"]], "atoms_info (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.atoms_info"]], "atoms_info (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.atoms_info"]], "atoms_info (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.atoms_info"]], "atoms_info (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.atoms_info"]], "atoms_info (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.atoms_info"]], "atoms_info (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.atoms_info"]], "atoms_info (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.atoms_info"]], "atoms_info (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.atoms_info"]], "atoms_info (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.atoms_info"]], "atoms_info (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atoms_info"]], "b_factor_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.b_factor_cutoff"]], "b_histogram (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_histogram"]], "b_iso (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.b_iso"]], "b_iso (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.b_iso"]], "b_iso (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.b_iso"]], "b_iso (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.b_iso"]], "b_iso (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.b_iso"]], "b_iso (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.b_iso"]], "b_iso (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.b_iso"]], "b_iso (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.b_iso"]], "b_iso_mean (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.b_iso_mean"]], "b_max (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_max"]], "b_mean (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_mean"]], "b_min (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_min"]], "bad_adps (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.bad_adps"]], "beta_ideal (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.beta_ideal"]], "bond (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bond"]], "bonds (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bonds"]], "bonds (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.bonds"]], "bonds (mmtbx.validation.rna_validate.rna_validation attribute)": [[326, "mmtbx.validation.rna_validate.rna_validation.bonds"]], "build_name_hash() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.build_name_hash"]], "c_alpha (class in mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.c_alpha"]], "calculate_ideal_and_deviation (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation"]], "cbeta (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.cbeta"]], "cbetadev (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.cbetadev"]], "cc (mmtbx.validation.experimental.residue_real_space property)": [[326, "mmtbx.validation.experimental.residue_real_space.cc"]], "cc (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.cc"]], "cc (mmtbx.validation.waters.water property)": [[326, "mmtbx.validation.waters.water.cc"]], "chain (class in mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.chain"]], "chain_id (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.chain_id"]], "chain_id (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.chain_id"]], "chain_id (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.chain_id"]], "chain_id (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.chain_id"]], "chain_id (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.chain_id"]], "chain_id (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.chain_id"]], "chain_id (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.chain_id"]], "chain_id (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.chain_id"]], "chain_id (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.chain_id"]], "chain_id (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.chain_id"]], "chain_id (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.chain_id"]], "chain_id (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.chain_id"]], "chain_id (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.chain_id"]], "chain_id (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.chain_id"]], "chain_id (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.chain_id"]], "chain_id (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.chain_id"]], "chain_type (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.chain_type"]], "chain_type (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.chain_type"]], "check_and_add_hydrogen() (in module mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.check_and_add_hydrogen"]], "check_and_report_reduce_failure() (in module mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.check_and_report_reduce_failure"]], "chi_angles (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.chi_angles"]], "chi_angles (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.chi_angles"]], "chiralities (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.chiralities"]], "chiralities (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.chiralities"]], "chirality (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.chirality"]], "clash (class in mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.clash"]], "clash_dict (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clash_dict"]], "clash_dict_b_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clash_dict_b_cutoff"]], "clashscore (class in mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.clashscore"]], "clashscore (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clashscore"]], "clashscore_b_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clashscore_b_cutoff"]], "combined (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.combined"]], "compare_ligands() (in module mmtbx.validation.ligands)": [[326, 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"mmtbx.validation.rotalyze.construct_complete_sidechain"]], "construct_fourth() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.construct_fourth"]], "coot_todo() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.coot_todo"]], "coot_todo() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.coot_todo"]], "count_dict_values() (mmtbx.validation.test_utils method)": [[326, "mmtbx.validation.test_utils.count_dict_values"]], "d_max (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.d_max"]], "d_max_outer (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.d_max_outer"]], "d_min (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.d_min"]], "d_min_outer (mmtbx.validation.experimental.data_statistics attribute)": [[326, 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(mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.delta"]], "delta (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.delta"]], "delta (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.delta"]], "delta_angle (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.delta_angle"]], "delta_max (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.delta_max"]], "deviation (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.deviation"]], "deviation (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.deviation"]], "different_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, 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method)": [[326, "mmtbx.validation.graphics.rotarama_plot_mixin.draw_plot"]], "draw_ramachandran_plot() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.draw_ramachandran_plot"]], "draw_rotamer_plot() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.draw_rotamer_plot"]], "dummy_validation (class in mmtbx.validation)": [[326, "mmtbx.validation.dummy_validation"]], "element (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.element"]], "element (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.element"]], "element (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.element"]], "element (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.element"]], "element (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.element"]], "entity (class in mmtbx.validation)": [[326, "mmtbx.validation.entity"]], "epsilon_angle (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.epsilon_angle"]], "evalscore() (mmtbx.validation.ramalyze.ramalyze static method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evalScore"]], "evaluatescore() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evaluateScore"]], "evaluatescore() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.evaluateScore"]], "evaluate_residue() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_residue"]], "evaluate_residue() (mmtbx.validation.rotalyze.residue_evaluator method)": [[326, "mmtbx.validation.rotalyze.residue_evaluator.evaluate_residue"]], "evaluate_rotamer() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_rotamer"]], "evaluation (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.evaluation"]], "evaluation (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.evaluation"]], "everything (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.everything"]], "exercise() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.exercise"]], "export_ramachandran_distribution() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.export_ramachandran_distribution"]], "export_rotamer_distribution() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.export_rotamer_distribution"]], "extent (mmtbx.validation.graphics.rotarama_plot_mixin attribute)": [[326, "mmtbx.validation.graphics.rotarama_plot_mixin.extent"]], "extent (mmtbx.validation.ramalyze.ramachandran_plot_mixin attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_plot_mixin.extent"]], "extract_atoms_from_residue_group() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.extract_atoms_from_residue_group"]], "extract_coordinates() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.extract_coordinates"]], "extract_ligand_atom_group() (in module mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.extract_ligand_atom_group"]], "extract_ligand_residue() (in module mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.extract_ligand_residue"]], "extract_residue_groups() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.extract_residue_groups"]], "fast (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.fast"]], "fav_percent (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.fav_percent"]], "filter_dicts() (mmtbx.validation.clashscore.probe_clashscore_manager method)": [[326, 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"mmtbx.validation.ramalyze.ramachandran.format_old"]], "format_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.format_old"]], "format_ramachandran_plot_title() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.format_ramachandran_plot_title"]], "format_score() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.format_score"]], "format_values() (mmtbx.validation.restraints.planarity method)": [[326, "mmtbx.validation.restraints.planarity.format_values"]], "format_values() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_angle method)": [[326, "mmtbx.validation.rna_validate.rna_angle.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_bond method)": [[326, "mmtbx.validation.rna_validate.rna_bond.format_values"]], "format_values() (mmtbx.validation.rna_validate.rna_pucker method)": [[326, "mmtbx.validation.rna_validate.rna_pucker.format_values"]], "formate_values() (mmtbx.validation.restraints.bond method)": [[326, "mmtbx.validation.restraints.bond.formate_values"]], "fsc (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.fsc"]], "get_alignment() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_alignment"]], "get_allowed_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_count_and_fraction"]], "get_allowed_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_goal"]], "get_altloc() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.get_altloc"]], "get_altloc_from_id_str() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_id_str"]], "get_altloc_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_three"]], "get_atoms_info() (in module mmtbx.validation)": [[326, "mmtbx.validation.get_atoms_info"]], "get_beta_ideal() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_beta_ideal"]], "get_bin() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_bin"]], "get_bonds_angles_rmsds() (mmtbx.validation.restraints.combined method)": [[326, "mmtbx.validation.restraints.combined.get_bonds_angles_rmsds"]], "get_cas_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_cas_from_three"]], "get_center() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_center"]], "get_chi1_chi2() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.get_chi1_chi2"]], "get_cis_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_cis_pro_count_and_fraction"]], "get_clashscore() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore"]], "get_clashscore_b_cutoff() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore_b_cutoff"]], "get_condensed_clashes() (mmtbx.validation.clashscore.probe_clashscore_manager method)": [[326, "mmtbx.validation.clashscore.probe_clashscore_manager.get_condensed_clashes"]], "get_contours() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_contours"]], "get_coordinates_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_range"]], "get_coordinates_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_ranges"]], "get_dihedral() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_dihedral"]], "get_expected_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_expected_count"]], "get_favored_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_count_and_fraction"]], "get_favored_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_goal"]], "get_favored_goal() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_favored_goal"]], "get_favored_peaks() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_peaks"]], "get_favored_regions() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_regions"]], "get_general_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_general_count_and_fraction"]], "get_gly_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_gly_count_and_fraction"]], "get_highlighted_residues() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_highlighted_residues"]], "get_ileval_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_ileval_count_and_fraction"]], "get_inverted_atoms() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_inverted_atoms"]], "get_master_phil() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_master_phil"]], "get_matching_atom_group() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_matching_atom_group"]], "get_mean_coordinate() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_mean_coordinate"]], "get_mean_coordinate_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_range"]], "get_mean_coordinate_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_ranges"]], "get_mean_xyz() (in module mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.get_mean_xyz"]], "get_missing_chains() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_missing_chains"]], "get_n_total_by_model() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_n_total_by_model"]], "get_n_total_by_model() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_n_total_by_model"]], "get_n_total_by_model() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_n_total_by_model"]], "get_occupancy() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_occupancy"]], "get_omega() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_omega"]], "get_omega_atoms() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_omega_atoms"]], "get_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_count"]], "get_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_percent"]], "get_outlier_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_outlier_plot_values"]], "get_outliers() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_outliers"]], "get_outliers() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_outliers"]], "get_outliers_count_and_fraction() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_count_and_fraction"]], "get_outliers_fraction_for_model() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_fraction_for_model"]], "get_outliers_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_outliers_goal"]], "get_outliers_goal() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_outliers_goal"]], "get_outliers_goal() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_goal"]], "get_outliers_table() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_outliers_table"]], "get_phi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_phi"]], "get_phi_psi_dict() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.get_phi_psi_dict"]], "get_phi_psi_residues_count() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_phi_psi_residues_count"]], "get_plot_data() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plot_data"]], "get_plot_data() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_plot_data"]], "get_plots() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plots"]], "get_prepro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_prepro_count_and_fraction"]], "get_psi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_psi"]], "get_ranges() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_ranges"]], "get_real_space_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_real_space_plot_values"]], "get_relative_sequence_copy_number() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_relative_sequence_copy_number"]], "get_residue_key() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_residue_key"]], "get_residue_range() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_residue_range"]], "get_result_class() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_class"]], "get_result_class() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_result_class"]], "get_result_class() (mmtbx.validation.experimental.real_space method)": [[326, "mmtbx.validation.experimental.real_space.get_result_class"]], "get_result_class() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_result_class"]], "get_result_class() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_angles method)": [[326, "mmtbx.validation.rna_validate.rna_angles.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_bonds method)": [[326, "mmtbx.validation.rna_validate.rna_bonds.get_result_class"]], "get_result_class() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_result_class"]], "get_result_class() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_result_class"]], "get_result_class() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_result_class"]], "get_result_class() (mmtbx.validation.waters.waters method)": [[326, "mmtbx.validation.waters.waters.get_result_class"]], "get_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_count"]], "get_rna_backbone_dihedrals() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rna_backbone_dihedrals"]], "get_rna_pucker_ref() (mmtbx.validation.rna_validate.rna_pucker_ref method)": [[326, "mmtbx.validation.rna_validate.rna_pucker_ref.get_rna_pucker_ref"]], "get_rotarama_data() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rotarama_data"]], "get_segid_as_chainid() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_segid_as_chainid"]], "get_selected() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_selected"]], "get_sequence_n_copies() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies"]], "get_sequence_n_copies_from_files() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies_from_files"]], "get_sugar_xyz_mean() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_sugar_xyz_mean"]], "get_table_data() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_table_data"]], "get_trans_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_trans_pro_count_and_fraction"]], "get_weighted_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_count"]], "get_weighted_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_percent"]], "get_weighted_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_result_count"]], "group_chains_and_sequences() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.group_chains_and_sequences"]], "gui_formats (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_formats"]], "gui_formats (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_formats"]], "gui_formats (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_formats"]], "gui_formats (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_formats"]], "gui_formats (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_formats"]], "gui_formats (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_formats"]], "gui_formats (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.gui_formats"]], "gui_formats (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.gui_formats"]], "gui_formats (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.gui_formats"]], "gui_formats (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.gui_formats"]], "gui_formats (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.gui_formats"]], "gui_formats (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.gui_formats"]], "gui_formats (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.gui_formats"]], "gui_list_headers (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_list_headers"]], "gui_list_headers (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_list_headers"]], "gui_list_headers (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_list_headers"]], "gui_list_headers (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_list_headers"]], "gui_list_headers (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_list_headers"]], "gui_list_headers (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.gui_list_headers"]], "gui_list_headers (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.gui_list_headers"]], "gui_list_headers (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.gui_list_headers"]], "gui_list_headers (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.gui_list_headers"]], "has_heavy_atoms() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.has_heavy_atoms"]], "header() (mmtbx.validation.cbetadev.cbeta static method)": [[326, "mmtbx.validation.cbetadev.cbeta.header"]], "header() (mmtbx.validation.clashscore.clash static method)": [[326, "mmtbx.validation.clashscore.clash.header"]], "header() (mmtbx.validation.entity static method)": [[326, "mmtbx.validation.entity.header"]], "header() (mmtbx.validation.experimental.residue_real_space static method)": [[326, "mmtbx.validation.experimental.residue_real_space.header"]], "header() (mmtbx.validation.ramalyze.ramachandran static method)": [[326, "mmtbx.validation.ramalyze.ramachandran.header"]], "header() (mmtbx.validation.restraints.bond static method)": [[326, "mmtbx.validation.restraints.bond.header"]], "header() (mmtbx.validation.restraints.planarity static method)": [[326, "mmtbx.validation.restraints.planarity.header"]], "header() (mmtbx.validation.restraints.restraint static method)": [[326, "mmtbx.validation.restraints.restraint.header"]], "header() (mmtbx.validation.rna_validate.rna_angle static method)": [[326, "mmtbx.validation.rna_validate.rna_angle.header"]], "header() (mmtbx.validation.rna_validate.rna_bond static method)": [[326, "mmtbx.validation.rna_validate.rna_bond.header"]], "header() (mmtbx.validation.rna_validate.rna_pucker static method)": [[326, "mmtbx.validation.rna_validate.rna_pucker.header"]], "header() (mmtbx.validation.rotalyze.rotamer static method)": [[326, "mmtbx.validation.rotalyze.rotamer.header"]], "header() (mmtbx.validation.waters.water static method)": [[326, "mmtbx.validation.waters.water.header"]], "icode (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.icode"]], "icode (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.icode"]], "icode (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.icode"]], "icode (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.icode"]], "icode (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.icode"]], "icode (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.icode"]], "icode (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.icode"]], "icode (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.icode"]], "icode (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.icode"]], "icode (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.icode"]], "icode (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.icode"]], "icode (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.icode"]], "icode (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.icode"]], "icode (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.icode"]], "icode (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.icode"]], "icode (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.icode"]], "id_str (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.id_str"]], "id_str (mmtbx.validation.ramalyze.c_alpha attribute)": [[326, "mmtbx.validation.ramalyze.c_alpha.id_str"]], "id_str() (mmtbx.validation.atom_base method)": [[326, "mmtbx.validation.atom_base.id_str"]], "id_str() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str"]], "id_str() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.id_str"]], "id_str() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.id_str"]], "id_str() (mmtbx.validation.model_properties.atom_occupancy method)": [[326, "mmtbx.validation.model_properties.atom_occupancy.id_str"]], "id_str() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.id_str"]], "id_str() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.id_str"]], "id_str() (mmtbx.validation.rna_validate.rna_angle method)": [[326, "mmtbx.validation.rna_validate.rna_angle.id_str"]], "id_str() (mmtbx.validation.rna_validate.rna_bond method)": [[326, "mmtbx.validation.rna_validate.rna_bond.id_str"]], "id_str() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.id_str"]], "id_str_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_no_atom_name"]], "id_str_old() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.id_str_old"]], "id_str_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.id_str_old"]], "id_str_src_atom_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_src_atom_no_atom_name"]], "ideal (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.ideal"]], "ideal_xyz (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.ideal_xyz"]], "idealized_calpha_angles() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.idealized_calpha_angles"]], "ignore_hd (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.ignore_hd"]], "incomplete (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.incomplete"]], "incomplete (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.incomplete"]], "increment_category_counts() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.increment_category_counts"]], "info (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.info"]], "isprepro() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.isPrePro"]], "is_bad_water() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_bad_water"]], "is_cis_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_cis_peptide"]], "is_cis_peptide() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.is_cis_peptide"]], "is_delta_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_delta_outlier"]], "is_epsilon_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_epsilon_outlier"]], "is_handedness_swap() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_handedness_swap"]], "is_heavy_atom() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_heavy_atom"]], "is_in_chain() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_in_chain"]], "is_outlier() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_outlier"]], "is_pseudochiral() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_pseudochiral"]], "is_same_residue() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue"]], "is_same_residue_group() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue_group"]], "is_similar() (mmtbx.validation.clashscore.probe_line_info method)": [[326, "mmtbx.validation.clashscore.probe_line_info.is_similar"]], "is_single_residue_object() (mmtbx.validation.atom method)": [[326, "mmtbx.validation.atom.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_single_residue_object"]], "is_single_residue_object() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_single_residue_object"]], "is_trans_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_trans_peptide"]], "iter_residue_groups() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.iter_residue_groups"]], "iter_results() (mmtbx.validation.model_properties.xray_structure_statistics method)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.iter_results"]], "iter_results() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.iter_results"]], "kinemage_header (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.kinemage_header"]], "kinemage_header (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.kinemage_header"]], "kinemage_key() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.kinemage_key"]], "label (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.label"]], "label (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.label"]], "label (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.label"]], "labels (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.labels"]], "ligand_validation (class in mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.ligand_validation"]], "ligands (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.ligands"]], "list_dict (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.list_dict"]], "local_altloc_from_atoms() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.local_altloc_from_atoms"]], "macromolecules (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.macromolecules"]], "marks (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.marks"]], "markup (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.markup"]], "markup (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.markup"]], "match_dihedral_to_name() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.match_dihedral_to_name"]], "max (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.max"]], "max (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.max"]], "max (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.max"]], "max (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.max"]], "max (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.max"]], "max (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.max"]], "max_b_factor (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.max_b_factor"]], "mean (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.mean"]], "mean (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.mean"]], "mean (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.mean"]], "mean (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.mean"]], "mean (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.mean"]], "mean (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.mean"]], "merge_dict() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.merge_dict"]], "merge_two_dicts() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.merge_two_dicts"]], "merging_and_model_statistics() (in module mmtbx.validation.experimental)": [[326, "mmtbx.validation.experimental.merging_and_model_statistics"]], "min (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.min"]], "min (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.min"]], "min (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.min"]], "min (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.min"]], "min (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.min"]], "min (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.min"]], "mmtbx.validation": [[326, "module-mmtbx.validation"]], "mmtbx.validation.analyze_peptides": [[326, "module-mmtbx.validation.analyze_peptides"]], "mmtbx.validation.cbetadev": [[326, "module-mmtbx.validation.cbetadev"]], "mmtbx.validation.clashscore": [[326, "module-mmtbx.validation.clashscore"]], "mmtbx.validation.experimental": [[326, "module-mmtbx.validation.experimental"]], "mmtbx.validation.graphics": [[326, "module-mmtbx.validation.graphics"]], "mmtbx.validation.ligands": [[326, "module-mmtbx.validation.ligands"]], "mmtbx.validation.model_properties": [[326, "module-mmtbx.validation.model_properties"]], "mmtbx.validation.ramalyze": [[326, "module-mmtbx.validation.ramalyze"]], "mmtbx.validation.restraints": [[326, "module-mmtbx.validation.restraints"]], "mmtbx.validation.rna_validate": [[326, "module-mmtbx.validation.rna_validate"]], "mmtbx.validation.rotalyze": [[326, "module-mmtbx.validation.rotalyze"]], "mmtbx.validation.sequence": [[326, "module-mmtbx.validation.sequence"]], "mmtbx.validation.utils": [[326, "module-mmtbx.validation.utils"]], "mmtbx.validation.waters": [[326, "module-mmtbx.validation.waters"]], "model (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.model"]], "model (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.model"]], "model (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.model"]], "model (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.model"]], "model (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.model"]], "model_id (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.model_id"]], "model_id (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.model_id"]], "model_id (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.model_id"]], "model_id (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.model_id"]], "model_id (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.model_id"]], "model_id (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.model_id"]], "model_id (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.model_id"]], "model_id (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.model_id"]], "model_id (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.model_id"]], "model_id (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.model_id"]], "model_id (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.model_id"]], "model_statistics (class in mmtbx.validation.model_properties)": [[326, "mmtbx.validation.model_properties.model_statistics"]], "molprobity_score() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.molprobity_score"]], "molprobity_table_labels (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.molprobity_table_labels"]], "multi_criterion_plot_mixin (class in mmtbx.validation.graphics)": [[326, "mmtbx.validation.graphics.multi_criterion_plot_mixin"]], "n_all (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_all"]], "n_allowed (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.n_allowed"]], "n_allowed (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.n_allowed"]], "n_allowed_by_model (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.n_allowed_by_model"]], "n_allowed_by_model (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.n_allowed_by_model"]], "n_aniso (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_aniso"]], "n_aniso_h (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_aniso_h"]], "n_atoms (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.n_atoms"]], "n_atoms (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_atoms"]], "n_atoms (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.n_atoms"]], "n_atoms (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.n_atoms"]], "n_atoms (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.n_atoms"]], "n_atoms (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.n_atoms"]], "n_atoms() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.n_atoms"]], "n_bad (mmtbx.validation.waters.waters attribute)": [[326, "mmtbx.validation.waters.waters.n_bad"]], "n_below_fofc_cutoff (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.n_below_fofc_cutoff"]], "n_below_two_fofc_cutoff (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.n_below_two_fofc_cutoff"]], "n_chiral_by_model (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.n_chiral_by_model"]], "n_favored (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.n_favored"]], "n_favored (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.n_favored"]], "n_favored_by_model (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.n_favored_by_model"]], "n_favored_by_model (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.n_favored_by_model"]], "n_free (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_free"]], "n_free_outer (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_free_outer"]], "n_handedness_by_model (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.n_handedness_by_model"]], "n_hbonds (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.n_hbonds"]], "n_hd 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attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.xyz_center"]], "z_max (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_max"]], "z_max (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_max"]], "z_max (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_max"]], "z_max (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_max"]], "z_max (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_max"]], "z_max (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_max"]], "z_mean (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_mean"]], "z_mean (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_mean"]], "z_mean (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_mean"]], "z_mean (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_mean"]], "z_mean (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_mean"]], "z_mean (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_mean"]], "z_min (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.z_min"]], "z_min (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.z_min"]], "z_min (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.z_min"]], "z_min (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.z_min"]], "z_min (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.z_min"]], "z_min (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.z_min"]], "zero_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.zero_occ"]], "zoom_info() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.zoom_info"]], "molprobityparser (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.MolProbityParser"]], "molprobitytemplate (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.MolProbityTemplate"]], "add_default_options() (mmtbx.validation.molprobity.molprobityparser method)": [[327, "mmtbx.validation.molprobity.MolProbityParser.add_default_options"]], "add_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.add_outlier"]], "adp_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.adp_stats"]], "altloc (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.altloc"]], "angle_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.angle_rmsd"]], "as_mmcif_records() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.as_mmcif_records"]], "as_multi_criterion_view() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.as_multi_criterion_view"]], "atom_selection (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.atom_selection"]], "atoms_to_observations_ratio() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.atoms_to_observations_ratio"]], "b_iso_mean() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.b_iso_mean"]], "binned_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.binned_data"]], "bond_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.bond_rmsd"]], "c_beta_deviations (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.c_beta_deviations"]], "cbeta_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.cbeta_outliers"]], "cbetadev (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.cbetadev"]], "chain_id (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.chain_id"]], "clashes (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.clashes"]], "clashscore (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.clashscore"]], "clashscore() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.clashscore"]], "crystal_symmetry (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.crystal_symmetry"]], "d_max (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.d_max"]], "d_max_min() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.d_max_min"]], "d_min (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.d_min"]], "d_min (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.d_min"]], "d_min() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.d_min"]], "data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.data"]], "data_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.data_stats"]], "display_wx_plots() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.display_wx_plots"]], "display_wx_plots() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.display_wx_plots"]], "file_name (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.file_name"]], "finalize_coords() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.finalize_coords"]], "find_missing_atoms() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.find_missing_atoms"]], "fmodel_statistics_by_resolution() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_by_resolution"]], "fmodel_statistics_graph_data() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_graph_data"]], "formats (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.formats"]], "get_altloc() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_altloc"]], "get_atoms_str() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_atoms_str"]], "get_bond_and_angle_outliers() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_bond_and_angle_outliers"]], "get_master_phil() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_master_phil"]], "get_outlier_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_outlier_plot_values"]], "get_polygon_statistics() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_polygon_statistics"]], "get_real_space_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_real_space_plot_values"]], "get_residue_group_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_residue_group_data"]], "get_results_as_pdb_json() (mmtbx.validation.molprobity.molprobitytemplate method)": [[327, "mmtbx.validation.molprobity.MolProbityTemplate.get_results_as_PDB_JSON"]], "get_statistics_for_phenix_gui() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_statistics_for_phenix_gui"]], "get_y_limits() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_y_limits"]], "header_info (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.header_info"]], "hydrogens (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.hydrogens"]], "i_seq (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.i_seq"]], "icode (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.icode"]], "is_cbeta_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_cbeta_outlier"]], "is_clash_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_clash_outlier"]], "is_geometry_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_geometry_outlier"]], "is_map_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_map_outlier"]], "is_phenix_refinement() (mmtbx.validation.molprobity.pdb_header_info method)": [[327, "mmtbx.validation.molprobity.pdb_header_info.is_phenix_refinement"]], "is_populated (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.is_populated"]], "is_ramachandran_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_ramachandran_outlier"]], "is_rotamer_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_rotamer_outlier"]], "iter_molprobity_gui_fields() (mmtbx.validation.molprobity.summary method)": [[327, "mmtbx.validation.molprobity.summary.iter_molprobity_gui_fields"]], "kinemage_file (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.kinemage_file"]], "labels (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.labels"]], "merging (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.merging"]], "missing_atoms (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.missing_atoms"]], "mmtbx.validation.molprobity": [[327, "module-mmtbx.validation.molprobity"]], "mmtbx.validation.molprobity.mp_geo": [[327, "module-mmtbx.validation.molprobity.mp_geo"]], "mmtbx.validation.molprobity.nqh_minimize": [[327, "module-mmtbx.validation.molprobity.nqh_minimize"]], "model (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model"]], "model_statistics_geometry (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_statistics_geometry"]], "model_statistics_geometry_result (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_statistics_geometry_result"]], "model_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_stats"]], "model_stats_new (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.model_stats_new"]], "molprobity (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity"]], "molprobity_flags() (in module mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity_flags"]], "molprobity_score() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.molprobity_score"]], "molprobity_version_number (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.molprobity_version_number"]], "mpscore (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.mpscore"]], "multi_criterion_view (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.multi_criterion_view"]], "n_confs (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.n_confs"]], "n_tls_groups (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.n_tls_groups"]], "neutron_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.neutron_stats"]], "nqh_flips (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.nqh_flips"]], "occupancy (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.occupancy"]], "omegalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.omegalyze"]], "outlier (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outlier"]], "outliers (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outliers"]], "parse_user_mods() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.parse_user_mods"]], "pdb_header_info (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.pdb_header_info"]], "pdb_hierarchy (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.pdb_hierarchy"]], "polygon_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.polygon_stats"]], "process_outliers() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.process_outliers"]], "program (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.program"]], "r_free (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.r_free"]], "r_free (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.r_free"]], "r_free() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.r_free"]], "r_work (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.r_work"]], "r_work (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.r_work"]], "r_work() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.r_work"]], "rama_allowed() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_allowed"]], "rama_favored (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rama_favored"]], "rama_favored() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_favored"]], "rama_outliers (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rama_outliers"]], "rama_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rama_outliers"]], "ramalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.ramalyze"]], "real_space (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.real_space"]], "refinement_program (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.refinement_program"]], "residue_multi_criterion (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion"]], "residues (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.residues"]], "resname (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.resname"]], "resseq (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.resseq"]], "restraints (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.restraints"]], "rms_angles (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.rms_angles"]], "rms_angles() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rms_angles"]], "rms_bonds (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.rms_bonds"]], "rms_bonds() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rms_bonds"]], "rna (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.rna"]], "rota_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.rota_outliers"]], "rotalyze (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.rotalyze"]], "rotamer_outliers (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.rotamer_outliers"]], "run() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.run"]], "run() (in module mmtbx.validation.molprobity.nqh_minimize)": [[327, "mmtbx.validation.molprobity.nqh_minimize.run"]], "run_molprobity_program() (in module mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.run_molprobity_program"]], "score (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.score"]], "segid (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.segid"]], "sequence (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.sequence"]], "show() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.show"]], "show() (mmtbx.validation.molprobity.pdb_header_info method)": [[327, "mmtbx.validation.molprobity.pdb_header_info.show"]], "show() (mmtbx.validation.molprobity.summary method)": [[327, "mmtbx.validation.molprobity.summary.show"]], "show_summary() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.show_summary"]], "space_group() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.space_group"]], "space_group_info() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.space_group_info"]], "summarize() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.summarize"]], "summary (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.summary"]], "twin_law() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.twin_law"]], "unit_cell() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.unit_cell"]], "waters (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.waters"]], "wilson_b (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.wilson_b"]], "write_coot_script() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.write_coot_script"]], "xtriage (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.xtriage"]], "xyz (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.xyz"]], "add_nodes_to_query_if_needed_in_place() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.add_nodes_to_query_if_needed_in_place"]], "alt_atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.alt_atom_id"]], "atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.atom_id"]], "atoms (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.atoms"]], "ccp4_partial_charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ccp4_partial_charge"]], "ccp4_type_energy (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ccp4_type_energy"]], "charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.charge"]], "chem_comp_atom (class in mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom"]], "chemical_id_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.chemical_id_search"]], "combine_split_structure() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.combine_split_structure"]], "comp_id (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.comp_id"]], "count_non_hydrogen_atoms() (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.count_non_hydrogen_atoms"]], "descriptor (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.descriptor"]], "fetch_pdb_data() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.fetch_pdb_data"]], "filter_pdb_file (class in mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.filter_pdb_file"]], "find_data_arrays() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.find_data_arrays"]], "get_cif_float() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_float"]], "get_cif_int() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_int"]], "get_cif_number() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_number"]], "get_high_resolution_and_residue_count_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_and_residue_count_for_structures"]], "get_high_resolution_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_for_structures"]], "get_ligand_info_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_ligand_info_for_structures"]], "get_program() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.get_program"]], "get_r_work_rfree_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_r_work_rfree_for_structures"]], "mmtbx.wwpdb": [[328, "module-mmtbx.wwpdb"]], "mmtbx.wwpdb.rcsb_web_services": [[328, "module-mmtbx.wwpdb.rcsb_web_services"]], "mmtbx.wwpdb.standard_geometry_cif": [[328, "module-mmtbx.wwpdb.standard_geometry_cif"]], "mmtbx.wwpdb.utils": [[328, "module-mmtbx.wwpdb.utils"]], "pdbx_align (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_align"]], "pdbx_aromatic_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_aromatic_flag"]], "pdbx_leaving_atom_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_leaving_atom_flag"]], "pdbx_model_cartn_x_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_x_ideal"]], "pdbx_model_cartn_y_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_y_ideal"]], "pdbx_model_cartn_z_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_model_cartn_z_ideal"]], "pdbx_ordinal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_ordinal"]], "pdbx_stereo_config (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.pdbx_stereo_config"]], "polymeric_type_filter() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.polymeric_type_filter"]], "post_query() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_query"]], "post_report_query_with_pdb_list() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_report_query_with_pdb_list"]], "process_chem_comp_atom_buffer (class in mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer"]], "process_chem_comps() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comps"]], "ref_radii_asa_probe (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ref_radii_asa_probe"]], "resolution_filter() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.resolution_filter"]], "sequence_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.sequence_search"]], "site_ideal() (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.site_ideal"]], "type_symbol (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.type_symbol"]], "accessor() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.accessor"]], "accessor() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.accessor"]], "accessor() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.accessor"]], "accessor() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.accessor"]], "accessor() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.accessor"]], "accessor() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.accessor"]], "accessor() (scitbx.array_family.flex.py_object method)": [[331, "scitbx.array_family.flex.py_object.accessor"]], "accessor() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.accessor"]], "accessor() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.accessor"]], "accessor() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.accessor"]], "accessor() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.accessor"]], "accessor() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.accessor"]], "accessor() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.accessor"]], "add_selected() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.add_selected"]], "add_selected() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.add_selected"]], "all() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all"]], "all() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all"]], "all() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all"]], "all() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all"]], "all() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.all"]], "all() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all"]], "all() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all"]], "all() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all"]], "all() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all"]], "all() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.all"]], "all() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.all"]], "all() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.all"]], "all() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.all"]], "all_approx_equal() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal"]], "all_approx_equal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal"]], "all_approx_equal_relatively() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal_relatively"]], "all_approx_equal_relatively() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal_relatively"]], "all_eq() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all_eq"]], "all_eq() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_eq"]], "all_eq() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_eq"]], "all_eq() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_eq"]], "all_eq() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_eq"]], "all_eq() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_eq"]], "all_eq() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_eq"]], "all_eq() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_eq"]], "all_ge() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_ge"]], "all_ge() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_ge"]], "all_ge() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_ge"]], "all_ge() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_ge"]], "all_ge() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_ge"]], "all_gt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_gt"]], "all_gt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_gt"]], "all_gt() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_gt"]], "all_gt() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_gt"]], "all_gt() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_gt"]], "all_le() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_le"]], "all_le() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_le"]], "all_le() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_le"]], "all_le() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_le"]], "all_le() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_le"]], "all_lt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_lt"]], "all_lt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_lt"]], "all_lt() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_lt"]], "all_lt() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_lt"]], "all_lt() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_lt"]], "all_ne() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all_ne"]], "all_ne() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_ne"]], "all_ne() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_ne"]], "all_ne() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_ne"]], "all_ne() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_ne"]], "all_ne() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_ne"]], "all_ne() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_ne"]], "all_ne() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_ne"]], "all_size (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.all_size"]], "angle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.angle"]], "angle() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.angle"]], "append() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.append"]], "append() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.append"]], "append() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.append"]], "append() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.append"]], "append() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.append"]], "append() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.append"]], "append() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.append"]], "append() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.append"]], "append() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.append"]], "append() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.append"]], "append() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.append"]], "append() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.append"]], "as_1d() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.as_1d"]], "as_1d() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.as_1d"]], "as_1d() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.as_1d"]], "as_1d() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.as_1d"]], "as_1d() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.as_1d"]], "as_1d() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.as_1d"]], "as_1d() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.as_1d"]], "as_1d() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.as_1d"]], "as_1d() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.as_1d"]], "as_1d() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.as_1d"]], "as_1d() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.as_1d"]], "as_1d() (scitbx.array_family.flex.vec3_int method)": 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"scitbx.array_family.flex.sym_mat3_double.as_double"]], "as_double() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.as_double"]], "as_double() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.as_double"]], "as_float() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.as_float"]], "as_int() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.as_int"]], "as_int() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.as_int"]], "as_int() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.as_int"]], "as_long() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.as_long"]], "as_long() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.as_long"]], "as_numpy_array() (scitbx.array_family.flex.bool method)": [[331, 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(in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.lower_bidiagonal"]], "mathematica_form() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.mathematica_form"]], "matrix_back_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_back_substitution"]], "matrix_back_substitution_given_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_back_substitution_given_transpose"]], "matrix_copy_block() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.matrix_copy_block"]], "matrix_copy_block() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_copy_block"]], "matrix_copy_block() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_block"]], "matrix_copy_block() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_copy_block"]], "matrix_copy_block() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_copy_block"]], "matrix_copy_column() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_column"]], "matrix_copy_lower_to_upper_triangle_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_lower_to_upper_triangle_in_place"]], "matrix_copy_lower_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_lower_triangle"]], "matrix_copy_upper_to_lower_triangle_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_upper_to_lower_triangle_in_place"]], "matrix_copy_upper_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_upper_triangle"]], "matrix_determinant_via_lu() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_determinant_via_lu"]], "matrix_diagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal"]], "matrix_diagonal_add_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_add_in_place"]], "matrix_diagonal_product() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_product"]], "matrix_diagonal_set_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_set_in_place"]], "matrix_diagonal_sum() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_sum"]], "matrix_forward_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_forward_substitution"]], "matrix_forward_substitution_given_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_forward_substitution_given_transpose"]], "matrix_inversion() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_inversion"]], "matrix_inversion_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_inversion_in_place"]], "matrix_is_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_is_symmetric"]], "matrix_is_symmetric() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_is_symmetric"]], "matrix_is_symmetric() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_is_symmetric"]], "matrix_lower_bidiagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lower_bidiagonal"]], "matrix_lower_triangle_as_packed_l() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lower_triangle_as_packed_l"]], "matrix_lu_back_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lu_back_substitution"]], "matrix_lu_decomposition_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lu_decomposition_in_place"]], "matrix_multiply() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_multiply"]], "matrix_multiply() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply"]], "matrix_multiply_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_packed_u"]], "matrix_multiply_packed_u_multiply_lhs_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_packed_u_multiply_lhs_transpose"]], "matrix_multiply_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_transpose"]], "matrix_norm_1() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_1"]], "matrix_norm_frobenius() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_frobenius"]], "matrix_norm_inf() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_inf"]], "matrix_outer_product() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_outer_product"]], "matrix_packed_l_as_lower_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_l_as_lower_triangle"]], "matrix_packed_l_as_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_l_as_symmetric"]], "matrix_packed_u_as_symmetric() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_packed_u_as_symmetric"]], "matrix_packed_u_as_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_as_symmetric"]], "matrix_packed_u_as_upper_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_as_upper_triangle"]], "matrix_packed_u_diagonal() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_packed_u_diagonal"]], "matrix_packed_u_diagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_diagonal"]], "matrix_packed_u_diagonal_add_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_diagonal_add_in_place"]], "matrix_packed_u_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_swap_rows_and_columns_in_place"]], "matrix_paste_block_in_place() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.matrix_paste_block_in_place"]], "matrix_paste_block_in_place() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_paste_block_in_place"]], "matrix_paste_block_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_paste_block_in_place"]], "matrix_paste_block_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_paste_block_in_place"]], "matrix_paste_block_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_paste_block_in_place"]], "matrix_paste_column_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_paste_column_in_place"]], "matrix_rot90() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_rot90"]], "matrix_rot90() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_rot90"]], "matrix_rot90() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_rot90"]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_swap_columns_in_place"]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_swap_columns_in_place"]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_swap_columns_in_place"]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_swap_rows_in_place"]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_swap_rows_in_place"]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_swap_rows_in_place"]], "matrix_symmetric_as_packed_l() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_as_packed_l"]], "matrix_symmetric_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_as_packed_u"]], "matrix_symmetric_upper_triangle_quadratic_form() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_upper_triangle_quadratic_form"]], "matrix_symmetric_upper_triangle_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_upper_triangle_swap_rows_and_columns_in_place"]], "matrix_trace() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_trace"]], "matrix_transpose() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_transpose"]], "matrix_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose"]], "matrix_transpose_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_in_place"]], "matrix_transpose_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_transpose_in_place"]], "matrix_transpose_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_transpose_in_place"]], "matrix_transpose_multiply() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply"]], "matrix_transpose_multiply_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply_as_packed_u"]], "matrix_transpose_multiply_diagonal_multiply_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply_diagonal_multiply_as_packed_u"]], "matrix_upper_bidiagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_upper_bidiagonal"]], "matrix_upper_triangle_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_upper_triangle_as_packed_u"]], "max() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.max"]], "max() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max"]], "max_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.max_default"]], "max_distance() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.max_distance"]], "max_distance() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max_distance"]], "max_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max_distance_between_any_pair_with_id"]], "max_element_length() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.max_element_length"]], "md5() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.md5"]], "mean() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.mean"]], "mean() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.mean"]], "mean_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.mean_default"]], "mean_weighted() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.mean_weighted"]], "mean_weighted() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.mean_weighted"]], "min() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min"]], "min() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min"]], "min_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.min_default"]], "min_distance_between_any_pair() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min_distance_between_any_pair"]], "min_distance_between_any_pair() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min_distance_between_any_pair"]], "min_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min_distance_between_any_pair_with_id"]], "min_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min_distance_between_any_pair_with_id"]], "min_max_mean() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.min_max_mean"]], "nd() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.nd"]], "nd() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.nd"]], "nd() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.nd"]], "nd() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.nd"]], "nd() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.nd"]], "nd() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.nd"]], "nd() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.nd"]], "nd() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.nd"]], "nd() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.nd"]], "nd() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.nd"]], "nd() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.nd"]], "nd() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.nd"]], "nd() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.nd"]], "next_permutation() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.next_permutation"]], "norm() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.norm"]], "norm() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.norm"]], "norm() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.norm"]], "norm() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.norm"]], "norm_1() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.norm_1"]], "norm_inf() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.norm_inf"]], "norm_inf() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.norm_inf"]], "norm_inf() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.norm_inf"]], "norm_inf() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.norm_inf"]], "norm_inf() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.norm_inf"]], "norms() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.norms"]], "norms() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.norms"]], "origin() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.origin"]], "origin() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.origin"]], "origin() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.origin"]], "origin() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.origin"]], "origin() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.origin"]], "origin() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.origin"]], "origin() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.origin"]], "origin() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.origin"]], "origin() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.origin"]], "origin() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.origin"]], "origin() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.origin"]], "origin() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.origin"]], "origin() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.origin"]], "part_names() (scitbx.array_family.flex.complex_double static method)": [[331, "scitbx.array_family.flex.complex_double.part_names"]], "part_names() (scitbx.array_family.flex.vec3_double static method)": [[331, "scitbx.array_family.flex.vec3_double.part_names"]], "parts() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.parts"]], "parts() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.parts"]], "parts() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.parts"]], "permutation_generator() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.permutation_generator"]], "pop_back() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.pop_back"]], "pop_back() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.pop_back"]], "pop_back() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.pop_back"]], "pop_back() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.pop_back"]], "pop_back() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.pop_back"]], "pop_back() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.pop_back"]], "pop_back() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.pop_back"]], "pop_back() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.pop_back"]], "pop_back() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.pop_back"]], "pop_back() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.pop_back"]], "pop_back() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.pop_back"]], "pop_back() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.pop_back"]], "py_object (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.py_object"]], "quadratic_interpolation_with_gradients() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.quadratic_interpolation_with_gradients"]], "random_selection() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.random_selection"]], "reserve() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.reserve"]], "reserve() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.reserve"]], "reserve() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.reserve"]], "reserve() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.reserve"]], "reserve() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.reserve"]], "reserve() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.reserve"]], "reserve() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.reserve"]], "reserve() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.reserve"]], "reserve() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.reserve"]], "reserve() (scitbx.array_family.flex.vec2_double method)": [[331, 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method)": [[331, "scitbx.array_family.flex.bool.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.shallow_copy"]], "shallow_copy() (scitbx.array_family.flex.sym_mat3_double method)": [[331, 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(scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_blas_2 property)": [[333, "scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_BLAS_2.debug_info"]], "description (scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_blas_2 property)": [[333, "scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_BLAS_2.description"]], "do() (scitbx.lstbx.normal_eqns_solving.iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.do"]], "do() (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations.do"]], "do() (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns method)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns.do"]], "do() (scitbx.lstbx.normal_eqns_solving.naive_iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations.do"]], "do() 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"max_shift_over_esd (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit.max_shift_over_esd"]], "mu (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations property)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations.mu"]], "n_max_iterations (scitbx.lstbx.normal_eqns_solving.iterations attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.n_max_iterations"]], "naive_iterations (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations"]], "naive_iterations_with_damping (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping"]], "naive_iterations_with_damping_and_shift_limit (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit"]], 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"each_abs() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.each_abs"]], "each_mod_short() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.each_mod_short"]], "extract_block() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.extract_block"]], "identity (class in scitbx.matrix)": [[334, "scitbx.matrix.identity"]], "inverse() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.inverse"]], "inversion (class in scitbx.matrix)": [[334, "scitbx.matrix.inversion"]], "is_approx_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_approx_zero"]], "is_col_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_col_zero"]], "is_r3_identity_matrix() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_identity_matrix"]], "is_r3_rotation_matrix() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_rotation_matrix"]], "is_r3_rotation_matrix_rms() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_rotation_matrix_rms"]], "is_square() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_square"]], "is_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_zero"]], "length() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.length"]], "length_sq() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.length_sq"]], "mathematica_form() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.mathematica_form"]], "matlab_form() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.matlab_form"]], "max() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.max"]], "max_index() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.max_index"]], "min() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.min"]], "min_index() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.min_index"]], "n_columns() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.n_columns"]], "n_rows() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.n_rows"]], "norm_sq() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.norm_sq"]], "normalize() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.normalize"]], "ortho() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.ortho"]], "outer_product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.outer_product"]], "product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.product"]], "quaternion_inverse() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.quaternion_inverse"]], "r3_rotation_matrix_as_unit_quaternion() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.r3_rotation_matrix_as_unit_quaternion"]], "r3_rotation_matrix_as_x_y_z_angles() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.r3_rotation_matrix_as_x_y_z_angles"]], "rec (class in scitbx.matrix)": [[334, "scitbx.matrix.rec"]], "resolve_partitions() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.resolve_partitions"]], "rotate() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.rotate"]], "rotate_2d() 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xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.add_tiles_to_cbf"]], "cbf_file_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.cbf_file_to_basis_dict"]], "copy_cbf_header() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.copy_cbf_header"]], "env_dxtbx_from_slac_metrology() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.env_dxtbx_from_slac_metrology"]], "format_object_from_data() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.format_object_from_data"]], "get_calib_file_path() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_calib_file_path"]], "get_cspad_cbf_handle() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_cspad_cbf_handle"]], "map_detector_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.map_detector_to_basis_dict"]], "metro_phil_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.metro_phil_to_basis_dict"]], "metrology2phil() (in module xfel.cftbx.detector.metrology2phil)": [[339, "xfel.cftbx.detector.metrology2phil.metrology2phil"]], "read_optical_metrology_from_flat_file() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.read_optical_metrology_from_flat_file"]], "sections2phil() (in module xfel.cftbx.detector.metrology2phil)": [[339, "xfel.cftbx.detector.metrology2phil.sections2phil"]], "write_cspad_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.write_cspad_cbf"]], "xfel.cftbx.detector": [[339, "module-xfel.cftbx.detector"]], "xfel.cftbx.detector.cspad_cbf_tbx": [[339, "module-xfel.cftbx.detector.cspad_cbf_tbx"]], "xfel.cftbx.detector.metrology2phil": [[339, "module-xfel.cftbx.detector.metrology2phil"]], "angstroms_to_ev (xfel.clustering.singleframe.singleframe attribute)": [[340, "xfel.clustering.singleframe.SingleFrame.ANGSTROMS_TO_EV"]], "cluster (class in xfel.clustering.cluster)": [[340, "xfel.clustering.cluster.Cluster"]], "singleframe (class in xfel.clustering.singleframe)": [[340, "xfel.clustering.singleframe.SingleFrame"]], "__dict__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__dict__"]], "__init__() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.__init__"]], "__init__() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.__init__"]], "__len__() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.__len__"]], "__module__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__module__"]], "__module__ (xfel.clustering.singleframe.singleframe attribute)": [[340, "xfel.clustering.singleframe.SingleFrame.__module__"]], "__weakref__ (xfel.clustering.cluster.cluster attribute)": [[340, "xfel.clustering.cluster.Cluster.__weakref__"]], "ab_cluster() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.ab_cluster"]], "all_frames_intensity_stats() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.all_frames_intensity_stats"]], "best_by_cc() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.best_by_CC"]], "distance_from() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.distance_from"]], "dump_as_mtz() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_as_mtz"]], "dump_file_list() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_file_list"]], "filter_negative_intensities() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.filter_negative_intensities"]], "from_crystal_symmetries() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_crystal_symmetries"]], "from_directories() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_directories"]], "from_expts() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_expts"]], "from_files() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_files"]], "from_iterable() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_iterable"]], "from_list() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_list"]], "init_calc_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.init_calc_wilson"]], "intensity_statistics() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.intensity_statistics"]], "make_g6() (xfel.clustering.singleframe.singleframe static method)": [[340, "xfel.clustering.singleframe.SingleFrame.make_g6"]], "make_sub_cluster() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.make_sub_cluster"]], "merge_dict() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.merge_dict"]], "n_reflections_by_sigi() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.n_reflections_by_sigi"]], "plot_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.plot_wilson"]], "point_group_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.point_group_filter"]], "polarization_correction() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.polarization_correction"]], "prime_postrefine() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.prime_postrefine"]], "print_ucs() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.print_ucs"]], "to_panda() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.to_panda"]], "to_pandas() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.to_pandas"]], "total_intensity_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.total_intensity_filter"]], "trim_res_limit() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.trim_res_limit"]], "uc_feature_vector() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.uc_feature_vector"]], "unit_cell_info() (in module xfel.clustering.cluster_groups)": [[340, "xfel.clustering.cluster_groups.unit_cell_info"]], "visualise_orientational_distribution() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.visualise_orientational_distribution"]], "xfel.clustering.cluster": [[340, "module-xfel.clustering.cluster"]], "xfel.clustering.cluster_groups": [[340, "module-xfel.clustering.cluster_groups"]], "xfel.clustering.singleframe": [[340, "module-xfel.clustering.singleframe"]], "outliercellerror": [[341, "xfel.command_line.cxi_merge.OutlierCellError"]], "pixelfiterror": [[341, "xfel.command_line.view_pixel_histograms.PixelFitError"]], "wrongbravaiserror": [[341, "xfel.command_line.cxi_merge.WrongBravaisError"]], "add_cell() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cell"]], "add_cells() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cells"]], "add_frame() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.add_frame"]], "apply_sub_pixel_metrology() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.apply_sub_pixel_metrology"]], "check_image() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.check_image"]], "check_pixel_histogram_fit() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.check_pixel_histogram_fit"]], "consistent_set_and_model() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.consistent_set_and_model"]], "convert_2x2() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.convert_2x2"]], "convert_detector() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.convert_detector"]], "convert_detector() (in module xfel.command_line.convert_gain_map_cbf)": [[341, "xfel.command_line.convert_gain_map_cbf.convert_detector"]], "crystfel_to_cctbx_coord_system() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.crystfel_to_cctbx_coord_system"]], "data() (xfel.command_line.convert_gain_map.fake_cspad_elementv2 method)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2.data"]], "determine_mean_i_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.determine_mean_I_mproc"]], "distance() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.distance"]], "estimate_signal_to_noise() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.estimate_signal_to_noise"]], "estimate_signal_to_noise() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.estimate_signal_to_noise"]], "fake_config (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_config"]], "fake_cspad_elementv2 (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2"]], "fake_env (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_env"]], "fake_evt (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_evt"]], "fake_get_config() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_get_config"]], "finalize_and_save_data() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.finalize_and_save_data"]], "fit_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.fit_one_histogram"]], "fourier_filter() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.fourier_filter"]], "full_width_half_max() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.full_width_half_max"]], "generate_data_from_streams() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_data_from_streams"]], "generate_streams_from_path() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_streams_from_path"]], "getconfig() (xfel.command_line.convert_gain_map.fake_env method)": [[341, "xfel.command_line.convert_gain_map.fake_env.getConfig"]], "getcspadquads() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getCsPadQuads"]], "gettime() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getTime"]], "get_average_cell_dimensions() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.get_average_cell_dimensions"]], "get_boundaries_from_sensor_id() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_boundaries_from_sensor_ID"]], "get_observations() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_observations"]], "get_overall_correlation() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.get_overall_correlation"]], "get_phil() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.get_phil"]], "get_plot_statistics() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.get_plot_statistics"]], "get_tile_center() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_center"]], "get_tile_coords() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_coords"]], "get_tile_id() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_id"]], "hist_outline() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.hist_outline"]], "image_template() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.image_template"]], "interpolate() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.interpolate"]], "keywise_printout() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.keywise_printout"]], "load_result() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.load_result"]], "make_int_pickle() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.make_int_pickle"]], "match_runs() (in module xfel.command_line.auto_submit)": [[341, "xfel.command_line.auto_submit.match_runs"]], "pixel_histograms (class in xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms"]], "pixels() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.pixels"]], "plot() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot"]], "plot_gaussians() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_gaussians"]], "plot_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_one_histogram"]], "plot_overall_completeness() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_overall_completeness"]], "plot_statistics (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_statistics"]], "plot_statistics_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_statistics_histograms"]], "plot_unit_cell_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_unit_cell_histograms"]], "point_in_polygon() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_in_polygon"]], "point_inside_circle() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_inside_circle"]], "postrefine_by_frame_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.postrefine_by_frame_mproc"]], "pyplot_label_axes() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.pyplot_label_axes"]], "quad() (xfel.command_line.convert_gain_map.fake_cspad_elementv2 method)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2.quad"]], "quadmask() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.quadMask"]], "read_all_mysql() (xfel.command_line.cxi_xmerge.xscaling_manager method)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager.read_all_mysql"]], "read_input() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.read_input"]], "reset() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.reset"]], "resolution_bin (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.resolution_bin"]], "roimask() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.roiMask"]], "run() (in module xfel.command_line.auto_submit)": [[341, "xfel.command_line.auto_submit.run"]], "run() (in module xfel.command_line.brehm_diederichs)": [[341, "xfel.command_line.brehm_diederichs.run"]], "run() (in module xfel.command_line.cbf_average)": [[341, "xfel.command_line.cbf_average.run"]], "run() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.run"]], "run() (in module xfel.command_line.convert_gain_map_cbf)": [[341, "xfel.command_line.convert_gain_map_cbf.run"]], "run() (in module xfel.command_line.cxi_cspad_pinwheel)": [[341, "xfel.command_line.cxi_cspad_pinwheel.run"]], "run() (in module xfel.command_line.cxi_diff)": [[341, "xfel.command_line.cxi_diff.run"]], "run() (in module xfel.command_line.cxi_lsf)": [[341, "xfel.command_line.cxi_lsf.run"]], "run() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.run"]], "run() (in module xfel.command_line.cxi_pbs)": [[341, "xfel.command_line.cxi_pbs.run"]], "run() (in module xfel.command_line.cxi_plotcv)": [[341, "xfel.command_line.cxi_plotcv.run"]], "run() (in module xfel.command_line.cxi_psana)": [[341, "xfel.command_line.cxi_psana.run"]], "run() (in module xfel.command_line.cxi_pyana)": [[341, "xfel.command_line.cxi_pyana.run"]], "run() (in module xfel.command_line.cxi_xmerge)": [[341, "xfel.command_line.cxi_xmerge.run"]], "run() (in module xfel.command_line.list_db_metadata)": [[341, "xfel.command_line.list_db_metadata.run"]], "run() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.run"]], "run() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.run"]], "run() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.run"]], "run() (in module xfel.command_line.plot_to_subpixel)": [[341, "xfel.command_line.plot_to_subpixel.run"]], "run() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.run"]], "run() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.run"]], "run() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.run"]], "run() (in module xfel.command_line.trial_stats)": [[341, "xfel.command_line.trial_stats.run"]], "run() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.run"]], "scale_all() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_all"]], "scale_all() (xfel.command_line.cxi_xmerge.xscaling_manager method)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager.scale_all"]], "scale_frame() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_frame"]], "scale_frame_by_mean_i_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.scale_frame_by_mean_I_mproc"]], "scale_frame_detail() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.scale_frame_detail"]], "scaling_manager (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.scaling_manager"]], "scaling_result (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.scaling_result"]], "sections() (xfel.command_line.convert_gain_map.fake_config method)": [[341, "xfel.command_line.convert_gain_map.fake_config.sections"]], "show_all_pyplot() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.show_all_pyplot"]], "show_histograms() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.show_histograms"]], "show_overall_observations() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.show_overall_observations"]], "show_tiles() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.show_tiles"]], "show_unit_cell_histograms() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.show_unit_cell_histograms"]], "signal_to_noise_statistical() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.signal_to_noise_statistical"]], "single_peak_fit() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.single_peak_fit"]], "single_reflection_histograms() (xfel.command_line.cxi_merge.scaling_manager static method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.single_reflection_histograms"]], "sliding_average() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.sliding_average"]], "subtract_background() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.subtract_background"]], "sum_intensities() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.sum_intensities"]], "unit_cell_distribution (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution"]], "unit_cell_to_symetry_object() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.unit_cell_to_symetry_object"]], "validate_phil() (in module xfel.command_line.metrology)": [[341, "xfel.command_line.metrology.validate_phil"]], "view_raw_image() (in module xfel.command_line.quadrants)": [[341, "xfel.command_line.quadrants.view_raw_image"]], "xfel.command_line": [[341, "module-xfel.command_line"]], "xfel.command_line.auto_submit": [[341, "module-xfel.command_line.auto_submit"]], "xfel.command_line.brehm_diederichs": [[341, "module-xfel.command_line.brehm_diederichs"]], "xfel.command_line.cbf_average": [[341, "module-xfel.command_line.cbf_average"]], "xfel.command_line.convert_gain_map": [[341, "module-xfel.command_line.convert_gain_map"]], "xfel.command_line.convert_gain_map_cbf": [[341, "module-xfel.command_line.convert_gain_map_cbf"]], "xfel.command_line.cxi_apply_metrology": [[341, "module-xfel.command_line.cxi_apply_metrology"]], "xfel.command_line.cxi_cspad_pinwheel": [[341, "module-xfel.command_line.cxi_cspad_pinwheel"]], "xfel.command_line.cxi_diff": [[341, "module-xfel.command_line.cxi_diff"]], "xfel.command_line.cxi_display_metrology": [[341, "module-xfel.command_line.cxi_display_metrology"]], "xfel.command_line.cxi_generate_circular_gain_mask": [[341, "module-xfel.command_line.cxi_generate_circular_gain_mask"]], "xfel.command_line.cxi_index": [[341, "module-xfel.command_line.cxi_index"]], "xfel.command_line.cxi_lsf": [[341, "module-xfel.command_line.cxi_lsf"]], "xfel.command_line.cxi_merge": [[341, "module-xfel.command_line.cxi_merge"]], "xfel.command_line.cxi_optical2cbfheader": [[341, "module-xfel.command_line.cxi_optical2cbfheader"]], "xfel.command_line.cxi_pbs": [[341, "module-xfel.command_line.cxi_pbs"]], "xfel.command_line.cxi_pickle2cbf": [[341, "module-xfel.command_line.cxi_pickle2cbf"]], "xfel.command_line.cxi_plotcv": [[341, "module-xfel.command_line.cxi_plotcv"]], "xfel.command_line.cxi_psana": [[341, "module-xfel.command_line.cxi_psana"]], "xfel.command_line.cxi_pyana": [[341, "module-xfel.command_line.cxi_pyana"]], "xfel.command_line.cxi_spots": [[341, "module-xfel.command_line.cxi_spots"]], "xfel.command_line.cxi_stream_to_pickle": [[341, "module-xfel.command_line.cxi_stream_to_pickle"]], "xfel.command_line.cxi_view": [[341, "module-xfel.command_line.cxi_view"]], "xfel.command_line.cxi_xmerge": [[341, "module-xfel.command_line.cxi_xmerge"]], "xfel.command_line.histogram_finalise": [[341, "module-xfel.command_line.histogram_finalise"]], "xfel.command_line.list_db_metadata": [[341, "module-xfel.command_line.list_db_metadata"]], "xfel.command_line.make_mask": [[341, "module-xfel.command_line.make_mask"]], "xfel.command_line.metrology": [[341, "module-xfel.command_line.metrology"]], "xfel.command_line.monitor_detectors": [[341, "module-xfel.command_line.monitor_detectors"]], "xfel.command_line.monitor_trials": [[341, "module-xfel.command_line.monitor_trials"]], "xfel.command_line.overlay_spectra": [[341, "module-xfel.command_line.overlay_spectra"]], "xfel.command_line.plot_to_subpixel": [[341, "module-xfel.command_line.plot_to_subpixel"]], "xfel.command_line.postrefine": [[341, "module-xfel.command_line.postrefine"]], "xfel.command_line.print_pickle": [[341, "module-xfel.command_line.print_pickle"]], "xfel.command_line.quadrants": [[341, "module-xfel.command_line.quadrants"]], "xfel.command_line.radial_average": [[341, "module-xfel.command_line.radial_average"]], "xfel.command_line.smooth_spectrum": [[341, "module-xfel.command_line.smooth_spectrum"]], "xfel.command_line.subtract_background": [[341, "module-xfel.command_line.subtract_background"]], "xfel.command_line.trial_stats": [[341, "module-xfel.command_line.trial_stats"]], "xfel.command_line.view_pixel_histograms": [[341, "module-xfel.command_line.view_pixel_histograms"]], "xfel.command_line.xes_finalise": [[341, "module-xfel.command_line.xes_finalise"]], "xfel.command_line.xes_histograms": [[341, "module-xfel.command_line.xes_histograms"]], "xscaling_manager (class in xfel.command_line.cxi_xmerge)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager"]], "imagefactory() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.ImageFactory"]], "imagefactory() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.ImageFactory"]], "apply_gaussian_noise() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.apply_gaussian_noise"]], "binned_correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.binned_correlation"]], "correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.correlation"]], "display() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.display"]], "display_with_callback() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.display_with_callback"]], "empty (class in xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.empty"]], "get_cursor() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_cursor"]], "get_frame_dictionary() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_frame_dictionary"]], "get_mmtbx_icalc() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.get_mmtbx_icalc"]], "img_add() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.img_add"]], "initialize_tables_and_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.initialize_tables_and_insert_command"]], "insert() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.insert"]], "integrate_one_image() (in module xfel.cxi.integrate_image_api)": [[342, "xfel.cxi.integrate_image_api.integrate_one_image"]], "integrate_one_image() (in module xfel.cxi.strong_zulu)": [[342, "xfel.cxi.strong_zulu.integrate_one_image"]], "is_odd_numbered() (in module xfel.cxi.util)": [[342, "xfel.cxi.util.is_odd_numbered"]], "is_pinwheel_region() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.is_pinwheel_region"]], "lines (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.lines"]], "literals() (xfel.cxi.correction_vector_plot.lines method)": [[342, "xfel.cxi.correction_vector_plot.lines.literals"]], "load_cc_data() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.load_cc_data"]], "main() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.main"]], "manage_sql (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.manage_sql"]], "r1_factor() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.r1_factor"]], "r_split() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.r_split"]], "run_cc() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.run_cc"]], "run_correction_vector_plot() (in module xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.run_correction_vector_plot"]], "run_one() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one"]], "run_one_index() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one_index"]], "run_one_index_core() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.run_one_index_core"]], "scale_factor() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.scale_factor"]], "send_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.send_insert_command"]], "split_sigma_test() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.split_sigma_test"]], "spot_add() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.spot_add"]], "superimpose_powder_arcs() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.superimpose_powder_arcs"]], "user_callback() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.user_callback"]], "vectors() (xfel.cxi.correction_vector_plot.lines method)": [[342, "xfel.cxi.correction_vector_plot.lines.vectors"]], "view_raw_image() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.view_raw_image"]], "wrapper_of_callback (class in xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.wrapper_of_callback"]], "xfel.cxi": [[342, "module-xfel.cxi"]], "xfel.cxi.average_spots": [[342, "module-xfel.cxi.average_spots"]], "xfel.cxi.correction_vector_plot": [[342, "module-xfel.cxi.correction_vector_plot"]], "xfel.cxi.cxi_cc": [[342, "module-xfel.cxi.cxi_cc"]], "xfel.cxi.display_powder_arcs": [[342, "module-xfel.cxi.display_powder_arcs"]], "xfel.cxi.display_spots": [[342, "module-xfel.cxi.display_spots"]], "xfel.cxi.integrate_image_api": [[342, "module-xfel.cxi.integrate_image_api"]], "xfel.cxi.strong_zulu": [[342, "module-xfel.cxi.strong_zulu"]], "xfel.cxi.util": [[342, "module-xfel.cxi.util"]], "cspad2x2image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPad2x2Image"]], "cspaddetector() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadDetector"]], "cspadelement() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadElement"]], "section (class in xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section"]], "statusframe_thread (class in xfel.cxi.cspad_ana.mod_daq_status)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread"]], "as_trace() (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis.as_trace"]], "average_mixin (class in xfel.cxi.cspad_ana.average_tbx)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin"]], "begincalibcycle() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.begincalibcycle"]], "beginjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.beginjob"]], "beginjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.beginjob"]], "calculate() (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis.calculate"]], "calib2sections() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2sections"]], "calib2tensor3() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2tensor3"]], "cbcaa() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.cbcaa"]], "chebyshev_common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.chebyshev_common_mode"]], "chebyshev_fit() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.chebyshev_fit"]], "commit_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.commit_entries"]], "commit_progress_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.commit_progress_entries"]], "common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.common_mode"]], "common_mode_correction (class in xfel.cxi.cspad_ana.common_mode)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction"]], "corners() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners"]], "corners_asic() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners_asic"]], "cspad2x2_bad_pixel_mask_cxi_run7() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad2x2_bad_pixel_mask_cxi_run7"]], "cspad_unbound_pixel_mask() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad_unbound_pixel_mask"]], "display_calib() (in module xfel.cxi.cspad_ana.display_calib)": [[343, "xfel.cxi.cspad_ana.display_calib.display_calib"]], "distl_filter() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.distl_filter"]], "distl_hitfinder (class in xfel.cxi.cspad_ana.hitfinder_tbx)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder"]], "do_photon_counting() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_photon_counting"]], "do_sigma_scaling() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_sigma_scaling"]], "dpack() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dpack"]], "dwritef() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef"]], "dwritef2() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef2"]], "endjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.endjob"]], "endjob() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.endjob"]], "endjob() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.endjob"]], "endjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.endjob"]], "env_distance() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_distance"]], "env_injector_xyz() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_injector_xyz"]], "env_laser_status() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_laser_status"]], "env_sifoil() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_sifoil"]], "env_wavelength_sxr() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_wavelength_sxr"]], "event() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.event"]], "event() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.event"]], "event() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.event"]], "event() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.event"]], "event() (xfel.cxi.cspad_ana.mod_dump.mod_dump method)": [[343, "xfel.cxi.cspad_ana.mod_dump.mod_dump.event"]], "event() (xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap method)": [[343, "xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap.event"]], "event() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.event"]], "event() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.event"]], "event() (xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5 method)": [[343, "xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5.event"]], "event() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.event"]], "event() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.event"]], "event() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.event"]], "event() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.event"]], "event() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.event"]], "event() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.event"]], "event() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.event"]], "event() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.event"]], "evt_beam_charge() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_beam_charge"]], "evt_get_quads() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_get_quads"]], "evt_pulse_energy() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_energy"]], "evt_pulse_length() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_length"]], "evt_repetition_rate() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_repetition_rate"]], "evt_seqno() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_seqno"]], "evt_time() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_time"]], "evt_timestamp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_timestamp"]], "evt_wavelength() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_wavelength"]], "filter_outlying_pixels() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.filter_outlying_pixels"]], "finalise_one_run (class in xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.finalise_one_run"]], "finalise_one_run (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.finalise_one_run"]], "first_moment_analysis (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis"]], "fread_matrix() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_matrix"]], "fread_tensor3() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_tensor3"]], "fread_vector() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.fread_vector"]], "getoptbool() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptBool"]], "getoptevalorstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptEvalOrString"]], "getoptfloat() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptFloat"]], "getoptinteger() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptInteger"]], "getoptroi() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptROI"]], "getoptstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptString"]], "getoptstrings() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptStrings"]], "get_active_data() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.get_active_data"]], "get_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.get_spectrum"]], "hdf5pack() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.hdf5pack"]], "histogram_finalise (class in xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.histogram_finalise"]], "image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image"]], "image_xpp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image_xpp"]], "initialize() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.initialize"]], "iplace() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.iplace"]], "laser_status (class in xfel.cxi.cspad_ana.mod_event_info)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status"]], "mod_average (class in xfel.cxi.cspad_ana.mod_average)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average"]], "mod_daq_status (class in xfel.cxi.cspad_ana.mod_daq_status)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status"]], "mod_dump (class in xfel.cxi.cspad_ana.mod_dump)": [[343, "xfel.cxi.cspad_ana.mod_dump.mod_dump"]], "mod_dump_bitmap (class in xfel.cxi.cspad_ana.mod_dump_bitmap)": [[343, "xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap"]], "mod_event_info (class in xfel.cxi.cspad_ana.mod_event_info)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info"]], "mod_filter (class in xfel.cxi.cspad_ana.mod_filter)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter"]], "mod_hdf5 (class in xfel.cxi.cspad_ana.mod_hdf5)": [[343, "xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5"]], "mod_hitfind (class in xfel.cxi.cspad_ana.mod_hitfind)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind"]], "mod_illumination_filter (class in xfel.cxi.cspad_ana.mod_illumination_filter)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter"]], "mod_mar (class in xfel.cxi.cspad_ana.mod_mar)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar"]], "mod_param (class in xfel.cxi.cspad_ana.mod_param)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param"]], "mod_pulnix_dump (class in xfel.cxi.cspad_ana.mod_pulnix_dump)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump"]], "mod_radial_average (class in xfel.cxi.cspad_ana.mod_radial_average)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average"]], "mod_xes (class in xfel.cxi.cspad_ana.mod_xes)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes"]], "ms_since_last_status_change() (xfel.cxi.cspad_ana.mod_event_info.laser_status method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.ms_since_last_status_change"]], "output_image() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_image"]], "output_matlab_form() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_matlab_form"]], "output_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_spectrum"]], "pathsubst() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.pathsubst"]], "pixel_histograms (class in xfel.cxi.cspad_ana.pixel_histograms)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms"]], "plot_energy() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.plot_energy"]], "q_size (xfel.cxi.cspad_ana.parse_calib.section attribute)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.q_size"]], "qrotate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.qrotate"]], "queue_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.queue_entry"]], "queue_progress_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.queue_progress_entry"]], "rplace() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.rplace"]], "run() (in module xfel.cxi.cspad_ana.xes_histograms)": [[343, "xfel.cxi.cspad_ana.xes_histograms.run"]], "run() (xfel.cxi.cspad_ana.mod_daq_status.statusframe_thread method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread.run"]], "set_status() (xfel.cxi.cspad_ana.mod_event_info.laser_status method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.set_status"]], "set_up_hitfinder() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.set_up_hitfinder"]], "skip_event_flag() (in module xfel.cxi.cspad_ana)": [[343, "xfel.cxi.cspad_ana.skip_event_flag"]], "spec_plot() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.spec_plot"]], "srotate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.srotate"]], "start_local() (xfel.cxi.cspad_ana.mod_daq_status.statusframe_thread method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread.start_local"]], "status (xfel.cxi.cspad_ana.mod_event_info.laser_status property)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status"]], "status_change_timestamp (xfel.cxi.cspad_ana.mod_event_info.laser_status attribute)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status_change_timestamp"]], "translate() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.translate"]], "update_histograms() (in module xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.update_histograms"]], "update_plot() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.update_plot"]], "v2calib2sections() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.v2calib2sections"]], "write_tiff() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.write_tiff"]], "xes_finalise (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.xes_finalise"]], "xes_from_histograms (class in xfel.cxi.cspad_ana.xes_histograms)": [[343, "xfel.cxi.cspad_ana.xes_histograms.xes_from_histograms"]], "xfel.cxi.cspad_ana": [[343, "module-xfel.cxi.cspad_ana"]], "xfel.cxi.cspad_ana.average_tbx": [[343, "module-xfel.cxi.cspad_ana.average_tbx"]], "xfel.cxi.cspad_ana.common_mode": [[343, "module-xfel.cxi.cspad_ana.common_mode"]], "xfel.cxi.cspad_ana.cspad_tbx": [[343, "module-xfel.cxi.cspad_ana.cspad_tbx"]], "xfel.cxi.cspad_ana.display_calib": [[343, "module-xfel.cxi.cspad_ana.display_calib"]], "xfel.cxi.cspad_ana.histogram_finalise": [[343, "module-xfel.cxi.cspad_ana.histogram_finalise"]], "xfel.cxi.cspad_ana.hitfinder_tbx": [[343, "module-xfel.cxi.cspad_ana.hitfinder_tbx"]], "xfel.cxi.cspad_ana.mod_average": [[343, "module-xfel.cxi.cspad_ana.mod_average"]], "xfel.cxi.cspad_ana.mod_daq_status": [[343, "module-xfel.cxi.cspad_ana.mod_daq_status"]], "xfel.cxi.cspad_ana.mod_dump": [[343, "module-xfel.cxi.cspad_ana.mod_dump"]], "xfel.cxi.cspad_ana.mod_dump_bitmap": [[343, "module-xfel.cxi.cspad_ana.mod_dump_bitmap"]], "xfel.cxi.cspad_ana.mod_event_info": [[343, "module-xfel.cxi.cspad_ana.mod_event_info"]], "xfel.cxi.cspad_ana.mod_filter": [[343, "module-xfel.cxi.cspad_ana.mod_filter"]], "xfel.cxi.cspad_ana.mod_hdf5": [[343, "module-xfel.cxi.cspad_ana.mod_hdf5"]], "xfel.cxi.cspad_ana.mod_hitfind": [[343, "module-xfel.cxi.cspad_ana.mod_hitfind"]], "xfel.cxi.cspad_ana.mod_illumination_filter": [[343, "module-xfel.cxi.cspad_ana.mod_illumination_filter"]], "xfel.cxi.cspad_ana.mod_mar": [[343, "module-xfel.cxi.cspad_ana.mod_mar"]], "xfel.cxi.cspad_ana.mod_param": [[343, "module-xfel.cxi.cspad_ana.mod_param"]], "xfel.cxi.cspad_ana.mod_pulnix_dump": [[343, "module-xfel.cxi.cspad_ana.mod_pulnix_dump"]], "xfel.cxi.cspad_ana.mod_radial_average": [[343, "module-xfel.cxi.cspad_ana.mod_radial_average"]], "xfel.cxi.cspad_ana.mod_xes": [[343, "module-xfel.cxi.cspad_ana.mod_xes"]], "xfel.cxi.cspad_ana.parse_calib": [[343, "module-xfel.cxi.cspad_ana.parse_calib"]], "xfel.cxi.cspad_ana.pixel_histograms": [[343, "module-xfel.cxi.cspad_ana.pixel_histograms"]], "xfel.cxi.cspad_ana.xes_finalise": [[343, "module-xfel.cxi.cspad_ana.xes_finalise"]], "xfel.cxi.cspad_ana.xes_histograms": [[343, "module-xfel.cxi.cspad_ana.xes_histograms"]], "detectorplot (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot"]], "detectorplotframe (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame"]], "onpan() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnPan"]], "onsave() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.OnSave"]], "onsaveimage() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnSaveImage"]], "onsetrunnumber() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnSetRunNumber"]], "ontimelockcheck() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnTimeLockCheck"]], "ontimer() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnTimer"]], "ontimer() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.OnTimer"]], "onupdate() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnUpdate"]], "onzoom() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnZoom"]], "run (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.Run"]], "runnumberevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.RunNumberEvent"]], "saveimageevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.SaveImageEvent"]], "statusframe (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame"]], "statusplot (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusPlot"]], "trialsplot (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlot"]], "trialsplotframe (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame"]], "updateevent (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.UpdateEvent"]], "create_plot_panel() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.create_plot_panel"]], "create_plot_panel() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.create_plot_panel"]], "create_plot_panel() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.create_plot_panel"]], "cull_braggs() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.cull_braggs"]], "cull_braggs() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.cull_braggs"]], "draw_plot() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot"]], "draw_plot_to_file() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot_to_file"]], "find_logs() 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method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.set_params"]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplot method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot.set_run_id"]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_run_id"]], "set_watch_dir() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_watch_dir"]], "show_controls_default (xfel.cxi.gfx.status_plot.statusframe attribute)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.show_controls_default"]], "show_controls_default (xfel.cxi.gfx.trials_plot.trialsplotframe attribute)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.show_controls_default"]], "show_controls_default (xfel.cxi.gfx.wx_detectors.detectorplotframe attribute)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.show_controls_default"]], "show_plot() (xfel.cxi.gfx.status_plot.statusplot method)": 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"compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_2 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_2.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_3 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_3.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.compute_functional_and_gradients"]], "compute_functional_and_gradients() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.compute_functional_and_gradients"]], "consistency_controls() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.consistency_controls"]], "correction_vectors (class in xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.correction_vectors"]], "curvatures() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.curvatures"]], "curvatures() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.curvatures"]], "delrsq_functional() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.delrsq_functional"]], "detector_origin_analysis() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.detector_origin_analysis"]], "fit_translation (class in xfel.metrology.mark1)": [[347, "xfel.metrology.mark1.fit_translation"]], "fit_translation2 (class in xfel.metrology.mark3)": [[347, "xfel.metrology.mark3.fit_translation2"]], "fit_translation4 (class in xfel.metrology.mark10)": [[347, "xfel.metrology.mark10.fit_translation4"]], "get_frames_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_frames_from_mysql"]], "get_obs_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_obs_from_mysql"]], "get_phil() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.get_phil"]], "jacobian_frame_rotx (xfel.metrology.mark10.fit_translation4 attribute)": [[347, "xfel.metrology.mark10.fit_translation4.jacobian_frame_rotx"]], "nominal_tile_centers() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.nominal_tile_centers"]], "one_panel (class in xfel.metrology.quadrant)": [[347, "xfel.metrology.quadrant.one_panel"]], "one_sensor (class in xfel.metrology.quadrant)": [[347, "xfel.metrology.quadrant.one_sensor"]], "optimise_rectangle (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle"]], "optimise_rectangle_2 (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle_2"]], "optimise_rectangle_3 (class in xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.optimise_rectangle_3"]], "parameter_based_model() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.parameter_based_model"]], "parameter_based_model() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.parameter_based_model"]], "parameter_based_model_one_frame_detail() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.parameter_based_model_one_frame_detail"]], "parse_metrology() (in module xfel.metrology.flatfile)": [[347, "xfel.metrology.flatfile.parse_metrology"]], "post_min_recalc() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.post_min_recalc"]], "post_min_recalc() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.post_min_recalc"]], "print_table() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.print_table"]], "print_table() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.print_table"]], "print_table() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.print_table"]], "print_table() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.print_table"]], "print_table_2() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.print_table_2"]], "print_unit_translations() (xfel.metrology.mark10.fit_translation4 static method)": [[347, "xfel.metrology.mark10.fit_translation4.print_unit_translations"]], "radial_transverse_analysis() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.radial_transverse_analysis"]], "read_data() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.read_data"]], "run() (in module xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.run"]], "run() (in module xfel.metrology.mark1)": [[347, "xfel.metrology.mark1.run"]], "run() (in module xfel.metrology.mark3)": [[347, "xfel.metrology.mark3.run"]], "run_cycle_a() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.run_cycle_a"]], "run_cycle_b() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.run_cycle_b"]], "same_sensor_table() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.same_sensor_table"]], "same_sensor_table() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.same_sensor_table"]], "standalone_check() 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"xfel.mono_simulation.mono_treatment.refinement.contour_plot_DEPRECATED_DOES_NOT_APPLY_SUBPIXEL_METROLOGY"]], "grid (xfel.mono_simulation.mono_treatment.refinement attribute)": [[349, "xfel.mono_simulation.mono_treatment.refinement.grid"]], "grid (xfel.mono_simulation.mono_treatment.refinement2 attribute)": [[349, "xfel.mono_simulation.mono_treatment.refinement2.grid"]], "per_frame_helper_factory() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.per_frame_helper_factory"]], "post_outlier_rejection() (in module xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.post_outlier_rejection"]], "pre_get_predictions() (in module xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.pre_get_predictions"]], "refine_all() (xfel.mono_simulation.mono_treatment.refinement2 method)": [[349, "xfel.mono_simulation.mono_treatment.refinement2.refine_all"]], "refine_rotx_roty2() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.refine_rotx_roty2"]], "refinement (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement"]], "refinement2 (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement2"]], "refinement_base (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement_base"]], "show_plot() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.show_plot"]], "xfel.mono_simulation": [[349, "module-xfel.mono_simulation"]], "xfel.mono_simulation.mono_treatment": [[349, "module-xfel.mono_simulation.mono_treatment"]]}}) \ No newline at end of file