htdocs update

cctbx/cctbx.command_line.precession_view.html

@@ -121,7 +121,7 @@ <h3>Navigation</h3>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="cctbx.command_line.precession_view.run">
-<span class="sig-prename descclassname"><span class="pre">cctbx.command_line.precession_view.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.command_line.precession_view.run" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">cctbx.command_line.precession_view.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.command_line.precession_view.run" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </section>

mmtbx/mmtbx.building.html

@@ -79,7 +79,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.building.extend_sidechains.correct_sequence">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">correct_sequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequences</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">truncate_to_cbeta=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.correct_sequence" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">correct_sequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequences</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">truncate_to_cbeta=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.correct_sequence" title="Link to this definition">¶</a></dt>
 <dd><p>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 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.building.extend_sidechains.extend_and_refine">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">extend_and_refine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xray_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cif_objects=()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_model=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_map_coeffs=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_files=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset_segid=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.extend_and_refine" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">extend_and_refine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xray_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cif_objects=()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_model=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_map_coeffs=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_files=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset_segid=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.extend_and_refine" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>Run the combined sidechain extension and real-space fitting, and optionally
 write final model and map coefficients.</p>
@@ -149,7 +149,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.building.extend_sidechains.refit_residues">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">refit_residues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cif_objects</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_rotamers=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anneal=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_modified_residues=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.refit_residues" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.building.extend_sidechains.</span></span><span class="sig-name descname"><span class="pre">refit_residues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cif_objects</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_rotamers=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anneal=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_modified_residues=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.extend_sidechains.refit_residues" title="Link to this definition">¶</a></dt>
 <dd><p>Use real-space refinement tools to fit newly extended residues.</p>
 </dd></dl>
 
@@ -184,7 +184,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.building.make_library.extract_and_superpose">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.building.make_library.</span></span><span class="sig-name descname"><span class="pre">extract_and_superpose</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">search_directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nproc=&lt;libtbx.AutoType</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.make_library.extract_and_superpose" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.building.make_library.</span></span><span class="sig-name descname"><span class="pre">extract_and_superpose</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">search_directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nproc=&lt;libtbx.AutoType</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.make_library.extract_and_superpose" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
@@ -530,7 +530,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.building.show_chain_resseq_ranges">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.building.</span></span><span class="sig-name descname"><span class="pre">show_chain_resseq_ranges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">residues</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix=''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.show_chain_resseq_ranges" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.building.</span></span><span class="sig-name descname"><span class="pre">show_chain_resseq_ranges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">residues</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix=''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.building.show_chain_resseq_ranges" title="Link to this definition">¶</a></dt>
 <dd><p>Given a list of residues (either residue_group or atom_group objects),
 print a summary of the chains and residue ranges present.</p>
 </dd></dl>

mmtbx/mmtbx.scaling.html

@@ -1794,7 +1794,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <p>Main program driver for Xtriage.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.scaling.xtriage.change_symmetry">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.scaling.xtriage.</span></span><span class="sig-name descname"><span class="pre">change_symmetry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">space_group_symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.scaling.xtriage.change_symmetry" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.scaling.xtriage.</span></span><span class="sig-name descname"><span class="pre">change_symmetry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">space_group_symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.scaling.xtriage.change_symmetry" title="Link to this definition">¶</a></dt>
 <dd><p>Encapsulates all operations required to convert the original data to a
 different symmetry as suggested by Xtriage.</p>
 </dd></dl>

mmtbx/mmtbx.solvent.html

@@ -117,7 +117,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <span id="mmtbx-solvent-ordered-solvent-module"></span><h2>mmtbx.solvent.ordered_solvent module<a class="headerlink" href="#module-mmtbx.solvent.ordered_solvent" title="Link to this heading">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.solvent.ordered_solvent.manager">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.solvent.ordered_solvent.</span></span><span class="sig-name descname"><span class="pre">manager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_neutron_scat_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params=&lt;libtbx.phil.scope_extract</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_peaks_params=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.solvent.ordered_solvent.manager" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.solvent.ordered_solvent.</span></span><span class="sig-name descname"><span class="pre">manager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_neutron_scat_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params=&lt;libtbx.phil.scope_extract</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_peaks_params=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.solvent.ordered_solvent.manager" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.solvent.ordered_solvent.manager.refine_adp">