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Issue #59/refactor sdtether #73

Merged
merged 26 commits into from
Feb 1, 2024
Merged

Issue #59/refactor sdtether #73

merged 26 commits into from
Feb 1, 2024

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lpardey
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@lpardey lpardey commented Feb 1, 2024 •
edited by ggutierrez-sunbright
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This PR:

  • Add original sdtether script migrated to Python3.
  • Refactors sdtether into multiple modules for typing and decoupling internal components.
  • Adds a common module (used by both sdrmsd and sdtether).
  • Refactors sdrmsd.
  • Adds test integration for both original and improved version of sdtether, and initial test for common module functionality.

closes #71, closes #59

lpardey and others added 25 commits January 25, 2024 21:42
@lpardey
extract superpose3d and type modules to a common package
79fb739
@lpardey
add sdtether to project scritps
a0b5adc
@lpardey
add parser module
a473e73
@lpardey
add sdtether (wip)
5f0477e
@lpardey
add main file (wik)
154a4ea
@lpardey
migrate update_coordinates method to common package
1f6fdd4
@lpardey
refactor sdtether (wip)
3ba4ceb
@lpardey
add fixture data for testing sdtether
364f6d8
@ggutierrez-sunbright @lpardey
Update sdtether_original.py (CBDD#69)
c22199f
@ggutierrez-sunbright @lpardey
Hotfix sdtether indentation error (CBDD#70)
10b0764 
* Update sdtether_original.py
@lpardey
fix sdtether original argument parsing
60de90c
@lpardey
add basic test for sdtether
2971e1f
@lpardey
refactor rmsd method
0e4507a 
update typing
squared_distance method is not necessary anymore
@lpardey
fix variable names
57aced7
@lpardey
add matchids type
097f13e
@lpardey
refactor superpose3d:
14925a8 
modified the class interface and fix several bugs
class works with rmsd and sdtether as well
@lpardey
add sdtether main function
e42a272
@lpardey
refactor:
3154de6 
* remove _get_ref_matches_align_data, match_to_mask and get_matches functions.
*add show_matches_info function
* add ref_mol, ref_matches and ref_align_data as instance attributes
* update run, process_molecule and write_aligned_molecule functions
@lpardey
remove unnecessary modules
77c74c0
@lpardey
add test_get_centroid (from superposer3d)
8f91ef7
@lpardey
refactor
5dab432
@lpardey
update sdtether script location
b014db5 
add "build/*" to exclude in mypy
@lpardey
refactor
6ada371
@lpardey
remove temporary git ignore
de92039
@lpardey
Merge branch 'main' into Issue-CBDD#59/refactor-sdtether
5d0d59b
ggutierrez-sunbright
ggutierrez-sunbright reviewed Feb 1, 2024
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rdock-utils/rdock_utils/common/types.py Outdated
@@ -14,10 +10,10 @@
Matrix3x3 = numpy.ndarray[Any, numpy.dtype[numpy.float64]]
SingularValueDecomposition = tuple[Matrix3x3, Vector3D, Matrix3x3]
Superpose3DResult = tuple[CoordsArray, float, Matrix3x3]
MatchIds = tuple[tuple[int, int], ...]
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This name may be a bit misleading, as it is not related to the match ids from sdtether (?)

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MappingIds perhaps?

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AtomsMapping sounds fitting

ggutierrez-sunbright
ggutierrez-sunbright reviewed Feb 1, 2024
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rdock-utils/tests/test_all_ok.py Outdated
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test in peace, placeholder test

@lpardey
fix mypy
6262eee 
add show_mol_mathches_info feature
add skipped molecule logger info on process_molecule method
@ggutierrez-sunbright ggutierrez-sunbright merged commit 08a3b41 into CBDD:main Feb 1, 2024
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@ggutierrez-sunbright ggutierrez-sunbright self-assigned this Feb 1, 2024
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@ggutierrez-sunbright ggutierrez-sunbright ggutierrez-sunbright approved these changes

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enhancement New feature or request rdock-utils
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migrate sdtether migrate python scripts
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@lpardey @ggutierrez-sunbright