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Jonathan Bisson 8a2d034f8f Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332) 
* Add a new parameter to mol_adjust_query_properties for generic query parameters (#46)

Adds a new parameter to mol_adjust_query_properties:"setGenericQueryFromProperties"
that defaults to false (so no change of behavior until used).

This PR also removes the previous way of doing it that involved reprocessing the query molecule for every comparison.

On datasets of 200k molecules the speed-up is between 2 (large complex substructure searches with repeating units) to 5 times (tiny substructures search).

Add support for generic query in PG cartridge

* Add generic groups to the lib

* Move the querying with generic groups out of MolOps to not bloat the library.

* Fix Python calls

* Update doc

* Proof that last 3 commits are mine.

* Fix missing headers

* Fix typo

* Fix call

* Fix calls

* suggested changes

* Update Code/GraphMol/GenericGroups/GenericGroups.h

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Add adjustquery test with default parameters.

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2023-08-03 15:41:43 +02:00
..
Abbreviations
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
ChemTransforms
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
CIPLabeler
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Depictor
Fixed tests that weren't being ran in testDepictor.py (#6486)
2023-06-23 13:52:12 +02:00
Deprotect
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Descriptors
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
DetermineBonds
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
DistGeomHelpers
expose two missing tags to python (#6372)
2023-05-24 15:39:47 +02:00
FileParsers
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
FilterCatalog
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
Fingerprints
Fix a few broken docstrings (#6480)
2023-06-23 13:47:51 +02:00
FMCS
replace a try..catch block with an if clause (#6488)
2023-06-24 07:46:38 +02:00
ForceFieldHelpers
Add inlines to ForceFieldHelpers header functions (#6356)
2023-05-13 06:45:56 +02:00
FragCatalog
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
GeneralizedSubstruct
Add support for generalized substructure searching (#6443)
2023-06-22 10:54:35 +02:00
GenericGroups
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolAlign
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolCatalog
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolChemicalFeatures
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
MolDraw2D
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MolEnumerator
Fixes #6432 (#6433)
2023-06-03 06:37:15 +02:00
MolHash
Fixes #6505 (#6506)
2023-07-14 06:58:19 +02:00
MolInterchange
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MolStandardize
Add an in place version of most of the MolStandardize functionality (#6491)
2023-07-21 08:44:41 +02:00
MolTransforms
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
Fixes #6479 (#6482)
2023-07-13 19:29:06 +02:00
ScaffoldNetwork
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
ShapeHelpers
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
SLNParse
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
SmilesParse
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
StructChecker
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
Subgraphs
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Substruct
Add atom and bond property parameters to substruct matching (#6453)
2023-06-15 05:08:48 +02:00
SubstructLibrary
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
TautomerQuery
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
test_data
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Wrap
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
AddHs.cpp
Fixes Issue 6437 (#6438)
2023-06-06 17:41:03 +02:00
AdjustQuery.cpp
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
Aromaticity.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Atom.cpp
Remove check for ring information from Atom::Match (#6063)
2023-02-08 04:30:05 +01:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
Improved handling of organometallics (#6139)
2023-03-18 04:36:38 +01:00
atomic_data.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
AtomIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Bond.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Bond.h
add #include <utility> (#5060)
2022-03-17 04:56:34 +01:00
BondIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
BondIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
Canon.h
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_canon.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
catch_chirality.cpp
fix issue in stereo bonds with only implicit H (#6527)
2023-07-27 19:00:21 +02:00
catch_graphmol.cpp
Fixes Issue 6437 (#6438)
2023-06-06 17:41:03 +02:00
catch_molbundle.cpp
Add support for generalized substructure searching (#6443)
2023-06-22 10:54:35 +02:00
catch_moliterators.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
catch_organometallics.cpp
Fix _MolFileBondEndPts after dativeBondsToHaptic. (#6254)
2023-03-31 04:50:38 +02:00
catch_pickles.cpp
Fixes #6312: reduces the size of molecule pickles which include atom and bond properties (#6321)
2023-05-26 04:46:23 +02:00
catch_queries.cpp
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
Chirality.h
Fixes #6239 (#6240)
2023-04-11 10:42:56 +02:00
CMakeLists.txt
Add support for generalized substructure searching (#6443)
2023-06-22 10:54:35 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
ConjugHybrid.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
cptest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Do not include dative bonds in ring finding by default (#6231)
2023-03-30 18:09:24 +02:00
FindStereo.cpp
fix issue in stereo bonds with only implicit H (#6527)
2023-07-27 19:00:21 +02:00
GraphMol.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Fixes #5505: problems when kekulizing molecules with query bonds (#5550)
2022-09-13 14:49:45 +02:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolBundle.h
Add support for generalized substructure searching (#6443)
2023-06-22 10:54:35 +02:00
MolOps.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MolOps.h
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
molopstest.cpp
BondDir not cleared from bonds that aren't stereoactive (#6162)
2023-03-07 15:15:11 +01:00
MolPickler.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MolPickler.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
new_canon.cpp
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
new_canon.h
Add the option to wedge two bonds at chiral centers (#6108)
2023-03-11 05:25:03 +01:00
NontetrahedralStereo.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Enable optional visualization of complex query atoms in a more compact form (#6056)
2023-02-16 12:34:05 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
QueryOps.cpp
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
QueryOps.h
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
querytest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RDKitBase.h
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
RDKitQueries.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
regress.txt
Unset executable flag
2019-10-10 20:18:43 +09:00
Renumber.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
resMolSupplierTest.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Resonance.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
RingInfo.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
ROMol.h
Fix RWMol::addAtom docstring (#6477)
2023-06-23 13:49:01 +02:00
RWMol.cpp
Improved handling of organometallics (#6139)
2023-03-18 04:36:38 +01:00
RWMol.h
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
SanitException.h
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
StereoGroup.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
SubstanceGroup.cpp
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
SubstanceGroup.h
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
test1.cpp
Fixes a couple of query-related bugs (#3398)
2020-09-17 08:16:43 +02:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Allow removal of non-special H atoms in SGroups (#5399)
2022-07-07 11:05:18 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Fixes #6423 (#6424)
2023-06-06 17:39:56 +02:00