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b64aea50826312fd6addab9b5c0fcb11f64bbe3a
rdkit/Code/GraphMol
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Greg Landrum b64aea5082 apply query adjustments when makeAtomsGeneric is enabled (#8315) 
* apply query adjustments when makeAtomsGeneric is enabled

* changes in response to review

* I got Python in my C++
2025-03-04 13:50:24 +01:00
..
Abbreviations
Improve doc string for ParseAbbreviations in python wrapper. (#8049)
2024-11-28 13:54:04 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Implements #8222 adds react_idx (index of reactant) to product atoms (#8231)
2025-02-06 17:07:55 +01:00
ChemTransforms
Tweak mol fragmenter (#8277)
2025-02-20 05:56:01 +01:00
CIPLabeler
Fix some minor issues reported by ubsan and the compiler (#8015)
2024-11-20 09:09:22 +01:00
Depictor
remove no-op macros and dead code (pt 2) (#8035)
2025-01-11 14:10:00 +01:00
Deprotect
Fixes #7989 Incorrect benzyl deprotection reaction (#7990)
2024-11-07 18:34:59 +01:00
Descriptors
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
DetermineBonds
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
DistGeomHelpers
Expose basinThresh to the python layer (#8283)
2025-02-20 10:12:17 +01:00
FileParsers
Fix the way carbon is handed in cleanupOrganometallics() (#8301)
2025-03-03 17:30:41 +01:00
FilterCatalog
fix: apply modernize-use-nullptr (#8134)
2025-01-09 07:56:10 +01:00
Fingerprints
mem fixes (#8276)
2025-02-20 05:59:30 +01:00
FMCS
remove no-op macros and dead code (pt 1) (#8012)
2024-11-19 04:31:56 +01:00
ForceFieldHelpers
Fixes Github #7901 (#8264)
2025-02-13 12:46:56 +01:00
FragCatalog
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
GeneralizedSubstruct
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
GenericGroups
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
MMPA
Fix shifting of a potentially negative number (#8014)
2024-11-24 06:50:16 +01:00
MolAlign
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolCatalog
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolChemicalFeatures
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
MolDraw2D
Option for standard atom colours with highlighting (#8294)
2025-02-24 17:46:24 +01:00
MolEnumerator
Implements #8222 adds react_idx (index of reactant) to product atoms (#8231)
2025-02-06 17:07:55 +01:00
MolHash
improve handling of esters, amides, etc. in the v2 tautomer hash (#8173)
2025-01-24 16:11:38 +01:00
MolInteractionFields
fix (#8144)
2025-01-09 07:52:46 +01:00
MolInterchange
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
MolProcessing
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolStandardize
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
MolTransforms
Fix inversion of stereo with canonicalizeConformer (#7878)
2024-10-10 09:57:39 -04:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RascalMCES
Initial Rascal results sort the wrong way round on number of atoms and bonds. (#8258)
2025-02-15 15:34:16 +01:00
ReducedGraphs
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
RGroupDecomposition
Fix memory leaks (#8298)
2025-02-25 16:58:19 +01:00
ScaffoldNetwork
Allow inclusion of molecule names in ScaffoldNetwork (#7956)
2024-10-30 06:11:30 +01:00
ShapeHelpers
Fix inversion of stereo with canonicalizeConformer (#7878)
2024-10-10 09:57:39 -04:00
SLNParse
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
SmilesParse
trimethylcyclohexane chirality error (#8272)
2025-02-24 17:41:54 +01:00
StructChecker
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
SubstructLibrary
remove no-op macros and dead code (pt 1) (#8012)
2024-11-19 04:31:56 +01:00
SynthonSpaceSearch
Optimisation of fingerprint Synthon Search (#8223)
2025-01-30 04:59:19 +01:00
TautomerQuery
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
test_data
Fixes #7501 dative bonds in cdxml (#7757)
2024-08-28 05:59:43 +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
apply query adjustments when makeAtomsGeneric is enabled (#8315)
2025-03-04 13:50:24 +01:00
AddHs.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
AdjustQuery.cpp
apply query adjustments when makeAtomsGeneric is enabled (#8315)
2025-03-04 13:50:24 +01:00
Aromaticity.cpp
Fixes #8256 (#8257)
2025-02-12 15:34:28 +01:00
Atom.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
Atom.h
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
atomic_data.cpp
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
atomic_data.h
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
AtomIterators.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Atropisomers.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
Atropisomers.h
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +01:00
Bond.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
Bond.h
A collection of small improvements from Roger S (#7566)
2024-06-26 08:29:57 +02:00
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
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
Canon.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
Canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
catch_adjustquery.cpp
apply query adjustments when makeAtomsGeneric is enabled (#8315)
2025-03-04 13:50:24 +01:00
catch_canon.cpp
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
catch_chirality.cpp
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-10-21 04:55:08 +02:00
catch_graphmol.cpp
Fixes #5134 (#5136)
2025-01-30 16:10:57 +01:00
catch_molbundle.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
catch_moliterators.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_molops.cpp
Fix the way carbon is handed in cleanupOrganometallics() (#8301)
2025-03-03 17:30:41 +01:00
catch_organometallics.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_periodictable.cpp
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
catch_pickles.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Chirality.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
Chirality.h
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-10-21 04:55:08 +02:00
CMakeLists.txt
Add Molecular Interaction Fields (#7993)
2024-12-14 17:08:43 +01:00
Conformer.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
Conformer.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ConjugHybrid.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
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
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
FindStereo.cpp
trimethylcyclohexane chirality error (#8272)
2025-02-24 17:41:54 +01:00
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 across everything (#7849)
2024-09-26 13:39:02 +02:00
itertest.cpp
remove no-op macros and dead code (pt 2) (#8035)
2025-01-11 14:10:00 +01:00
Kekulize.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
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
Fix minimal build, allow building without boost::serialization (#6932)
2023-11-23 05:57:05 +01:00
MolOps.cpp
Fix the way carbon is handed in cleanupOrganometallics() (#8301)
2025-03-03 17:30:41 +01:00
MolOps.h
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
molopstest.cpp
Fixes #5134 (#5136)
2025-01-30 16:10:57 +01:00
MolPickler.cpp
GitHub 7865 haspropwithvaluequery leaks (#7872)
2024-10-30 06:12:40 +01:00
MolPickler.h
Expose propertyFlags to CFFI and MinimalLib (#7960)
2024-11-07 06:08:27 +01:00
MolProps.cpp
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
new_canon.cpp
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
new_canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
NontetrahedralStereo.cpp
fix: apply modernize-use-nullptr (#8134)
2025-01-09 07:56:10 +01:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryOps.cpp
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
QueryOps.h
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
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
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +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 across everything (#7849)
2024-09-26 13:39:02 +02:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
make sure outdated ring fusion information is recomputed before attempting to use it (#7274)
2024-03-20 09:37:10 +01:00
RingInfo.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ROMol.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
RWMol.cpp
fix #7782 (#7783)
2024-10-03 06:52:34 +02:00
RWMol.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +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
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
StereoGroup.h
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
SubstanceGroup.cpp
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
SubstanceGroup.h
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
test1.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
test_fixtures.h
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Fixes #7064 (#7141)
2024-02-22 06:46:39 +01:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00