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rdkit/Code/GraphMol
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Greg Landrum ef90a4bedf Allow adding custom atom and bond matcher functions for substructure searching (#8994) 
* extra SSS match functions for atoms/bonds
initial implementation and testing

* add baseline to test

* add a functor for matching atom coords

* support the extra checks in python

* refactor the way the python callbacks are handled

* test tolerances

* expose the AtomCoordsMatcher to python

* allow the extra checks to override the default matching

---------

Co-authored-by: = <=>
2025-12-12 20:03:31 +01:00
..
Abbreviations
Allow abbreviations without XBonds (#8933)
2025-11-06 16:33:25 +01:00
Basement/FeatTrees
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
ChemReactions
Do not reset the ringInfo information when adding bonds to RWMol (#8934)
2025-11-07 14:41:01 +01:00
ChemTransforms
propagate string_view (#8858)
2025-10-14 19:15:37 +02:00
CIPLabeler
Make assignCIPLabels Ctrl+c interruptable (#8589)
2025-06-27 08:27:44 +02:00
Depictor
Fixes #8776 (#8875)
2025-10-17 05:52:27 +02:00
Deprotect
Fixes #7989 Incorrect benzyl deprotection reaction (#7990)
2024-11-07 18:34:59 +01:00
Descriptors
add conditional logic for GETAWAY test (#8923)
2025-11-04 16:05:56 +01:00
DetermineBonds
Improve DetermineBonds and DetermineBondOrders performance (#8888)
2025-12-08 06:17:41 +01:00
DistGeomHelpers
strip whitespace from embedParametersToJSON() (#8989)
2025-12-04 06:57:08 +01:00
EnumerateStereoisomers
Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available (#8924)
2025-11-11 17:05:30 +01:00
FileParsers
Valence error when parsing SCSR (#8948)
2025-11-18 17:09:04 +01:00
FilterCatalog
Use std::string_view for property keys (#8844)
2025-10-09 16:14:48 +02:00
Fingerprints
Allow using generators for similarity maps (#8912)
2025-11-06 19:12:29 +01:00
FMCS
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
ForceFieldHelpers
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
FragCatalog
propagate string_view (#8858)
2025-10-14 19:15:37 +02:00
GeneralizedSubstruct
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
GenericGroups
Modernization of some substructure code (#8450)
2025-05-12 06:33:25 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MMPA
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolAlign
Allow Hs to be ignored in the RMSD alignment functions (#8976)
2025-12-04 18:37:59 +01:00
MolCatalog
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolChemicalFeatures
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolDraw2D
Better solid triangles (#8943)
2025-11-18 09:47:24 +01:00
MolEnumerator
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
MolHash
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolInteractionFields
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolInterchange
Switch from using RapidJSON to Boost::JSON for MolInterchange (#8859)
2025-11-11 11:54:44 +01:00
MolProcessing
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
MolStandardize
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
MolTransforms
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
PartialCharges
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
RascalMCES
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
ReducedGraphs
Fix off-by-one error in Reduced Graph fingerprint bitstring. (#8385)
2025-04-07 13:20:19 +02:00
RGroupDecomposition
Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition (#8813)
2025-10-29 21:50:19 +01:00
ScaffoldNetwork
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
ShapeHelpers
Minor refactor of the python wrappers (#8847)
2025-10-05 09:42:31 +02:00
SLNParse
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
SmilesParse
Fixes for nontetrahedral stereo parsing from SMILES/SMARTS (#8932)
2025-11-09 05:31:12 +01:00
StructChecker
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
Subgraphs
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +01:00
Substruct
Allow adding custom atom and bond matcher functions for substructure searching (#8994)
2025-12-12 20:03:31 +01:00
SubstructLibrary
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
SynthonSpaceSearch
Make incremental search callback take ownership of mols (#8940)
2025-11-11 17:10:29 +01:00
TautomerQuery
Modernization of some substructure code (#8450)
2025-05-12 06:33:25 +02:00
test_data
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-10 13:02:42 -05:00
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
Allow adding custom atom and bond matcher functions for substructure searching (#8994)
2025-12-12 20:03:31 +01:00
AddHs.cpp
Do not reset the ringInfo information when adding bonds to RWMol (#8934)
2025-11-07 14:41:01 +01:00
AdjustQuery.cpp
apply query adjustments when makeAtomsGeneric is enabled (#8315)
2025-03-04 13:50:24 +01:00
Aromaticity.cpp
fixes #5078 (#8795)
2025-09-22 11:06:42 +02:00
Atom.cpp
Merge simple AND queries onto atoms. (#8830)
2025-10-09 04:38:42 +02:00
Atom.h
Merge simple AND queries onto atoms. (#8830)
2025-10-09 04:38:42 +02:00
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
Fix for Issue 8602 (#8668)
2025-08-20 10:10:47 +02:00
Atropisomers.h
Fixes #7983 (#8342)
2025-03-20 07:40:33 +01:00
Bond.cpp
Merge simple AND queries onto atoms. (#8830)
2025-10-09 04:38:42 +02:00
Bond.h
Merge simple AND queries onto atoms. (#8830)
2025-10-09 04:38:42 +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
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
Canon.cpp
Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization (#8972)
2025-12-12 14:07:26 +01:00
Canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
catch_adjustquery.cpp
Partial fix to a problem with implicit Hs being written to SMARTS (#8893)
2025-10-24 07:50:06 +02:00
catch_canon.cpp
Small fix in ring stereo/canonicalization (#8962)
2025-12-12 13:56:01 +01:00
catch_chirality.cpp
Small fix in ring stereo/canonicalization (#8962)
2025-12-12 13:56:01 +01:00
catch_graphmol.cpp
Implements #8873 (#8904)
2025-11-04 16:10:56 +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
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +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
Modern stereo: fix stereo inversion in rings (#8957)
2025-11-21 07:50:16 +01:00
Chirality.h
style: apply modernize-use-override (#8137)
2025-04-25 12:24:58 +02:00
CMakeLists.txt
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +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
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
FindStereo.cpp
Small fix in ring stereo/canonicalization (#8962)
2025-12-12 13:56:01 +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
Stop using raw pointers in the canonicalization interface (#8990)
2025-12-12 14:00:23 +01:00
itertest.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
Kekulize.cpp
Synthon space bad chiral count (#8550)
2025-06-03 13:09:09 +02:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolBundle.h
Fix minimal build, allow building without boost::serialization (#6932)
2023-11-23 05:57:05 +01:00
MolOps.cpp
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +01:00
MolOps.h
Fixes #8726 (#8874)
2025-10-17 16:51:22 +02:00
molopstest.cpp
Convert graphmolMolOpsTest to catch2 (#8978)
2025-12-03 06:28:56 +01:00
MolPickler.cpp
Change extern types to static consts (#8765)
2025-11-07 05:15:22 +01:00
MolPickler.h
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MolProps.cpp
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
MonomerInfo.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
MonomerInfo.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
new_canon.cpp
Stop using raw pointers in the canonicalization interface (#8990)
2025-12-12 14:00:23 +01:00
new_canon.h
Stop using raw pointers in the canonicalization interface (#8990)
2025-12-12 14:00:23 +01:00
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
Github8353 (#8354)
2025-03-17 19:54:15 +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
Fix a couple issues related to atom list handling in V3000 mol blocks (#8824)
2025-10-09 05:26:01 +02:00
QueryOps.h
Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)
2025-03-29 07:26:03 +01:00
querytest.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +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
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
Resonance.cpp
Fix #8638 (#8639)
2025-07-25 14:33:32 +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
Do not add a __computedProps property to molecules when initializing them (#8931)
2025-11-18 19:09:36 -05:00
ROMol.h
add clearPropertyCache() (#8533)
2025-05-18 08:14:05 +02:00
RWMol.cpp
Do not reset the ringInfo information when adding bonds to RWMol (#8934)
2025-11-07 14:41:01 +01:00
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
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
StereoGroup.cpp
fix a problem with stereogroups involving bonds and getMolFrags() (#8558)
2025-05-27 16:43:20 +02:00
StereoGroup.h
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
Subset.cpp
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +01:00
Subset.h
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +01:00
SubstanceGroup.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
SubstanceGroup.h
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
test1.cpp
Do not add a __computedProps property to molecules when initializing them (#8931)
2025-11-18 19:09:36 -05:00
test_fixtures.h
Convert graphmolMolOpsTest to catch2 (#8978)
2025-12-03 06:28:56 +01:00
test-valgrind.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
testChirality.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
testMolBundle.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
testPickler.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
testPicklerGlobalSettings.cpp
Refactor iostreams includes (#8846)
2025-10-08 16:08:01 +02:00
testSGroup.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-10 13:02:42 -05:00