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

..

test_data

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Testing/Temporary

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Atom.cpp

Fixes #8877 (#8886)

2025-10-22 07:59:35 -04:00

Bond.cpp

Python Bond Inversion (#8951)

2025-11-19 05:54:04 +01:00

Chirality.cpp

Initial support for non-tetrahedral stereochemistry (#5084)

2022-05-20 09:07:16 +02:00

ChiralityOps.cpp

expose cleanupStereoGroups to python (#8515)

2025-05-11 05:08:38 +02:00

CMakeLists.txt

Allow adding custom atom and bond matcher functions for substructure searching (#8994)

2025-12-12 20:03:31 +01:00

CompressedSDMolSupplier.cpp

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

Conformer.cpp

Minor refactor of the python wrappers (#8847)

2025-10-05 09:42:31 +02:00

ContextManagers.h

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

EditableMol.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

ForwardSDMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

MaeMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

MaeWriter.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

Mol.cpp

Allow adding custom atom and bond matcher functions for substructure searching (#8994)

2025-12-12 20:03:31 +01:00

MolBundle.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolOps.cpp

Add extract mol fragment api (#8811)

2025-12-09 15:06:29 +01:00

MolSupplier.h

Improve MaeMolSupplier API (#6053)

2023-02-08 04:31:51 +01:00

MonomerInfo.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

MultithreadedMolSupplier.h

[GSoC-2020] Generalized and Multithreaded File Reader (#3363)

2020-10-09 04:31:05 +02:00

MultithreadedSDMolSupplier.cpp

remove no-op macros and dead code (pt 4) (#8037)

2025-01-26 07:49:50 +01:00

MultithreadedSmilesMolSupplier.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

PDBWriter.cpp

... and more mem errors fixed (#7924)

2024-10-25 07:01:34 +02:00

props.hpp

Fixes #8890 (#8891)

2025-10-23 08:52:27 -04:00

Queries.cpp

Expose replaceAtomWithQueryAtom to Python (#7380)

2024-05-07 06:50:59 +02:00

rdchem.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

rdchem.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

rdmolfiles.cpp

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

rdmolfiles.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

rdmolops.cpp

Updated code for chirality perception (#3324)

2020-09-02 15:00:29 +02:00

rdmolops.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

rdqueries.cpp

Remove extra calls to python::register_exception_translator

2016-03-01 06:36:54 +01:00

rdTrajectory.cpp

- added miising Code/GraphMol/Wrap/rdTrajectory.cpp

2016-05-11 19:56:32 +01:00

ResonanceMolSupplier.cpp

Fix #7112 (#8483)

2025-04-30 16:22:45 +02:00

RingInfo.cpp

Minor refactor of the python wrappers (#8847)

2025-10-05 09:42:31 +02:00

rough_test.py

Python Bond Inversion (#8951)

2025-11-19 05:54:04 +01:00

SDMolSupplier.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

SDWriter.cpp

... and more mem errors fixed (#7924)

2024-10-25 07:01:34 +02:00

seqs.hpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SmilesMolSupplier.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

SmilesWriter.cpp

... and more mem errors fixed (#7924)

2024-10-25 07:01:34 +02:00

StereoGroup.cpp

Update createStereoGroup to accept bond list (#8587)

2025-06-16 06:04:34 +02:00

SubstanceGroup.cpp

Use std::string_view for property keys (#8844)

2025-10-09 16:14:48 +02:00

substructmethods.h

Allow adding custom atom and bond matcher functions for substructure searching (#8994)

2025-12-12 20:03:31 +01:00

Table.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

TDTMolSupplier.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

TDTWriter.cpp

... and more mem errors fixed (#7924)

2024-10-25 07:01:34 +02:00

test_cdxml.py

Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)

2025-08-29 04:39:22 +02:00

test_subset.py

Add extract mol fragment api (#8811)

2025-12-09 15:06:29 +01:00

testConformer.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testMultithreadedMolSupplier.py

Revert "Fixes #8644 (#8768)" (#8787)

2025-09-16 16:28:01 +02:00

testPropertyLists.py

support bond property lists in SDF (#8778)

2025-09-17 16:17:12 +02:00

testSCSR.py

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

testSGroups.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testSubstructureMatch.py

Allow adding custom atom and bond matcher functions for substructure searching (#8994)

2025-12-12 20:03:31 +01:00

testThreads.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testTrajectory.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

Trajectory.cpp

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00