Greg Landrum a9477d2694 Modernization of some substructure code (#8450) ...

* use std::span for substruct match callbacks

This removes a copy from every evaluation of potential matches

* some cleanup/modernization

* some modernization

* deprecate chiralAtomCompat

* small optimization

* remove naked pointers

* improve new_timings.py script

* changes suggested in review

* response to review

* response to review

2025-05-12 06:33:25 +02:00

..

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

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +02:00

Bond.cpp

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +02:00

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

cmake cleanup (#6814)

2023-11-10 15:32:54 +01:00

CompressedSDMolSupplier.cpp

Fix some more mem errors in 2024.09.1 (#7899)

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

Conformer.cpp

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +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

Modernization of some substructure code (#8450)

2025-05-12 06:33:25 +02:00

MolBundle.cpp

Run clang-format across everything (#7849)

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

MolOps.cpp

Clarify Docstring of molzip when called with a Single mol object (#8470)

2025-04-28 15:33:25 +02:00

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

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +02:00

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 a custom CXSMILES feature to indicate Zero Order Bonds (#8454)

2025-04-22 09:56:58 +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

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

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

rough_test.py

expose cleanupStereoGroups to python (#8515)

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

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

Fixes #6208 (#6419)

2023-06-03 04:59:16 +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

add StereoGroup.getBonds() to Python wrapper (#8451)

2025-04-17 16:22:22 +02:00

SubstanceGroup.cpp

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +02:00

substructmethods.h

- Changed all unsigned to unsigned int for clarity (#6646)

2023-08-25 06:09:19 +02:00

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

Reformat Python code for 2023.03 release (#6294)

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

testConformer.py

Reformat Python code for 2023.03 release (#6294)

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

testMultithreadedMolSupplier.py

Reformat Python code for 2023.03 release (#6294)

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

testPropertyLists.py

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

testSGroups.py

Reformat Python code for 2023.03 release (#6294)

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

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