rdkit

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

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

ChemTransforms

Leak fixes for 2026.03.1 (#9198 )

2026-03-25 05:56:26 +01:00

CIPLabeler

Fixes #9153 (#9154 )

2026-03-12 18:29:59 +01:00

Depictor

[bot] Update molecular templates header (#9234 )

2026-04-10 15:02:46 +02:00

Deprotect

Fixes #7989 Incorrect benzyl deprotection reaction (#7990 )

2024-11-07 18:34:59 +01:00

Descriptors

Fix SMARTS for the strict definition of rotatable bonds (#9096 )

2026-02-09 17:50:12 +01:00

DetermineBonds

Add valence 1 as possible option for sulfur (#9120 )

2026-02-19 13:52:05 +01:00

DistGeomHelpers

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

EnumerateStereoisomers

Store CIP-ranked anchors after CIP labeling. (#9056 )

2026-01-29 18:23:44 +01:00

FileParsers

Leak fixes for 2026.03.1 (#9198 )

2026-03-25 05:56:26 +01:00

FilterCatalog

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

Fingerprints

Leak fixes for 2026.03.1 (#9198 )

2026-03-25 05:56:26 +01:00

FMCS

In verbose output, check that the query molecule exists before using it. (#9040 )

2026-01-08 06:06:52 +01:00

ForceFieldHelpers

Fixes #9143 (#9195 )

2026-03-24 10:03:02 +01:00

FragCatalog

propagate string_view (#8858 )

2025-10-14 19:15:37 +02:00

GaussianShape

Misplaced parentheses in shape code (#9222 )

2026-04-07 16:59:56 +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

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

MMPA

Fix for issue #8965 (#8968 )

2026-02-26 08:58:36 +01:00

MolAlign

MolAlign: brace-init BestAlignmentParams in wrapper (#9042 )

2026-01-08 07:31:22 +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

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

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

Hide data representation inside RDKit::Dict (#9113 )

2026-03-20 06:58:36 +01:00

MolProcessing

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

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

MolStandardize

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +02:00

MolTransforms

Gaussian shape overlays (#9095 )

2026-03-26 21:53:54 +01:00

PartialCharges

Refactor iostreams includes (#8846 )

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

RascalMCES

Deterministic kekulize, independent of atom and bond order (#9125 )

2026-03-19 08:43:13 +01:00

ReducedGraphs

Fix off-by-one error in Reduced Graph fingerprint bitstring. (#8385 )

2025-04-07 13:20:19 +02:00

RGroupDecomposition

Move some more tests over to catch2 (#9058 )

2026-01-24 07:03:04 +01:00

ScaffoldNetwork

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

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

ShapeHelpers

Move some more tests over to catch2 (#9058 )

2026-01-24 07:03:04 +01:00

SLNParse

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

SmilesParse

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

StructChecker

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

Subgraphs

Move some more tests over to catch2 (#9058 )

2026-01-24 07:03:04 +01:00

Substruct

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +02:00

SubstructLibrary

Move some more tests over to catch2 (#9058 )

2026-01-24 07:03:04 +01:00

SynthonSpaceSearch

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

TautomerQuery

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +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

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

AddHs.cpp

fix: kekulization failure for V3000 molblocks with aromatic bonds and explicit H (#9141 )

2026-03-14 06:50:01 +01:00

AdjustQuery.cpp

apply query adjustments when makeAtomsGeneric is enabled (#8315 )

2025-03-04 13:50:24 +01:00

Aromaticity.cpp

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

Atom.cpp

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +02:00

Atom.h

Store CIP-ranked anchors after CIP labeling. (#9056 )

2026-01-29 18:23:44 +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

atropisomer bond atoms are checked explicitly for SP2 hybridization (#8974 )

2025-12-29 18:04:40 +01:00

Atropisomers.h

Fixes #7983 (#8342 )

2025-03-20 07:40:33 +01:00

Bond.cpp

The precondition in Bond::getOtherAtomIdx() is redundant (#9092 )

2026-02-06 16:09:23 +01:00

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

Follow up to PR #8968 (#9168 )

2026-03-20 04:28:17 +01:00

Canon.h

More refactoring in Canon.cpp (#9155 )

2026-03-12 05:54:20 +01:00

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

Follow up to PR #8968 (#9168 )

2026-03-20 04:28:17 +01:00

catch_chirality.cpp

Fix for issue #8965 (#8968 )

2026-02-26 08:58:36 +01:00

catch_graphmol.cpp

Leak fixes for 2026.03.1 (#9198 )

2026-03-25 05:56:26 +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

make ringdecomposerlib a mandatory dependency (#9209 )

2026-03-27 18:17:27 +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

Add 'k' extension to SMARTS to support ringsize queries (#9172 )

2026-03-17 15:02:59 +01:00

catch_sgroups.cpp

Run clang-format across everything (#7849 )

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

Chirality.cpp

cleanup of stereogroups and wedges for non-chiral sites (#9051 )

2026-01-30 04:20:32 +01:00

Chirality.h

cleanup of stereogroups and wedges for non-chiral sites (#9051 )

2026-01-30 04:20:32 +01:00

CMakeLists.txt

make ringdecomposerlib a mandatory dependency (#9209 )

2026-03-27 18:17:27 +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

Normalize rings (#9208 )

2026-04-01 05:37:02 +02:00

FindStereo.cpp

Store CIP-ranked anchors after CIP labeling. (#9056 )

2026-01-29 18:23:44 +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

Deterministic kekulize, independent of atom and bond order (#9125 )

2026-03-19 08:43:13 +01:00

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

Deterministic kekulize, independent of atom and bond order (#9125 )

2026-03-19 08:43:13 +01:00

MolOps.h

Deterministic kekulize, independent of atom and bond order (#9125 )

2026-03-19 08:43:13 +01:00

molopstest.cpp

make ringdecomposerlib a mandatory dependency (#9209 )

2026-03-27 18:17:27 +01:00

MolPickler.cpp

Hide data representation inside RDKit::Dict (#9113 )

2026-03-20 06:58:36 +01:00

MolPickler.h

Move some fields and methods from AtomPDBResidueInfo to base class (#8863 )

2026-02-04 12:13:33 +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

Refactor iostreams includes (#8846 )

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

MonomerInfo.h

Move some fields and methods from AtomPDBResidueInfo to base class (#8863 )

2026-02-04 12:13:33 +01:00

new_canon.cpp

Fix modern stereo performance issue for large structures (#9100 )

2026-02-26 16:40:40 +01:00

new_canon.h

Stop using raw pointers in the canonicalization interface (#8990 )

2025-12-12 14:00:23 +01:00

NontetrahedralStereo.cpp

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +01:00

PeriodicTable.cpp

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +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

Add 'k' extension to SMARTS to support ringsize queries (#9172 )

2026-03-17 15:02:59 +01:00

QueryOps.h

Add 'k' extension to SMARTS to support ringsize queries (#9172 )

2026-03-17 15:02:59 +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 ringdecomposerlib a mandatory dependency (#9209 )

2026-03-27 18:17:27 +01:00

RingInfo.h

make ringdecomposerlib a mandatory dependency (#9209 )

2026-03-27 18:17:27 +01:00

Rings.h

Fix typo (#2862 )

2019-12-31 06:43:27 +01:00

ROMol.cpp

Speed-up tautomer canonicalization, no API changes (#9134 )

2026-03-31 06:42:40 +02:00

ROMol.h

add clearPropertyCache() (#8533 )

2025-05-18 08:14:05 +02:00

RWMol.cpp

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +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

style: apply readability-braces-around-statements (#8136 )

2026-02-09 12:10:50 +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

Move some fields and methods from AtomPDBResidueInfo to base class (#8863 )

2026-02-04 12:13:33 +01:00

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

cleanup of stereogroups and wedges for non-chiral sites (#9051 )

2026-01-30 04:20:32 +01:00