Yakov Pechersky 0986d22c58 Deterministic kekulize, independent of atom and bond order (#9125) ...

* Make kekulization deterministic

* Add tautomer order-independence regression (python)

* Adjust tautomer tests for deterministic kekulization

* Update graphmol wedged-bond kekulization checks

* SmilesParse: update aromatic bond index expectations

* SmilesParse: refresh cxsmilesTest expected files

* Depictor: update testDepictor expected MolBlocks

* Depictor: update depictorCatch expectations

* Depictor Wrap: update expected MolBlock for pyDepictor

* MarvinParse: update testMrvToMol expected outputs

* FileParsers: refresh testAtropisomers expected outputs

* FileParsers: update tests for deterministic kekulization

* MolDraw2D: refresh brittle bond assertions

* RascalMCES: update expected cluster size

* MinimalLib: make cffi wedging check order-independent

* documentation fix

* MinimalLib: update Kekulé bond table in aligned-coords test

* Hoist duplicated lambdas to TEST_CASE scope

* Remove unused originalWedges variable

* Remove redundant bounds check; clarify wedge-end preference

* Pre-sort allAtms by wedge-end + rank

* Use mol.atomNeighbors() for neighbor iteration

* Check inAllAtms before linear-scanning done

* Drop redundant optsV/wedgedOptsV sorts

* Remove unused Canon.h include

* Add canonical parameter to Kekulize; skip ranking during sanitization

* Test canonical re-kekulization preserves stereo across atom orderings

* MinimalLib: update Kekulé bond orders in invertedWedges

* Change Kekulize canonical default to false, expose in Python wrappers

* keep rank order, push_back

* Revert "RascalMCES: update expected cluster size"

This reverts commit a81bb39495.

* docstring change

* expose new flag to python wrapper

* document changes in ReleaseNotes.md

* revert minimallib test changes again

* canonical = true defaults

* Revert "revert minimallib test changes again"

This reverts commit 039e1d84da.

* Reapply "RascalMCES: update expected cluster size"

This reverts commit 7b83a7a3e8.

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>

2026-03-19 08:43:13 +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

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

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

ChemTransforms

Allow molzip to position fragments when joining them (#9021)

2026-01-07 10:33:03 -05:00

CIPLabeler

Fixes #9153 (#9154)

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

Depictor

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

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

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

strip whitespace from embedParametersToJSON() (#8989)

2025-12-04 06:57:08 +01:00

EnumerateStereoisomers

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

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

FileParsers

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

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

FilterCatalog

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

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

Fingerprints

Support serializing/deserializing FP generators to JSON (#9000)

2025-12-24 19:09:05 +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

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

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

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

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

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

2026-03-19 08:43:13 +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

Fix deprecated literal operators and macro redefinition warnings for modern compilers (#9055)

2026-01-19 08:14:52 +01:00

MolProcessing

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

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

MolStandardize

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +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

More refactoring in Canon.cpp (#9155)

2026-03-12 05:54:20 +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

Small refactor before PR #8968 follow up (#9135)

2026-03-01 07:24:59 +01:00

catch_chirality.cpp

Fix for issue #8965 (#8968)

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

catch_graphmol.cpp

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

2026-03-19 08:43:13 +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

Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds (#9118)

2026-02-20 19:54:13 +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

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

Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds (#9118)

2026-02-20 19:54:13 +01:00

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

Fix for issue #8965 (#8968)

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

MolPickler.cpp

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

2026-02-04 12:13:33 +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

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

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 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

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