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251353a217f52777533419e548bbac5fc32fb9c8
rdkit/Code/GraphMol
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Greg Landrum 251353a217 Ensure that StereoGroups don't have duplicate atoms or bonds (#9258) 
* check for duplicate atoms/bonds in StereoGroups

* explicit handling of duplicate stereogroup atoms in CTAB and CXSMILES parsers

---------

Co-authored-by: = <=>
2026-04-29 16:54:00 +02:00
..
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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
If templates match, skip ring number check (#9217)
2026-04-23 19:21:29 +02:00
Deprotect
Fixes #7989 Incorrect benzyl deprotection reaction (#7990)
2024-11-07 18:34:59 +01:00
Descriptors
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
2026-04-29 16:54:00 +02:00
FilterCatalog
style: apply readability-braces-around-statements (#8136)
2026-02-09 12:10:50 +01:00
Fingerprints
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
FMCS
In verbose output, check that the query molecule exists before using it. (#9040)
2026-01-08 06:06:52 +01:00
ForceFieldHelpers
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
FragCatalog
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +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
MolDraw2D: configurable legend position and vertical side legends (Issue #9023) (#9183)
2026-04-16 04:59:00 +02:00
MolEnumerator
Add safeSetattr to more params / options objects (#8842)
2025-10-08 16:15:20 +02:00
MolHash
Tautomer insensitive hash v2, E/Z and stereocenter-preservation (#9128)
2026-04-24 14:19:47 +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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
PartialCharges
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
RascalMCES
Deterministic kekulize, independent of atom and bond order (#9125)
2026-03-19 08:43:13 +01:00
ReducedGraphs
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
RGroupDecomposition
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
SmilesParse
Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
2026-04-29 16:54:00 +02:00
StructChecker
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
Subgraphs
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
2026-04-29 16:54:00 +02:00
catch_molbundle.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
catch_moliterators.cpp
Add some std::ranges support (#9218)
2026-04-13 17:13:04 +02:00
catch_molops.cpp
make ringdecomposerlib a mandatory dependency (#9209)
2026-03-27 18:17:27 +01:00
catch_molranges.cpp
Add some std::ranges support (#9218)
2026-04-13 17:13:04 +02:00
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/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
Chirality.h
cleanup of stereogroups and wedges for non-chiral sites (#9051)
2026-01-30 04:20:32 +01:00
CMakeLists.txt
Add some std::ranges support (#9218)
2026-04-13 17:13:04 +02:00
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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
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
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
resMolSupplierTest.cpp
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00
Resonance.cpp
Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +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 some std::ranges support (#9218)
2026-04-13 17:13:04 +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
Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
2026-04-29 16:54:00 +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