Yakov Pechersky 08552e56b1 atropisomer bond atoms are checked explicitly for SP2 hybridization (#8974) ...

* atropisomer bond atoms are checked explicitly for SP2 hybridization

before, we checked only on totalDegree = 2 or 3,
but this causes false positives for something like a chiral sulfoxide
since the S is tetrahedral (sp3) but has only 3 substituents.
the hybridization code relies on totalDegree,
but modified to include and making sure to include conjugation
so while this is more expensive per molecule, it is closer to intent

Closes #8973

* assert we got no warnings on sulfinamides

* cleanup

* bring back degree based check, quick pass so that we don't run expensive calc on all mols with wedge bonds

* bring conformer back

2025-12-29 18:04:40 +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

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +01:00

ChemTransforms

move molzip to its own file (#9013)

2025-12-22 10:42:23 -05:00

CIPLabeler

Make assignCIPLabels Ctrl+c interruptable (#8589)

2025-06-27 08:27:44 +02:00

Depictor

Fixes #8776 (#8875)

2025-10-17 05:52:27 +02:00

Deprotect

Fixes #7989 Incorrect benzyl deprotection reaction (#7990)

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

Descriptors

add conditional logic for GETAWAY test (#8923)

2025-11-04 16:05:56 +01:00

DetermineBonds

Improve DetermineBonds and DetermineBondOrders performance (#8888)

2025-12-08 06:17:41 +01:00

DistGeomHelpers

strip whitespace from embedParametersToJSON() (#8989)

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

EnumerateStereoisomers

Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available (#8924)

2025-11-11 17:05:30 +01:00

FileParsers

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

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

FilterCatalog

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

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

Fingerprints

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

2025-12-24 19:09:05 +01:00

FMCS

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

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

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

Refactor iostreams includes (#8846)

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

MMPA

Refactor iostreams includes (#8846)

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

MolAlign

Allow Hs to be ignored in the RMSD alignment functions (#8976)

2025-12-04 18:37:59 +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

Better solid triangles (#8943)

2025-11-18 09:47:24 +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

Last leak fixes for 2025! (#9006)

2025-12-13 20:22:59 +01:00

MolProcessing

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

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

MolStandardize

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

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

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

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

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

ReducedGraphs

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

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

RGroupDecomposition

Stop writing so many atom properties to cxsmiles (#9002)

2025-12-13 04:35:57 +01:00

ScaffoldNetwork

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

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

ShapeHelpers

A bunch of modernization of the ShapeHelpers code (#8954)

2025-12-15 15:49:00 -05:00

SLNParse

Refactor iostreams includes (#8846)

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

SmilesParse

Last leak fixes for 2025! (#9006)

2025-12-13 20:22:59 +01:00

StructChecker

Refactor iostreams includes (#8846)

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

Subgraphs

rename test, convert to catch (#9003)

2025-12-13 20:18:40 +01:00

Substruct

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

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

SubstructLibrary

Refactor iostreams includes (#8846)

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

SynthonSpaceSearch

Fixes Github9009 (#9012)

2025-12-22 06:26:23 +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

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

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

AddHs.cpp

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +01:00

AdjustQuery.cpp

apply query adjustments when makeAtomsGeneric is enabled (#8315)

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

Aromaticity.cpp

fixes #5078 (#8795)

2025-09-22 11:06:42 +02:00

Atom.cpp

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +02:00

Atom.h

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +02:00

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

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +02:00

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

Some more cleaning up in SMILES Writing (#8991)

2025-12-29 07:00:45 +01:00

Canon.h

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

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 fix in ring stereo/canonicalization (#8962)

2025-12-12 13:56:01 +01:00

catch_chirality.cpp

Small fix in ring stereo/canonicalization (#8962)

2025-12-12 13:56:01 +01:00

catch_graphmol.cpp

Implements #8873 (#8904)

2025-11-04 16:10:56 +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

Add extract mol fragment api (#8811)

2025-12-09 15:06:29 +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

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

catch_sgroups.cpp

Run clang-format across everything (#7849)

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

Chirality.cpp

Modern stereo: fix stereo inversion in rings (#8957)

2025-11-21 07:50:16 +01:00

Chirality.h

style: apply modernize-use-override (#8137)

2025-04-25 12:24:58 +02:00

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

Add SCSR parsing to RDKit (#8147)

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

FindStereo.cpp

Small fix in ring stereo/canonicalization (#8962)

2025-12-12 13:56:01 +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

Synthon space bad chiral count (#8550)

2025-06-03 13:09:09 +02:00

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

Add extract mol fragment api (#8811)

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

MolOps.h

Fixes #8726 (#8874)

2025-10-17 16:51:22 +02:00

molopstest.cpp

Convert graphmolMolOpsTest to catch2 (#8978)

2025-12-03 06:28:56 +01:00

MolPickler.cpp

Change extern types to static consts (#8765)

2025-11-07 05:15:22 +01:00

MolPickler.h

Refactor iostreams includes (#8846)

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

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

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

new_canon.cpp

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

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

new_canon.h

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

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

NontetrahedralStereo.cpp

fix: apply modernize-use-nullptr (#8134)

2025-01-09 07:56:10 +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

Fix a couple issues related to atom list handling in V3000 mol blocks (#8824)

2025-10-09 05:26:01 +02:00

QueryOps.h

Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)

2025-03-29 07:26:03 +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

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +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

Stop writing so many atom properties to cxsmiles (#9002)

2025-12-13 04:35:57 +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

Refactor iostreams includes (#8846)

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

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

Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)

2025-11-10 13:02:42 -05:00