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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
..
csharp_wrapper
Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
2025-08-29 04:39:22 +02:00
gmwrapper
Fix for issue #8965 (#8968)
2026-02-26 08:58:36 +01:00
Abbreviations.i
Add support for abbreviations (#3406)
2020-09-28 17:09:46 -04:00
AddHs.i
add svn props
2011-07-01 04:43:39 +00:00
Atom_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Atom.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
AtomIterators.i
add svn props
2011-07-01 04:43:39 +00:00
AtomPairs.i
add svn props
2011-07-01 04:43:39 +00:00
AvalonLib.i
Unset executable flag
2019-10-10 20:18:43 +09:00
BitOps.i
expose FPS functions to java; add tests for that (#897)
2016-05-02 14:39:48 -04:00
Bond_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Bond.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
BondIterators_doc.i
add svn props
2011-07-01 04:43:39 +00:00
BondIterators.i
add svn props
2011-07-01 04:43:39 +00:00
build_docs.sh
add
2011-04-08 02:48:25 +00:00
Canon.i
add svn props
2011-07-01 04:43:39 +00:00
ChemDraw.i
Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
2025-08-29 04:39:22 +02:00
ChemReactions_doc.i
add svn props
2011-07-01 04:43:39 +00:00
ChemReactions.i
cdxml parser (#5273)
2022-09-28 05:49:27 +02:00
ChemTransforms.i
Expose molzip functionality to MinimalLib (#7959)
2024-11-12 17:16:14 +01:00
CMakeLists.txt
Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
2025-08-29 04:39:22 +02:00
Conformer_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Conformer.i
- wrap types that are otherwise not accessible from SWIG wrappers (#6110)
2023-02-20 12:44:24 +01:00
Descriptors.i
remove USR references from SWIG wrappers
2013-10-08 05:48:40 +02:00
Dict.i
Use std::string_view for property keys (#8844)
2025-10-09 16:14:48 +02:00
DistGeom.i
Allow the sources of conformer generation failures to be retrieved (#5960)
2023-01-24 18:09:15 +01:00
DiversityPick.h
style: apply readability-braces-around-statements (#8136)
2026-02-09 12:10:50 +01:00
DiversityPick.i
add support for a diversity picker to java wrapper
2011-10-08 12:59:40 +00:00
ErrorGenerator.i
add svn props
2011-07-01 04:43:39 +00:00
ExplicitBitVect_doc.i
add svn props
2011-07-01 04:43:39 +00:00
ExplicitBitVect.i
Add some ExplicitBitVect operations to Swig (#7204)
2024-03-03 05:55:37 +01:00
extend_std_vector.i
Get the wrappers working with SWIG 4.0 (#5795)
2022-12-10 07:13:55 +01:00
FilterCatalog_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
FilterCatalog.i
fix several warnings originating from the swig wrappers (#7063)
2024-01-30 04:44:43 +01:00
FilterCatalogParams_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
FilterCatalogs_doc.i
Updated docs
2015-09-10 11:34:41 -04:00
Fingerprints.i
Get the wrappers working with SWIG 4.0 (#5795)
2022-12-10 07:13:55 +01:00
FMCS.i
fix several warnings originating from the swig wrappers (#7063)
2024-01-30 04:44:43 +01:00
ForceField.i
fix #8019 (#8020)
2024-11-20 09:09:56 +01:00
GeneralizedSubstruct.i
Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)
2023-12-19 04:44:06 +01:00
GenericRDKitException.h
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Inchi.i
add svn props
2011-07-01 04:43:39 +00:00
make_templates.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolBundle.i
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolDraw2D.i
- wrap types that are otherwise not accessible from SWIG wrappers (#6110)
2023-02-20 12:44:24 +01:00
MolEnumerator.i
Add support for SRUs to MolEnumerator (#4563)
2021-09-28 16:37:39 +02:00
MolHash.i
Fixes #2677 (#2687)
2019-10-03 18:07:26 -04:00
MolOps.i
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
MolStandardize.i
Fix memory leaks (#8298)
2025-02-25 16:58:19 +01:00
MolSupplier.i
V2 API for the MolSuppliers (#7168)
2024-02-29 06:46:56 +01:00
MolTransforms.i
add svn props
2011-07-01 04:43:39 +00:00
MolWriters.i
- Restore mol writing functions in the RDKFuncs module (#7544)
2024-06-21 05:51:18 +02:00
MonomerInfo.i
first java wrappers of pdb stuff
2013-10-11 18:06:09 +02:00
MorganFingerprints.h
fix: apply modernize-use-nullptr (#8134)
2025-01-09 07:56:10 +01:00
MorganFingerprints.i
Cart fixes (#2462)
2019-05-27 14:29:09 +02:00
msvc_stdint.i
Fixes csharp build for 64 bit systems (#1098)
2016-10-14 15:40:05 +02:00
parse_doxy_html.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
PeriodicTable_doc.i
add svn props
2011-07-01 04:43:39 +00:00
PeriodicTable.i
add svn props
2011-07-01 04:43:39 +00:00
Point3D_doc.i
add svn props
2011-07-01 04:43:39 +00:00
point.i
add svn props
2011-07-01 04:43:39 +00:00
Queries.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
QueryAtom_doc.i
add svn props
2011-07-01 04:43:39 +00:00
QueryAtom.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
QueryBond_doc.i
add svn props
2011-07-01 04:43:39 +00:00
QueryBond.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
QueryOps.i
GitHub 7865 haspropwithvaluequery leaks (#7872)
2024-10-30 06:12:40 +01:00
RascalMCES.i
C sharp rascal mcs wrapper (#7390)
2024-05-05 05:52:24 +02:00
RDKFuncs_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
RDKitExceptions.i
[v2 API] SMILES/SMARTS parsers (#6203)
2024-01-19 17:17:51 +01:00
RDLogger.i
Expose RDLog to SWIG wrappers (#5749)
2023-04-14 09:26:56 +02:00
RDProps.i
Handle query atoms and bonds in SWIG wrappers (#7431)
2024-05-23 07:18:49 +02:00
ReactionFingerprints.i
Fixes #1776 (#1780)
2018-03-20 10:10:40 -04:00
RGroupDecomposition.i
Replace awful enum reflection macros with Better Enums (#7913)
2024-10-25 08:17:07 +02:00
RingInfo_doc.i
add svn props
2011-07-01 04:43:39 +00:00
RingInfo.i
add svn props
2011-07-01 04:43:39 +00:00
Rings.i
add svn props
2011-07-01 04:43:39 +00:00
ROMol_doc.i
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
ROMol.i
Fixes #9107 (#9111)
2026-02-13 14:11:10 -05:00
RWMol_doc.i
add svn props
2011-07-01 04:43:39 +00:00
RWMol.i
Deterministic kekulize, independent of atom and bond order (#9125)
2026-03-19 08:43:13 +01:00
SanitException.i
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
ScaffoldNetwork.i
Add ScaffoldNetwork to csharp (#3289)
2020-07-13 14:48:34 +02:00
SDMolSupplier_doc.i
add svn props
2011-07-01 04:43:39 +00:00
SmartsWrite.i
add svn props
2011-07-01 04:43:39 +00:00
SmilesMolSupplier_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
SmilesParse.i
[v2 API] SMILES/SMARTS parsers (#6203)
2024-01-19 17:17:51 +01:00
SmilesWrite.i
Fixes #8654 (#8657)
2025-07-30 05:56:52 +02:00
SmilesWriter_doc.i
add svn props
2011-07-01 04:43:39 +00:00
std_tuple.i
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
StereoGroup.i
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
Streams.i
Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF (#4933)
2022-01-23 07:06:36 +01:00
Subgraphs.i
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Subset.i
Add extract mol fragment api (#8811)
2025-12-09 15:06:29 +01:00
SubstanceGroup.i
Add getUIntVectProp to RDProps (#7507)
2024-06-23 07:01:07 +02:00
SubstructLibrary.i
fix several warnings originating from the swig wrappers (#7063)
2024-01-30 04:44:43 +01:00
TautomerQuery.i
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
TDTMolSupplier_doc.i
add svn props
2011-07-01 04:43:39 +00:00
TDTWriter_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Trajectory.i
Java wrappers for Trajectory/Snapshot objects (#977)
2016-07-20 22:51:01 -04:00
Transform2D_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
Transform3D_doc.i
add svn props
2011-07-01 04:43:39 +00:00
transforms.i
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
types.i
add svn props
2011-07-01 04:43:39 +00:00