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
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