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Rody Arantes 5d9892575c Fix STEREOANY (wavy bond) loss during InChI roundtrip (#9315)
When converting molecules with wavy bonds (Bond::STEREOANY on double
bonds) through InChI and back, the stereo information was silently
dropped. This affected any workflow using InChI roundtrips for
canonicalization (e.g. with -SUU flag).

Two bugs in External/INCHI-API/inchi.cpp:

Reverse path (InchiToMol): The stereo0D processing loop skipped
INCHI_PARITY_UNDEFINED entries before they could reach the double bond
handler. The handler already had an else clause that correctly sets
Bond::STEREOANY, but it was never reached. Fix: only skip
INCHI_PARITY_NONE at the top level, and add a guard in the Tetrahedral
case to prevent UNDEFINED/UNKNOWN from incorrectly setting chirality.

Forward path (MolToInchi): STEREOANY double bonds were only handled by
collapsing the coordinates — InChI then produced no stereo annotation
under -SUU. Fix: also emit a stereo0D entry with INCHI_PARITY_UNKNOWN
parity so InChI's -SUU output correctly carries the "stereo unknown"
designation. StereoAtoms may be cleared for STEREOANY, so we locate
the two outer neighbors by iterating bonds.

New test testStereoAnyRoundtrip in External/INCHI-API/test.cpp covers
9 representative cases (Schiff base, oxime, cinnamic acid, chalcone,
crotonaldehyde, tamoxifen-like, retinal-like, plus two molecules with
a chiral center adjacent to the wavy bond).

Counts in rdkit/Chem/UnitTestInchi.py shift by 1 (689 same, 492
reasonable) because the new STEREOANY emission produces a more
accurate roundtrip for one entry in the test inventory.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-06-02 14:41:00 +02:00
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2025-10-08 16:08:01 +02:00
2025-11-18 17:02:04 +01:00