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020b755ad4
The standard re-wedging pattern is:
clearSingleBondDirFlags(mol); // saves _UnknownStereo=1, clears BondDir to NONE
WedgeMolBonds(mol, &conf); // re-derives wedges from chiral tags
// ... caller restores BondDir::UNKNOWN on bonds with _UnknownStereo=1 ...
Wiggly bonds at chiral centers should survive this round-trip but did
not: countChiralNbrs only checked BondDir to decide whether a chiral
atom's stereo was already expressed, missing the _UnknownStereo=1
marker that clearSingleBondDirFlags saved when it cleared BondDir to
NONE. With the marker invisible to countChiralNbrs, pickBondToWedge
would pick the wiggly bond itself (terminal neighbors are scored
lower), and the caller's subsequent restore of BondDir::UNKNOWN would
erase the wedge, leaving the chiral atom with no visible stereo.
Fix: extend countChiralNbrs to recognize bonds with _UnknownStereo=1
as equivalent to BondDir::UNKNOWN. The chiral atom is then pre-skipped
in pickBondsToWedge, the same way it already is for bonds that still
have BondDir::UNKNOWN set.
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>