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Preserve chirality when merging explicit Hs in MergeQueryHs - #9676
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Merging an explicit H neighbor into a chiral atom's query dropped the chiral tag entirely: updateProps() copies the property dictionary but not d_chiralTag, so the tag was lost when the atom was replaced by a QueryAtom. The merged query then matched both enantiomers. Carry the chiral tag across the replacement, and flip the tag when removing the H bonds changes the parity of the remaining bond order -- the same fixup removeHs() already performs per removal. Fixes rdkit#9675 Generated with [Devin](https://devin.ai) Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
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Reference Issue
Fixes #9675
What does this implement/fix? Explain your changes.
MolOps::mergeQueryHsdropped chirality when an explicit H neighbor of a tetrahedral stereo center was merged into the parent's query. Two things combine here.When the parent atom was not already a query atom, it was replaced by a
QueryAtomviaupdateProps(). That call copies the property dictionary but notd_chiralTag, so the tag was lost outright.And removing the H bonds changes the order of the remaining bonds about the center, which can flip the parity the tag encodes.
removeHs()already compensates for this per removal (getPerturbationOrder+invertChirality). The merge path did not.The change carries the tag across the replacement and applies the same parity fixup, computed over the kept bonds plus the removed bonds appended in original order.
The reported L-alanine case now keeps a chiral tag on the merged atom, and with
useChiralityon the query matchesC[C@@H](N)C(=O)Owhile rejectingC[C@H](N)C(=O)O. A regression test covers both assertions.Any other comments?
graphmolMolOpsTestpasses all 116 test cases andmolopsTestsCatchpasses 16/16, run withRDBASEset. The Python-side check from the issue was not run (no py312 bindings on this machine). The C++ test asserts the same behavior.