Fix _smilesAtomOutputOrder parsing for RDKit 2024.03.6 or newer (Issue #7749) #66
+110
−74
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Fixes #65
RDKit's rdkit/rdkit#7749 fixed an issue with the formatting of
_smilesAtomOutputOrder: before this bugfix, the code added an extra comma at the end of the list of atom indexes, which required some custom parsing code such as the one inget_atom_order_in_smiles().Once that patch was merged, the parsing code broke, as it expects the comma to be there.
After the patch,
_smilesAtomOutputOrdercan be parsed as json, or usingast.literal_eval(), which is what I'm adding here. For backwards compatibility with RDKit builds that do not include that patch, I added a couple of lines that remove the extra comma before usingast.literal_eval()to parse the list.