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This one was reported by @lucasmorin222 in the RDKit tracker (rdkit/rdkit#4845), but I've confirmed that it's a coordgen problem.
I don't have a straight reproducible for coordgen, but this bit of C++ using RDKit+Coordgen results in a segfault:
auto m1 = "C1C=CC=C2C1=CSC=C3C(=O)OOOC(=O)C(=CC(=O)N3)OC2=O"_smiles;
CoordGen::addCoords(*m1);
The crash occurs here:
https://github.com/schrodinger/coordgenlibs/blob/master/sketcherMinimizerAtom.cpp#L377
because lastPoppedIndex
is 1 and neighs.size()
is 1.
I'll do a PR.