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Segfault within coordgen for molecule #106

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greglandrum opened this issue Jan 4, 2022 · 0 comments
Open

Segfault within coordgen for molecule #106

greglandrum opened this issue Jan 4, 2022 · 0 comments
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greglandrum commented Jan 4, 2022 •
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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.
@greglandrum greglandrum self-assigned this Jan 4, 2022
@greglandrum greglandrum added the bug label Jan 4, 2022
greglandrum added a commit to greglandrum/coordgenlibs that referenced this issue Jan 4, 2022
@greglandrum
Fixes schrodinger#106
ac822d6
d-b-w pushed a commit that referenced this issue Jan 5, 2022
@greglandrum
Addresses SEGV in #106 (#107)
3ec1dfc 
But it doesn't address the root issue of NaN coordinates.
@greglandrum greglandrum mentioned this issue Jan 6, 2022
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d-b-w added a commit that referenced this issue Jan 11, 2022
@d-b-w
Refactor clockwiseOrderedNeighbors() to avoid NaN SEGV from #106 (#108)
ddc6ab2 
* Refactor clockwiseOrderedNeighbors() to avoid NaN SEGV

Although the SEGV when coordinates are NaN has already been
bypassed, I refactored this function when trying to understand
what it did. I find this version more readable, it also happens
to be more efficient (although that probably doesn't matter
with 3-5 substituents).
@bjonnh-work bjonnh-work mentioned this issue Jul 17, 2023
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