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Avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms (#8415)

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* avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms

* changes in response to review

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2025-04-08 09:32:59 +02:00
committed by GitHub
parent 5817e52db2
commit d8dc968eaa
2 changed files with 19 additions and 1 deletions
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16
Code/GraphMol/Depictor/catch_tests.cpp
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@@ -2337,3 +2337,19 @@ M END)CTAB"_ctab;
CHECK_THAT(ctd.x, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
CHECK_THAT(ctd.y, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
}
#ifdef RDK_BUILD_COORDGEN_SUPPORT
TEST_CASE("CoordGen should not segfault when bond has stereo spec but no stereo atoms") {
auto m = "C=C1C=CC(=O)CC1"_smiles;
REQUIRE(m);
CHECK(m->getNumBonds() == 8);
auto b = m->getBondWithIdx(0);
CHECK(b->getBondType() == Bond::DOUBLE);
b->setStereo(Bond::STEREOZ);
CHECK(b->getStereoAtoms().empty());
RDDepict::preferCoordGen = true;
RDDepict::compute2DCoords(*m);
RDDepict::preferCoordGen = false;
CHECK(m->getNumConformers() == 1);
}
#endif

4
External/CoordGen/CoordGen.h vendored
View File

@@ -154,8 +154,10 @@ unsigned int addCoords(T &mol, const CoordGenParams *params = nullptr) {
auto obnd = *bndit;
if (obnd->getBondType() != Bond::DOUBLE ||
obnd->getStereo() <= Bond::STEREOANY ||
obnd->getStereo() > Bond::STEREOTRANS)
obnd->getStereo() > Bond::STEREOTRANS ||
obnd->getStereoAtoms().size() < 2) {
continue;
}
sketcherMinimizerBondStereoInfo sinfo;
sinfo.atom1 = ats[obnd->getStereoAtoms()[0]];