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fixes #3967 (#4190)

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* fixes #3967

* modernize test

Co-authored-by: greg landrum <greg.landrum@gmail.com>
This commit is contained in:
jfkonecn
2021-06-02 23:13:13 -04:00
committed by greg landrum
parent 2b76d8e941
commit 435a6b64b5
3 changed files with 50 additions and 0 deletions
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2
.gitignore vendored
View File

@@ -8,6 +8,8 @@
#- Eclipse files
/.project
/.pydevproject
/.cproject
/.settings/
#- CLion files
/cmake-build-*

26
Code/GraphMol/Canon.cpp
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@@ -350,10 +350,25 @@ void canonicalizeDoubleBond(Bond *dblBond, UINT_VECT &bondVisitOrders,
// If we're not looking at the bonds used to determine the
// stereochemistry, we need to flip the setting on the other bond:
const INT_VECT &stereoAtoms = dblBond->getStereoAtoms();
auto isClosingRingBond = [](Bond *bond) {
if (bond == nullptr) {
return false;
}
auto beginIdx = bond->getBeginAtomIdx();
auto endIdx = bond->getEndAtomIdx();
return beginIdx > endIdx &&
beginIdx - endIdx > 1 &&
bond->hasProp(common_properties::_TraversalRingClosureBond);
};
auto isFlipped = false;
if (atom1->getDegree() == 3 &&
std::find(stereoAtoms.begin(), stereoAtoms.end(),
static_cast<int>(atom1ControllingBond->getOtherAtomIdx(
atom1->getIdx()))) == stereoAtoms.end()) {
isFlipped = true;
atom2Dir = (atom2Dir == Bond::ENDUPRIGHT) ? Bond::ENDDOWNRIGHT
: Bond::ENDUPRIGHT;
}
@@ -363,6 +378,17 @@ void canonicalizeDoubleBond(Bond *dblBond, UINT_VECT &bondVisitOrders,
std::find(stereoAtoms.begin(), stereoAtoms.end(),
static_cast<int>(firstFromAtom2->getOtherAtomIdx(
atom2->getIdx()))) == stereoAtoms.end()) {
isFlipped = true;
atom2Dir = (atom2Dir == Bond::ENDUPRIGHT) ? Bond::ENDDOWNRIGHT
: Bond::ENDUPRIGHT;
}
if (!isFlipped &&
(isClosingRingBond(dblBond) ||
(isClosingRingBond(secondFromAtom1) &&
!secondFromAtom1->getIsAromatic() &&
secondFromAtom1->getBondDir() != Bond::NONE))
) {
atom2Dir = (atom2Dir == Bond::ENDUPRIGHT) ? Bond::ENDDOWNRIGHT
: Bond::ENDUPRIGHT;
}

22
Code/GraphMol/SmilesParse/test.cpp
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@@ -4339,6 +4339,27 @@ void testOSSFuzzFailures() {
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub3967() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github Issue 3967: Double bond stereo gets "
"flipped by SMILES reader/writer"
<< std::endl;
{
auto mol = "C=c1s/c2n(c1=O)CCCCCCC\\N=2"_smiles;
TEST_ASSERT(mol);
auto smi = MolToSmiles(*mol);
TEST_ASSERT(smi == "C=c1s/c2n(c1=O)CCCCCCC\\N=2");
}
{
auto mol = "C1=C\\C/C=C2C3=C/C/C=C\\C=C/C\\3C\\2\\C=C/1"_smiles;
TEST_ASSERT(mol);
auto smi = MolToSmiles(*mol);
TEST_ASSERT(smi == "C1=C\\C/C=C2C3=C/C/C=C\\C=C/C\\3C\\2\\C=C/1");
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
@@ -4417,6 +4438,7 @@ int main(int argc, char *argv[]) {
testdoRandomSmileGeneration();
testGithub1028();
testGithub3139();
testGithub3967();
#endif
testOSSFuzzFailures();
}