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Modern stereo: fix stereo inversion in rings (#8957)

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* Modern stereo: fix stereo inversion in rings

* Update Code/GraphMol/catch_chirality.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* Update Code/GraphMol/catch_chirality.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* Update Code/GraphMol/catch_chirality.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* review comments

* Update Code/GraphMol/catch_chirality.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* gregs comment

---------

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
This commit is contained in:
Rachel Walker
2025-11-20 22:50:16 -08:00
committed by GitHub
parent 79b595de20
commit 3320d7b454
2 changed files with 33 additions and 9 deletions
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20
Code/GraphMol/Chirality.cpp
View File

@@ -1450,7 +1450,8 @@ void findAtomNeighborsHelper(const ROMol &mol, const Atom *atom,
}
// conditions for an atom to be a candidate for ring stereochem:
// 1) two non-ring neighbors that have different ranks
// 1) two non-ring neighbors that have different ranks (the ring neighbors
// will have the same rank)
// 2) one non-ring neighbor and two ring neighbors (the ring neighbors will
// have the same rank)
// 3) four ring neighbors with three different ranks
@@ -1462,7 +1463,6 @@ bool atomIsCandidateForRingStereochem(
const std::vector<unsigned int> &atomRanks) {
PRECONDITION(atom, "bad atom");
bool res = false;
std::set<unsigned int> nbrRanks;
if (!atom->getPropIfPresent(common_properties::_ringStereochemCand, res)) {
const RingInfo *ringInfo = mol.getRingInfo();
if (ringInfo->isInitialized() && ringInfo->numAtomRings(atom->getIdx())) {
@@ -1477,33 +1477,35 @@ bool atomIsCandidateForRingStereochem(
}
std::vector<const Atom *> nonRingNbrs;
std::vector<const Atom *> ringNbrs;
std::set<unsigned int> ringNbrRanks;
for (const auto bond : mol.atomBonds(atom)) {
if (!ringInfo->numBondRings(bond->getIdx())) {
nonRingNbrs.push_back(bond->getOtherAtom(atom));
} else {
const Atom *nbr = bond->getOtherAtom(atom);
ringNbrs.push_back(nbr);
nbrRanks.insert(atomRanks[nbr->getIdx()]);
ringNbrRanks.insert(atomRanks[nbr->getIdx()]);
}
}
// std::cerr << "!!!! " << atom->getIdx() << " " << nbrRanks.size() << " "
// std::cerr << "!!!! " << atom->getIdx() << " " << ringNbrRanks.size() << " "
// << ringNbrs.size() << " " << nonRingNbrs.size() << std::endl;
switch (nonRingNbrs.size()) {
case 2:
// they have to be different
// the ranks of the non ring neighbors must be different AND
// the ranks of the ring neighbors must be the same (see issue #8956)
res = atomRanks[nonRingNbrs[0]->getIdx()] !=
atomRanks[nonRingNbrs[1]->getIdx()];
res &= (ringNbrs.size() != ringNbrRanks.size());
break;
case 1:
if (ringNbrs.size() > nbrRanks.size()) {
if (ringNbrs.size() > ringNbrRanks.size()) {
res = true;
}
break;
case 0:
if (ringNbrs.size() == 4 && nbrRanks.size() == 3) {
if (ringNbrs.size() == 4 && ringNbrRanks.size() == 3) {
res = true;
} else if (ringNbrs.size() == 3 && nbrRanks.size() == 2) {
} else if (ringNbrs.size() == 3 && ringNbrRanks.size() == 2) {
res = true;
} else {
res = false;

22
Code/GraphMol/catch_chirality.cpp
View File

@@ -6348,6 +6348,28 @@ TEST_CASE("extra ring stereo with new stereo perception") {
CHECK(atm->hasProp(common_properties::_ringStereoAtoms));
}
}
SECTION("#8956 ensure ring stereochemistry is not inverted on round trip") {
auto useLegacy = GENERATE(true, false);
CAPTURE(useLegacy);
UseLegacyStereoPerceptionFixture fx(useLegacy);
auto [smi1, smi2] = GENERATE(
std::make_pair("CC[C@]1(C)CCC[C@](C)(O)C1",
"CC[C@@]1(C)CCC[C@@](C)(O)C1"),
std::make_pair("C[C@H]1CCC[C@](C)(O)C1", "C[C@@H]1CCC[C@@](C)(O)C1"));
auto m1 = v2::SmilesParse::MolFromSmiles(smi1);
REQUIRE(m1);
auto m2 = v2::SmilesParse::MolFromSmiles(smi2);
REQUIRE(m2);
MolOps::assignStereochemistry(*m1, true, true, true);
MolOps::assignStereochemistry(*m2, true, true, true);
auto roundtrip1 = MolToSmiles(*m1);
auto roundtrip2 = MolToSmiles(*m2);
CHECK(roundtrip1 == smi1);
CHECK(roundtrip2 == smi2);
CHECK(roundtrip2 != roundtrip1);
}
}
TEST_CASE("ring stereo basics with new stereo") {
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);