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allow specified chiral features to SSS match unspecified features (#8115)

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This commit is contained in:
Greg Landrum
2024-12-18 20:37:17 +01:00
committed by GitHub
parent 74fc77f959
commit e77d4e3f6a
5 changed files with 80 additions and 9 deletions
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17
Code/GraphMol/Substruct/SubstructMatch.cpp
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@@ -246,6 +246,9 @@ bool MolMatchFinalCheckFunctor::operator()(const std::uint32_t q_c[],
}
const Atom *mAt = d_mol.getAtomWithIdx(m_c[i]);
if (!detail::hasChiralLabel(mAt)) {
if (d_params.specifiedStereoQueryMatchesUnspecified) {
continue;
}
return false;
}
if (qAt->getDegree() > mAt->getDegree()) {
@@ -327,10 +330,15 @@ bool MolMatchFinalCheckFunctor::operator()(const std::uint32_t q_c[],
const Bond *mBnd = d_mol.getBondBetweenAtoms(
q_to_mol[qBnd->getBeginAtomIdx()], q_to_mol[qBnd->getEndAtomIdx()]);
CHECK_INVARIANT(mBnd, "Matching bond not found");
if (mBnd->getBondType() != Bond::DOUBLE ||
qBnd->getStereo() <= Bond::STEREOANY) {
if (mBnd->getBondType() != Bond::DOUBLE) {
continue;
}
if (!d_params.specifiedStereoQueryMatchesUnspecified &&
mBnd->getStereo() <= Bond::STEREOANY) {
return false;
}
// don't think this can actually happen, but check to be sure:
if (mBnd->getStereoAtoms().size() != 2) {
continue;
@@ -386,6 +394,7 @@ class AtomLabelFunctor {
AtomLabelFunctor(const ROMol &query, const ROMol &mol,
const SubstructMatchParameters &ps)
: d_query(query), d_mol(mol), d_params(ps) {};
bool operator()(unsigned int i, unsigned int j) const {
bool res = false;
if (d_params.useChirality) {
@@ -393,7 +402,8 @@ class AtomLabelFunctor {
if (qAt->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
qAt->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) {
const Atom *mAt = d_mol.getAtomWithIdx(j);
if (mAt->getChiralTag() != Atom::CHI_TETRAHEDRAL_CW &&
if (!d_params.specifiedStereoQueryMatchesUnspecified &&
mAt->getChiralTag() != Atom::CHI_TETRAHEDRAL_CW &&
mAt->getChiralTag() != Atom::CHI_TETRAHEDRAL_CCW) {
return false;
}
@@ -421,6 +431,7 @@ class BondLabelFunctor {
qBnd->getStereo() > Bond::STEREOANY) {
const Bond *mBnd = d_mol[j];
if (mBnd->getBondType() == Bond::DOUBLE &&
!d_params.specifiedStereoQueryMatchesUnspecified &&
mBnd->getStereo() <= Bond::STEREOANY) {
return false;
}