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Revert "Fix WedgeMolBonds stealing wiggly bonds from adjacent chiral atoms (#…" (#9293)

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This reverts commit 020b755ad4.
This commit is contained in:
Greg Landrum
2026-05-22 04:39:08 +02:00
committed by GitHub
parent 020b755ad4
commit 4ad9f33bf6
2 changed files with 4 additions and 93 deletions
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20
Code/GraphMol/WedgeBonds.cpp
View File

@@ -54,23 +54,11 @@ namespace detail {
std::pair<bool, INT_VECT> countChiralNbrs(const ROMol &mol, int noNbrs) {
INT_VECT nChiralNbrs(mol.getNumAtoms(), noNbrs);
// start by looking for bonds that are already wedged. A wiggly bond with
// BondDir::NONE plus _UnknownStereo=1 (the state left by
// clearSingleBondDirFlags) is treated the same as one that still has
// BondDir::UNKNOWN: an intentional stereo annotation we should not overwrite.
// start by looking for bonds that are already wedged
for (const auto bond : mol.bonds()) {
bool isDirected = bond->getBondDir() == Bond::BEGINWEDGE ||
bond->getBondDir() == Bond::BEGINDASH ||
bond->getBondDir() == Bond::UNKNOWN;
if (!isDirected) {
int unknownStereo = 0;
if (bond->getPropIfPresent(common_properties::_UnknownStereo,
unknownStereo) &&
unknownStereo) {
isDirected = true;
}
}
if (isDirected) {
if (bond->getBondDir() == Bond::BEGINWEDGE ||
bond->getBondDir() == Bond::BEGINDASH ||
bond->getBondDir() == Bond::UNKNOWN) {
if (bond->getBeginAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
bond->getBeginAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) {
nChiralNbrs[bond->getBeginAtomIdx()] = noNbrs + 1;

77
Code/GraphMol/catch_chirality.cpp
View File

@@ -6554,80 +6554,3 @@ TEST_CASE(
REQUIRE(m);
CHECK(*labels_reference == get_bond_stereo_labels(*m));
}
TEST_CASE(
"WedgeMolBonds does not steal a wiggly bond from an adjacent chiral "
"atom across clearSingleBondDirFlags") {
// CC[C@@H](Cl)N: atom 2 (C@@H) is the chiral center; atom 4 (N) is a
// degree-1 terminal neighbor. The existing countChiralNbrs handling for
// BondDir::UNKNOWN treats a wiggly bond as the stereo annotation for the
// adjacent chiral atom and pre-skips it. After clearSingleBondDirFlags,
// the bond's BondDir is NONE and only _UnknownStereo=1 remains as a
// marker; countChiralNbrs must recognize that marker so the same
// pre-skip behavior applies. Without this, pickBondToWedge would pick
// the wiggly bond (terminal neighbors are preferred) and the caller's
// subsequent restore of BondDir::UNKNOWN would erase the wedge, leaving
// the chiral atom with no visible stereo.
std::string smi =
"CC[C@@H](Cl)N "
"|(-2.078461,0.000000,;-0.779423,0.750000,;0.519615,-0.000000,;"
"0.519615,-1.500000,;1.818653,0.750000,)|";
std::unique_ptr<RWMol> m{SmilesToMol(smi)};
REQUIRE(m);
auto *chiralAtom = m->getAtomWithIdx(2);
REQUIRE(chiralAtom->getChiralTag() != Atom::ChiralType::CHI_UNSPECIFIED);
const auto originalChiralTag = chiralAtom->getChiralTag();
// Mark the bond to N (atom 4, terminal) as a wiggly bond
auto *wigglyBond = m->getBondBetweenAtoms(2, 4);
REQUIRE(wigglyBond != nullptr);
wigglyBond->setBondDir(Bond::BondDir::UNKNOWN);
// Simulate the typical re-wedging pattern: clearSingleBondDirFlags saves
// _UnknownStereo=1 for bonds with BondDir::UNKNOWN and then clears BondDir
// to NONE, so that stale wedge directions are removed before re-wedging.
MolOps::clearSingleBondDirFlags(*m);
REQUIRE(wigglyBond->getBondDir() == Bond::BondDir::NONE);
Chirality::wedgeMolBonds(*m, &m->getConformer());
// No bond at the chiral center should be wedged: the wiggly bond is the
// intentional stereo annotation, matching the BondDir::UNKNOWN behavior
// before clearSingleBondDirFlags.
for (const auto b : m->atomBonds(chiralAtom)) {
CHECK(b->getBondDir() != Bond::BondDir::BEGINWEDGE);
CHECK(b->getBondDir() != Bond::BondDir::BEGINDASH);
}
// Round-trip preserves the chiral tag itself; only the visual wedging
// representation is affected by the wiggly-bond annotation.
CHECK(chiralAtom->getChiralTag() == originalChiralTag);
}
TEST_CASE(
"pickBondsToWedge respects _UnknownStereo=1 marker when called directly") {
// pickBondsToWedge is part of the public API (Chirality.h); callers can
// invoke it without going through wedgeMolBonds, so the recognition of
// the _UnknownStereo=1 marker has to live in countChiralNbrs itself.
std::string smi =
"CC[C@@H](Cl)N "
"|(-2.078461,0.000000,;-0.779423,0.750000,;0.519615,-0.000000,;"
"0.519615,-1.500000,;1.818653,0.750000,)|";
std::unique_ptr<RWMol> m{SmilesToMol(smi)};
REQUIRE(m);
auto *wigglyBond = m->getBondBetweenAtoms(2, 4);
REQUIRE(wigglyBond != nullptr);
wigglyBond->setBondDir(Bond::BondDir::UNKNOWN);
MolOps::clearSingleBondDirFlags(*m);
REQUIRE(wigglyBond->getBondDir() == Bond::BondDir::NONE);
auto wedgeBonds =
Chirality::pickBondsToWedge(*m, nullptr, &m->getConformer());
// The chiral atom's stereo is already expressed by the wiggly bond, so
// pickBondsToWedge must not pick any bond to wedge for it. The molecule
// has no atropisomers, so the returned map should be empty.
CHECK(wedgeBonds.empty());
}