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Fix potential iterator invalidation (#8944)

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The iterator in the loop over bonds (changed in utils.cpp) is potentially
invalidated by adding bonds to the molecule. We copy the bonds into a vector to
ensure safety.
This commit is contained in:
Max Rietmann
2025-11-11 17:03:05 +01:00
committed by GitHub
parent 45681a1c04
commit 3802eaaac9
1 changed files with 15 additions and 2 deletions
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17
External/ChemDraw/utils.cpp vendored
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@@ -108,8 +108,16 @@ struct FragmentReplacement {
auto bond_ordering =
replacement_atom->getProp<std::vector<int>>(CDX_BOND_ORDERING);
// The "addBond" lower in the loop potentially modifies the atomBonds
// iterator. To ensure safety, we copy the bonds first.
std::vector<Bond *> replacement_bonds(
mol.atomBonds(replacement_atom).begin(),
mol.atomBonds(replacement_atom).end());
std::vector<Bond *> xbonds; // Reuse this vector to reduce repeated allocations
// Find the connecting atoms and and do the replacement
for (auto bond : mol.atomBonds(replacement_atom)) {
for (auto bond : replacement_bonds) {
// find the position of the attachment bonds in the bond ordering
unsigned bond_id = 0;
if (!bond->getPropIfPresent<unsigned int>(CDX_BOND_ID, bond_id)) {
@@ -134,7 +142,12 @@ struct FragmentReplacement {
auto &xatom = fragment_atoms[pos];
for (auto &xbond : mol.atomBonds(xatom)) {
// The "addBond" lower in the loop potentially modifies the atomBonds
// iterator. To ensure safety, we copy the bonds first.
xbonds.assign(mol.atomBonds(xatom).begin(),
mol.atomBonds(xatom).end());
for (auto &xbond : xbonds) {
// xatom is the fragment dummy atom
// xbond is the fragment bond
if (bond->getBeginAtom() == replacement_atom) {