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Fixes two out-of-bounds bugs in the InChI wrapper (#8126)

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This commit is contained in:
Greg Landrum
2024-12-25 21:32:35 +01:00
committed by greg landrum
parent bcef6669fa
commit df2a783c8b
2 changed files with 41 additions and 7 deletions
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19
External/INCHI-API/inchi.cpp vendored
View File

@@ -1840,11 +1840,14 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
}
// convert tetrahedral chirality info to Stereo0D
if (atom->getChiralTag() != Atom::CHI_UNSPECIFIED ||
atom->hasProp("molParity")) {
// we ignore the molParity if the number of neighbors are below 3
if (atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW ||
atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW) {
atom->calcImplicitValence();
if (atom->getNumImplicitHs() + atom->getDegree() < 3) {
if (auto tval = atom->getTotalValence(); tval < 3 || tval > 4) {
BOOST_LOG(rdWarningLog)
<< "tetrahedral chirality on atom with <3 or >4 neighbors will be ignored."
<< std::endl;
continue;
}
inchi_Stereo0D stereo0D;
@@ -1865,7 +1868,6 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
// std::cerr<<" at: "<<atom->getIdx();
for (const auto &p : neighbors) {
stereo0D.neighbor[nid++] = p.second;
// std::cerr<<" "<<p.second;
}
if (nid == 3) {
// std::cerr<<" nid==3, reorder";
@@ -1964,6 +1966,13 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
// neighbor
unsigned int idx = inchiAtoms[atomIndex1].num_bonds;
// The InChI code has a max number of neighbors allowed:
if (idx >= MAXVAL) {
BOOST_LOG(rdErrorLog)
<< " atom " << atomIndex1 << " has too many bonds: " << idx
<< ". The InChI library supports at most " << MAXVAL << std::endl;
return "";
}
inchiAtoms[atomIndex1].neighbor[idx] = atomIndex2;
// bond type

29
External/INCHI-API/test.cpp vendored
View File

@@ -909,17 +909,41 @@ void testGithub5311() {
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
std::cerr << "!!! " << inchi << std::endl;
TEST_ASSERT(inchi == "InChI=1S/H3O2P/c1-3-2/h3H2,(H,1,2)");
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
}
void testGithub8123() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github #8123" << std::endl;
{
// fails due to the presence of a dative bond
auto m =
"Cc1cc(C)c(N2CCN(c3c(C)cc(C)cc3C)C2[Ru@OH28]2(Cl)(Cl)=Cc3cc([S@SP3](=O)(=O)N(C)C)ccc3O->2C(C)C)c(C)c1"_smiles;
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi.empty());
}
{
auto m =
"CC[C@H]1OC(=O)C[C@@H](O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)[C@@H](O)C(N(C)C)C2O)[C@@H](CC=O)C[C@@H](C)C(=O)/C=C/C(C)=C/[C@@H]1CO.CC[C@H]1OC(=O)C[C@@H](O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)[C@@H](O[C@H]3CC(C)(O)[C@@H](O)C(C)O3)C(N(C)C)C2O)[C@@H](CC=O)C[C@@H](C)C(=O)/C=C/C(C)=C/[C@@H]1CO[C@@H]1OC(C)[C@@H](O)[C@H](OC)C1OC.[3H][Y]([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])[3H]"_smiles;
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
boost::logging::enable_logs("rdApp.info");
testGithubIssue3();
testGithubIssue8();
testGithubIssue40();
@@ -938,4 +962,5 @@ int main() {
test_clean_up_on_kekulization_error();
testGithub6172();
testGithub5311();
testGithub8123();
}