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Fixes #9020 (#9025)

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* Fixes #9020

* add another test

---------

Co-authored-by: = <=>
This commit is contained in:
Greg Landrum
2026-01-03 06:42:09 +01:00
committed by greg landrum
parent 6ee39bd992
commit 25ce3f3602
2 changed files with 165 additions and 1 deletions
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17
Code/GraphMol/AddHs.cpp
View File

@@ -1064,7 +1064,22 @@ void removeHs(RWMol &mol, const RemoveHsParameters &ps, bool sanitize) {
if (!atomsToRemove.empty() && ps.removeNonimplicit && sanitize) {
sanitizeMol(mol);
}
};
// if we removed Hs and any chiral atoms now have more than 1 explict H,
// remove those
if (!atomsToRemove.empty()) {
for (auto atom : mol.atoms()) {
if (!atom->getNoImplicit() &&
atom->getChiralTag() != Atom::CHI_UNSPECIFIED) {
unsigned int numExplicitHs = atom->getNumExplicitHs();
if (numExplicitHs > 1) {
atom->setNumExplicitHs(0);
atom->updatePropertyCache(false);
}
}
}
}
}
ROMol *removeHs(const ROMol &mol, const RemoveHsParameters &ps, bool sanitize) {
auto *res = new RWMol(mol);
try {

149
Code/GraphMol/FileParsers/molfile_stereo_catch.cpp
View File

@@ -639,3 +639,152 @@ M END
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREONONE);
}
}
TEST_CASE("github #9020: implicit/explicit H labels depend on 3D conformers") {
SECTION("as reported") {
auto mb3 = R"CTAB(
RDKit 3D
6 5 0 0 0 0 0 0 0 0999 V2000
-0.3698 0.0026 0.0028 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8980 -0.5748 -0.1191 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6741 -0.1194 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3142 1.0665 -0.3155 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0830 -0.5246 -0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5432 0.1497 0.0240 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
M END)CTAB";
{
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 3);
}
{
v2::FileParsers::MolFileParserParams params;
params.removeHs = false;
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3, params);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
MolOps::removeHs(*mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 3);
}
}
SECTION("With a quaternary N") {
auto mb3 = R"CTAB(
RDKit 3D
6 5 0 0 0 0 0 0 0 0999 V2000
-0.3698 0.0026 0.0028 N 0 0 0 0 0 0 0 0 0 0 0 0
0.8980 -0.5748 -0.1191 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6741 -0.1194 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3142 1.0665 -0.3155 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0830 -0.5246 -0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5432 0.1497 0.0240 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
M CHG 1 1 1
M END)CTAB";
{
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3);
REQUIRE(mol3);
// mol3->debugMol(std::cerr);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 3);
CHECK(mol3->getAtomWithIdx(1)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(1)->getNumImplicitHs() == 1);
}
{
v2::FileParsers::MolFileParserParams params;
params.removeHs = false;
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3, params);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
MolOps::removeHs(*mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 3);
CHECK(mol3->getAtomWithIdx(1)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(1)->getNumImplicitHs() == 1);
}
}
SECTION("actually chiral") {
auto mb3 = R"CTAB(
RDKit 3D
6 5 0 0 0 0 0 0 0 0999 V2000
-0.3698 0.0026 0.0028 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8980 -0.5748 -0.1191 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6741 -0.1194 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3142 1.0665 -0.3155 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.0830 -0.5246 -0.6430 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1.5432 0.1497 0.0240 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
M END)CTAB";
{
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 1);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
}
{
v2::FileParsers::MolFileParserParams params;
params.removeHs = false;
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3, params);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
MolOps::removeHs(*mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 1);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
}
}
SECTION("not chiral, one H") {
auto mb3 = R"CTAB(
RDKit 3D
6 5 0 0 0 0 0 0 0 0999 V2000
-0.3698 0.0026 0.0028 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8980 -0.5748 -0.1191 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6741 -0.1194 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3142 1.0665 -0.3155 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.0830 -0.5246 -0.6430 F 0 0 0 0 0 0 0 0 0 0 0 0
1.5432 0.1497 0.0240 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
M END)CTAB";
{
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 1);
}
{
v2::FileParsers::MolFileParserParams params;
params.removeHs = false;
auto mol3 = v2::FileParsers::MolFromMolBlock(mb3, params);
REQUIRE(mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 0);
MolOps::removeHs(*mol3);
CHECK(mol3->getAtomWithIdx(0)->getNumExplicitHs() == 0);
CHECK(mol3->getAtomWithIdx(0)->getNumImplicitHs() == 1);
}
}
}