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Cleanup/get atoms and bonds (#9243)

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This commit is contained in:
Greg Landrum
2026-04-18 05:22:09 +02:00
committed by GitHub
parent db025bd6b0
commit e35f7db009
44 changed files with 405 additions and 535 deletions
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17
External/FreeSASA/RDFreeSASA.cpp vendored
View File

@@ -89,8 +89,7 @@ bool classifyAtoms(ROMol &mol, std::vector<double> &radii,
}
bool success = true;
for (ROMol::AtomIterator at = mol.beginAtoms(); at != mol.endAtoms(); ++at) {
Atom *atom = *at;
for (const auto atom : mol.atoms()) {
freesasa_atom_class cls = FREESASA_ATOM_UNKNOWN;
std::string classification = "Unclassified";
double radius = 0.0;
@@ -168,9 +167,9 @@ double internalCalcSASA(const ROMol &mol, const std::vector<double> &radii,
double sasa = res->total;
mol.setProp(common_properties::Molecule::SASA, sasa);
size_t i = 0;
for (ROMol::ConstAtomIterator at = mol.beginAtoms(); at != mol.endAtoms();
++at, ++i) {
(*at)->setProp(common_properties::Atom::SASA, res->sasa[i]);
for (const auto atom : mol.atoms()) {
atom->setProp(common_properties::Atom::SASA, res->sasa[i]);
++i;
}
freesasa_result_free(res);
@@ -184,10 +183,10 @@ double calcSASA(const RDKit::ROMol &mol, const std::vector<double> &radii,
double result = internalCalcSASA(mol, radii, confIdx, opts);
if (query) {
result = 0.0f;
for (ROMol::ConstQueryAtomIterator at = mol.beginQueryAtoms(query);
at != mol.endQueryAtoms(); ++at) {
const Atom *atom = *at;
result += atom->getProp<double>("SASA");
for (const auto atom : mol.atoms()) {
if (query->Match(atom)) {
result += atom->getProp<double>("SASA");
}
}
}
return result;

85
External/INCHI-API/inchi.cpp vendored
View File

@@ -1149,97 +1149,96 @@ bool _Valence3ClCleanUp1(RWMol &mol, Atom *atom) {
}
void cleanUp(RWMol &mol) {
ROMol::AtomIterator ai;
bool aromHolder;
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ++ai) {
switch ((*ai)->getAtomicNum()) {
for (const auto atom : mol.atoms()) {
switch (atom->getAtomicNum()) {
case 7:
if ((*ai)->calcExplicitValence(false) == 4) {
if (_Valence4NCleanUp1(mol, *ai)) {
if (atom->calcExplicitValence(false) == 4) {
if (_Valence4NCleanUp1(mol, atom)) {
continue;
}
if ((*ai)->getFormalCharge() == -1) {
if (_Valence4NCleanUp2(mol, *ai)) {
if (atom->getFormalCharge() == -1) {
if (_Valence4NCleanUp2(mol, atom)) {
continue;
}
}
continue;
}
if ((*ai)->getFormalCharge()) {
if (atom->getFormalCharge()) {
continue;
}
aromHolder = (*ai)->getIsAromatic();
(*ai)->setIsAromatic(0);
aromHolder = atom->getIsAromatic();
atom->setIsAromatic(0);
if ((*ai)->calcExplicitValence(false) == 5) {
if (atom->calcExplicitValence(false) == 5) {
// rings CN1=CCN=CC=1, CN1=NCOCC=1, [N]=C1N=CN=N1, [N]=C1C=CN=N1
(_Valence5NCleanUp6(mol, *ai)) || (_Valence5NCleanUp7(mol, *ai)) ||
(_Valence5NCleanUp8(mol, *ai)) ||
(_Valence5NCleanUp9(mol, *ai)) ||
(_Valence5NCleanUpA(mol, *ai)) ||
(_Valence5NCleanUp6(mol, atom)) || (_Valence5NCleanUp7(mol, atom)) ||
(_Valence5NCleanUp8(mol, atom)) ||
(_Valence5NCleanUp9(mol, atom)) ||
(_Valence5NCleanUpA(mol, atom)) ||
// try search for valence-5 N connected to a N+
(_Valence5NCleanUp1(mol, *ai)) ||
(_Valence5NCleanUp1(mol, atom)) ||
// connected to N- through a tiple then single bond
(_Valence5NCleanUp2(mol, *ai)) ||
(_Valence5NCleanUp2(mol, atom)) ||
// directly to a N
(_Valence5NCleanUp3(mol, *ai)) ||
(_Valence5NCleanUp3(mol, atom)) ||
// to two Si- via double bonds
(_Valence5NCleanUp4(mol, *ai)) ||
(_Valence5NCleanUp4(mol, atom)) ||
// alternating bonds to O
(_Valence5NCleanUp5(mol, *ai, 8)) ||
(_Valence5NCleanUp5(mol, atom, 8)) ||
// alternating bonds to S
(_Valence5NCleanUp5(mol, *ai, 16)) ||
(_Valence5NCleanUp5(mol, atom, 16)) ||
// alternating bonds to S
(_Valence5NCleanUp5(mol, *ai, 9)) ||
(_Valence5NCleanUp5(mol, atom, 9)) ||
// alternating bonds to S
(_Valence5NCleanUp5(mol, *ai, 17)) ||
(_Valence5NCleanUp5(mol, atom, 17)) ||
// last resort
(_Valence5NCleanUpB(mol, *ai));
(_Valence5NCleanUpB(mol, atom));
}
if (aromHolder) {
(*ai)->setIsAromatic(1);
atom->setIsAromatic(1);
}
break;
case 17:
if ((*ai)->calcExplicitValence(false) == 8 &&
_Valence8ClCleanUp1(mol, *ai)) {
if (atom->calcExplicitValence(false) == 8 &&
_Valence8ClCleanUp1(mol, atom)) {
continue;
}
if ((*ai)->calcExplicitValence(false) == 5 &&
_Valence5ClCleanUp1(mol, *ai)) {
if (atom->calcExplicitValence(false) == 5 &&
_Valence5ClCleanUp1(mol, atom)) {
continue;
}
if ((*ai)->calcExplicitValence(false) == 3 &&
_Valence3ClCleanUp1(mol, *ai)) {
if (atom->calcExplicitValence(false) == 3 &&
_Valence3ClCleanUp1(mol, atom)) {
continue;
}
break;
case 16:
if ((*ai)->calcExplicitValence(false) == 7) {
if (_Valence7SCleanUp1(mol, *ai)) {
if (atom->calcExplicitValence(false) == 7) {
if (_Valence7SCleanUp1(mol, atom)) {
continue;
}
if (_Valence7SCleanUp2(mol, *ai)) {
if (_Valence7SCleanUp2(mol, atom)) {
continue;
}
if (_Valence7SCleanUp3(mol, *ai)) {
if (_Valence7SCleanUp3(mol, atom)) {
continue;
}
_Valence8SCleanUp1(mol, *ai);
} else if ((*ai)->calcExplicitValence(false) == 8) {
_Valence8SCleanUp1(mol, *ai);
_Valence8SCleanUp1(mol, atom);
} else if (atom->calcExplicitValence(false) == 8) {
_Valence8SCleanUp1(mol, atom);
}
break;
case 35:
if ((*ai)->calcExplicitValence(false) == 3 &&
(*ai)->getFormalCharge() == 0) {
if (atom->calcExplicitValence(false) == 3 &&
atom->getFormalCharge() == 0) {
// connected to Se. Example: PubChem 10787526
if ((*ai)->getDegree() == 1) {
if (atom->getDegree() == 1) {
RWMol::ADJ_ITER nid, end;
boost::tie(nid, end) = mol.getAtomNeighbors(*ai);
boost::tie(nid, end) = mol.getAtomNeighbors(atom);
if (mol.getAtomWithIdx(*nid)->getAtomicNum() == 34) {
mol.getBondBetweenAtoms((*ai)->getIdx(), *nid)
mol.getBondBetweenAtoms(atom->getIdx(), *nid)
->setBondType(Bond::SINGLE);
}
}