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Fixes #3330 (#3869)

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This commit is contained in:
Greg Landrum
2021-03-06 01:59:37 +01:00
committed by GitHub
parent 31169bdc4e
commit 6fbe4f788d
2 changed files with 57 additions and 31 deletions
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72
Code/GraphMol/MolOps.cpp
View File

@@ -264,45 +264,55 @@ void assignRadicals(RWMol &mol) {
!atom->getAtomicNum()) {
continue;
}
double accum = 0.0;
RWMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
accum += mol[*beg]->getValenceContrib(atom);
++beg;
}
accum += atom->getNumExplicitHs();
int totalValence = static_cast<int>(accum + 0.1);
const auto &valens =
PeriodicTable::getTable()->getValenceList(atom->getAtomicNum());
int chg = atom->getFormalCharge();
int nOuter =
PeriodicTable::getTable()->getNouterElecs(atom->getAtomicNum());
int baseCount = 8;
if (atom->getAtomicNum() == 1 || atom->getAtomicNum() == 2) {
baseCount = 2;
}
if (valens.size() != 1 || valens[0] != -1) {
double accum = 0.0;
RWMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
accum += mol[*beg]->getValenceContrib(atom);
++beg;
}
accum += atom->getNumExplicitHs();
int totalValence = static_cast<int>(accum + 0.1);
int baseCount = 8;
if (atom->getAtomicNum() == 1 || atom->getAtomicNum() == 2) {
baseCount = 2;
}
// applies to later (more electronegative) elements:
int numRadicals = baseCount - nOuter - totalValence + chg;
if (numRadicals < 0) {
numRadicals = 0;
// can the atom be "hypervalent"? (was github #447)
const INT_VECT &valens =
PeriodicTable::getTable()->getValenceList(atom->getAtomicNum());
if (valens.size() > 1) {
for (auto val : valens) {
if (val - totalValence + chg >= 0) {
numRadicals = val - totalValence + chg;
break;
// applies to later (more electronegative) elements:
int numRadicals = baseCount - nOuter - totalValence + chg;
if (numRadicals < 0) {
numRadicals = 0;
// can the atom be "hypervalent"? (was github #447)
const INT_VECT &valens =
PeriodicTable::getTable()->getValenceList(atom->getAtomicNum());
if (valens.size() > 1) {
for (auto val : valens) {
if (val - totalValence + chg >= 0) {
numRadicals = val - totalValence + chg;
break;
}
}
}
}
// applies to earlier elements:
int numRadicals2 = nOuter - totalValence - chg;
if (numRadicals2 >= 0) {
numRadicals = std::min(numRadicals, numRadicals2);
}
atom->setNumRadicalElectrons(numRadicals);
} else {
// if this is an atom where we have no preferred valence info at all,
// e.g. for transition metals, then we shouldn't be guessing. This was
// #3330
auto nValence = nOuter - chg;
atom->setNumRadicalElectrons(nValence % 2);
}
// applies to earlier elements:
int numRadicals2 = nOuter - totalValence - chg;
if (numRadicals2 >= 0) {
numRadicals = std::min(numRadicals, numRadicals2);
}
atom->setNumRadicalElectrons(numRadicals);
}
}

16
Code/GraphMol/catch_graphmol.cpp
View File

@@ -1481,4 +1481,20 @@ TEST_CASE("needsHs function", "[chemistry]") {
REQUIRE(m);
CHECK(!MolOps::needsHs(*m));
}
}
TEST_CASE(
"github #3330: incorrect number of radicals electrons calculated for "
"metals",
"[chemistry][metals]") {
SECTION("basics") {
std::vector<std::pair<std::string, unsigned int>> data = {
{"[Mn+2]", 1}, {"[Mn+1]", 0}, {"[Mn]", 1}, {"[Mn-1]", 0},
{"[C]", 4}, {"[C+1]", 3}, {"[C-1]", 3}};
for (const auto &pr : data) {
std::unique_ptr<ROMol> m(SmilesToMol(pr.first));
REQUIRE(m);
CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == pr.second);
}
}
}