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Fixes #1850 (#2087)

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* Fixes #1850

* docstring update in response to review

* return immediately if the conformer isn't 3D
also header update
This commit is contained in:
Greg Landrum
2018-10-04 14:29:50 +02:00
committed by Brian Kelley
parent a453b8510a
commit b917fd4159
4 changed files with 53 additions and 7 deletions
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16
Code/GraphMol/Chirality.cpp
View File

@@ -326,7 +326,7 @@ void findAtomNeighborDirHelper(const ROMol &mol, const Atom *atom,
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const Bond* bond = mol[*beg];
const Bond *bond = mol[*beg];
// check whether this bond is explictly set to have unknown stereo
if (!hasExplicitUnknownStereo) {
int explicit_unknown_stereo;
@@ -396,7 +396,7 @@ void findAtomNeighborsHelper(const ROMol &mol, const Atom *atom,
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const Bond* bond = mol[*beg];
const Bond *bond = mol[*beg];
Bond::BondDir dir = bond->getBondDir();
if (bond->getBondType() == Bond::SINGLE &&
bond->getIdx() != refBond->getIdx()) {
@@ -432,7 +432,7 @@ bool atomIsCandidateForRingStereochem(const ROMol &mol, const Atom *atom) {
std::vector<const Atom *> nonRingNbrs;
std::vector<const Atom *> ringNbrs;
while (beg != end) {
const Bond* bond = mol[*beg];
const Bond *bond = mol[*beg];
if (!ringInfo->numBondRings(bond->getIdx())) {
nonRingNbrs.push_back(bond->getOtherAtom(atom));
} else {
@@ -933,7 +933,7 @@ void rerankAtoms(const ROMol &mol, UINT_VECT &ranks) {
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const Bond* oBond = mol[*beg];
const Bond *oBond = mol[*beg];
if (oBond->getBondType() == Bond::DOUBLE) {
if (oBond->getStereo() == Bond::STEREOE) {
invars[i] += 1;
@@ -957,7 +957,7 @@ void rerankAtoms(const ROMol &mol, UINT_VECT &ranks) {
}
#endif
}
} // end of chirality namespace
} // namespace Chirality
namespace MolOps {
@@ -1025,7 +1025,7 @@ void assignStereochemistry(ROMol &mol, bool cleanIt, bool force,
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds((*bondIt)->getBeginAtom());
while (!hasStereoBonds && beg != end) {
const Bond* nbond = mol[*beg];
const Bond *nbond = mol[*beg];
++beg;
if (nbond->getBondDir() == Bond::ENDDOWNRIGHT ||
nbond->getBondDir() == Bond::ENDUPRIGHT) {
@@ -1034,7 +1034,7 @@ void assignStereochemistry(ROMol &mol, bool cleanIt, bool force,
}
boost::tie(beg, end) = mol.getAtomBonds((*bondIt)->getEndAtom());
while (!hasStereoBonds && beg != end) {
const Bond* nbond = mol[*beg];
const Bond *nbond = mol[*beg];
++beg;
if (nbond->getBondDir() == Bond::ENDDOWNRIGHT ||
nbond->getBondDir() == Bond::ENDUPRIGHT) {
@@ -1878,6 +1878,8 @@ void detectBondStereochemistry(ROMol &mol, int confId) {
void assignStereochemistryFrom3D(ROMol &mol, int confId,
bool replaceExistingTags) {
if (!mol.getNumConformers() || !mol.getConformer(confId).is3D()) return;
detectBondStereochemistry(mol, confId);
assignChiralTypesFrom3D(mol, confId, replaceExistingTags);
bool force = true;

1
Code/GraphMol/MolOps.h
View File

@@ -839,6 +839,7 @@ RDKIT_GRAPHMOL_EXPORT void assignChiralTypesFrom3D(
\param replaceExistingTags if this flag is true, any existing info about
stereochemistry will be replaced
If the conformer provided is not a 3D conformer, nothing will be done.
*/
RDKIT_GRAPHMOL_EXPORT void assignStereochemistryFrom3D(
ROMol &mol, int confId = -1, bool replaceExistingTags = true);

17
Code/GraphMol/Wrap/MolOps.cpp
View File

@@ -1575,6 +1575,23 @@ struct molops_wrapper {
python::arg("flagPossibleStereoCenters") = false),
docString.c_str());
// ------------------------------------------------------------------------
docString =
"Uses a conformer (should be 3D) to assign ChiralTypes to a molecule's atoms\n\
and stereo flags to its bonds\n\
\n\
ARGUMENTS:\n\
\n\
- mol: the molecule to use\n\
- confId: (optional) the conformation to use \n\
- replaceExistingTags: (optional) replace any existing information about stereochemistry\n\
\n";
python::def("AssignStereochemistryFrom3D",
MolOps::assignStereochemistryFrom3D,
(python::arg("mol"), python::arg("confId") = -1,
python::arg("replaceExistingTags") = true),
docString.c_str());
// ------------------------------------------------------------------------
docString =
"Find bonds than can be cis/trans in a molecule and mark them as 'any'.\n\

26
Code/GraphMol/Wrap/rough_test.py
View File

@@ -4891,6 +4891,32 @@ width='200px' height='200px' >
with self.assertRaises(RuntimeError):
mol = Chem.MolFromRDKitSVG("bad svg")
def testAssignStereochemistryFrom3D(self):
def _stereoTester(mol,expectedCIP,expectedStereo):
mol.UpdatePropertyCache()
self.assertEqual(mol.GetNumAtoms(),9)
self.assertFalse(mol.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(mol.GetBondWithIdx(3).GetStereo(),Chem.BondStereo.STEREONONE)
for bond in mol.GetBonds():
bond.SetBondDir(Chem.BondDir.NONE)
Chem.AssignStereochemistryFrom3D(mol)
self.assertTrue(mol.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(mol.GetAtomWithIdx(1).GetProp("_CIPCode"),expectedCIP)
self.assertEqual(mol.GetBondWithIdx(3).GetStereo(),expectedStereo)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'test_data',
'stereochem.sdf')
suppl = Chem.SDMolSupplier(fileN, sanitize=False)
expected = (
("R",Chem.BondStereo.STEREOZ),
("R",Chem.BondStereo.STEREOE),
("S",Chem.BondStereo.STEREOZ),
("S",Chem.BondStereo.STEREOE),
)
for i,mol in enumerate(suppl):
cip,stereo = expected[i]
_stereoTester(mol,cip,stereo)
def testGitHub2082(self):
ctab="""
MJ150720