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progress on #563

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This commit is contained in:
Greg Landrum
2015-08-14 07:19:52 +02:00
parent a43f63dd46
commit 55f6fed10d
3 changed files with 30 additions and 25 deletions
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40
Code/GraphMol/DistGeomHelpers/Embedder.cpp
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@@ -140,24 +140,21 @@ namespace RDKit {
void _findChiralSets(const ROMol &mol, DistGeom::VECT_CHIRALSET &chiralCenters) {
ROMol::ConstAtomIterator ati;
INT_PAIR_VECT nbrs;
INT_VECT nbrs;
ROMol::OEDGE_ITER beg,end;
Atom *oatom;
for (ati = mol.beginAtoms(); ati != mol.endAtoms(); ati++) {
if ((*ati)->getAtomicNum() != 1) { //skip hydrogens
if ((*ati)->hasProp(common_properties::_CIPCode)) {
Atom::ChiralType chiralType=(*ati)->getChiralType();
if (chiralType==Atom::CHI_TETRAHEDRAL_CW || chiralType==Atom::CHI_TETRAHEDRAL_CCW) {
// make a chiral set from the neighbors
nbrs.clear();
nbrs.reserve(4);
// find the neighbors of this atom and enter them into the
// nbr list along with their CIPRanks
// nbr list
boost::tie(beg,end) = mol.getAtomBonds(*ati);
while (beg != end) {
oatom = mol[*beg]->getOtherAtom(*ati);
unsigned int rank;
oatom->getProp(common_properties::_CIPRank, rank);
INT_PAIR rAid(rank, oatom->getIdx());
nbrs.push_back(rAid);
nbrs.push_back(mol[*beg]->getOtherAtomIdx(*ati));
++beg;
}
// if we have less than 4 heavy atoms as neighbors,
@@ -166,33 +163,26 @@ namespace RDKit {
bool includeSelf = false;
CHECK_INVARIANT(nbrs.size() >= 3, "Cannot be a chiral center");
std::sort(nbrs.begin(), nbrs.end());
if (nbrs.size() < 4) {
unsigned int rank;
(*ati)->getProp(common_properties::_CIPRank, rank);
INT_PAIR rAid(rank, (*ati)->getIdx());
nbrs.insert(nbrs.begin(), rAid);
nbrs.insert(nbrs.begin(), (*ati)->getIdx());
includeSelf = true;
}
// now create a chiral set and set the upper and lower bound on the volume
std::string cipCode;
(*ati)->getProp(common_properties::_CIPCode, cipCode);
if (cipCode == "S") {
if (chiralType == Atom::CHI_TETRAHEDRAL_CW) {
// postive chiral volume
DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0].second,
nbrs[1].second,
nbrs[2].second,
nbrs[3].second,
DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0],
nbrs[1],
nbrs[2],
nbrs[3],
5.0, 100.0);
DistGeom::ChiralSetPtr cptr(cset);
chiralCenters.push_back(cptr);
} else {
DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0].second,
nbrs[1].second,
nbrs[2].second,
nbrs[3].second,
DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0],
nbrs[1],
nbrs[2],
nbrs[3],
-100.0, -5.0);
DistGeom::ChiralSetPtr cptr(cset);
chiralCenters.push_back(cptr);

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Regress/Data/chembl_20_chiral.smi.gz Normal file
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15
Regress/Scripts/chiral_embed.py Normal file
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@@ -0,0 +1,15 @@
from rdkit import Chem
from rdkit.Chem import AllChem
suppl = Chem.SmilesMolSupplier('../Data/chembl_20_chiral.smi')
for i,mol in enumerate(suppl):
csmi = Chem.MolToSmiles(mol,True)
for j in range(100):
mh = Chem.AddHs(mol)
AllChem.EmbedMolecule(mh,randomSeed=j+1)
Chem.AssignAtomChiralTagsFromStructure(mh)
nm = Chem.RemoveHs(mh)
smi = Chem.MolToSmiles(nm,True)
if smi!=csmi:
print('%d %d %s:\n%s\n%s'%(i,j,mol.GetProp('_Name'),csmi,smi))