def check_mol( mol ):
match, mList = EmbedLib.MatchPharmacophoreToMol( mol, feat_fact, pcophore)
if match:
res = []
num_match = len( mList )
for i in range( num_match ):
num_feature = len( mList[i] )
for j in range( num_feature ):
print mList[i][j].GetAtomIds(), mList[i][j].GetFamily()
bounds = rdDistGeom.GetMoleculeBoundsMatrix( mol )
pList = EmbedLib.GetAllPharmacophoreMatches( mList, bounds, pcophore )
#pList = EmbedLib.MatchPharmacophore( mList, bounds, pcophore )
print pList
#print raw_input("-----")
num_match = len( pList )
print num_match
phMatches = []
for i in range( num_match ):
num_feature = len( pList[i] )
phMatch = []
for j in range( num_feature ):
phMatch.append( pList[i][j].GetAtomIds() )
phMatches.append( phMatch )
for phMatch in phMatches:
bm, embeds, nFail = EmbedLib.EmbedPharmacophore( mol, phMatch, pcophore, count=20, silent=1 )
print "-----> embeds num:", len( embeds )
for embed in embeds:
AllChem.UFFOPtimizeMolecule( embed )
align_data = rdAliginment.GetAlignmetTransform( bm, bounds )
AllChem.TransformMol( embed, align_data[1] )
res.append( embed )
return res
def check_mol(mol):
res = []
mol.RemoveAllConformers()
match, mList = EmbedLib.MatchPharmacophoreToMol(mol, feat_fact, pcophore)
#mList = [ m for m in Set( mList ) ]
if match:
num_match = len(mList)
for i in range(num_match):
num_feature = len(mList[i])
for j in range(num_feature):
print mList[i][j].GetAtomIds(), mList[i][j].GetFamily()
bounds = rdDistGeom.GetMoleculeBoundsMatrix(mol)
pList = EmbedLib.GetAllPharmacophoreMatches(mList, bounds, pcophore)
num_match = len(pList)
phMatches = []
for i in range(num_match):
num_feature = len(pList[i])
phMatch = []
for j in range(num_feature):
phMatch.append(pList[i][j].GetAtomIds())
phMatches.append(phMatch)
for phMatch in phMatches:
bm, embeds, nFail = EmbedLib.EmbedPharmacophore(mol,
phMatch,
pcophore,
count=5,
silent=1)
print "-----> embeds num:", len(embeds)
for embed in embeds:
AllChem.UFFOptimizeMolecule(embed)
feats = feat_fact.GetFeaturesForMol(embed)
feats_dict = GetFeatsPerAtoms(feats)
match_feats = [feats_dict[atomid] for atomid in phMatch]
pro_mat = [list(feat.GetPos()) for feat in match_feats]
align_data = rdAlignment.GetAlignmentTransform(
ref_mat, pro_mat, maxIterations=200)
AllChem.TransformMol(embed, align_data[1])
print align_data[0]
print align_data[1]
res.append(embed)
else:
print "no hits"
return res