Dear all,
I am new to working with the Pharm3D module and I have a question regarding
pharmacophore matching: Is it possible to match a molecule to a pharmacophore
that requires one atom to match to two different features (e.g. H-bond acceptor
and donor)? Here is a dummy code example for a case where I am trying to match
ethanol back to all of its pharmacophore features (I am using rdkit version
2022.09.4):
import os
from rdkit import Chem, RDConfig
from rdkit.Chem import AllChem, ChemicalFeatures, rdDistGeom
from rdkit.Chem.Pharm3D import Pharmacophore, EmbedLib
feature_definition_file = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef')
featFactory = ChemicalFeatures.BuildFeatureFactory(feature_definition_file)
m1 = Chem.MolFromSmiles('CCO') # ethanol
m1 = Chem.AddHs(m1)
AllChem.EmbedMolecule(m1)
features = featFactory.GetFeaturesForMol(m1)
# This is to keep track of features
for i in features:
print(i.GetFamily())
#features = features[1:] #removing donor feature will make it work
print()
for i in features:
print(i.GetFamily())
pcophore = Pharmacophore.Pharmacophore(features)
m2 = Chem.MolFromSmiles('CCO') # ethanol again
m2 = Chem.AddHs(m2)
AllChem.EmbedMolecule(m2)
bool_match, matches = EmbedLib.MatchPharmacophoreToMol(m2, featFactory,
pcophore)
print("bool_match =", bool_match)
boundsMat = rdDistGeom.GetMoleculeBoundsMatrix(m2)
failed, boundsMatMatched, matched, matchDetails =
EmbedLib.MatchPharmacophore(matches, boundsMat, pcophore, useDownsampling=True)
print("matched =", matched)
MatchPharmacophore() appears to be working only by removing one of the two
features derived from the oxygen. Am I doing something wrong or is there a neat
way to fix this?
Kind regards,
Mattis
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