Hello,
I have a question regarding Chemical Features module on RDKit. I realized
that for molecule with SMILES representation "OC1CC1O" from QM9 dataset,
using the code
fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef')
factory = ChemicalFeatures.BuildFeatureFactory(fdefName)
mol = Chem.MolFromSmiles('OC1CC1O')
feats = factory.GetFeaturesForMol(mol)
I get a feature vector with length four, 2 of which are Donor and 2 are
Acceptors. In other words, the output for
for i in range(0, len(feats)):
if feats[i].GetFamily() == 'Donor':
print('feat donor: ',i)
print(feats[i].GetAtomIds())
elif feats[i].GetFamily() == 'Acceptor':
print('feat acptr: ',i)
print(feats[i].GetAtomIds())
is
feat donor: 0
(0,)
feat donor: 1
(4,)
feat acptr: 2
(0,)
feat acptr: 3
(4,)
I was wondering if there is a difference between the two Donors and why I
have two separate donor features? Why it doesn't give a single donor
feature with nodes (0, 4) instead? Thanks you.
Sincerely,
Navid
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