Hi RDKit community,
I am not familiar with how partial charges are calculated and I couldn't
seem to find anything in my searches.
If you run the code below, you'll see that the partial charges are always
the same, even though the embedded mol is different - which leads me to
believe these partial charge calculations are not dependent on conformers
(which I always thought they were?)
Can someone with more knowledge than me confirm my hypothesis? Also does
rdkit have any partial charge calculators that are dependent on conformers?
mol = Chem.MolFromSmiles('C[C@@](CC1=CC(O)=C(O)C=C1)(NN)C(O)=O')
AllChem.EmbedMolecule(mol, AllChem.ETKDG())
AllChem.ComputeGasteigerCharges(mol)
contribs = [float(mol.GetAtomWithIdx(i).GetProp('_GasteigerCharge')) for i
in range(mol.GetNumAtoms())]
fps = AllChem.MMFFGetMoleculeProperties(mol)
mmff_partial_charges = [fps.GetMMFFPartialCharge(x) for x in
range(mol.GetNumAtoms())]
print(mmff_partial_charges)
print(contribs)
Thanks,
Hao
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