The following code changes the bond order correctly but does not change the
charges accordingly
Any idea what I am doing wrong?
Thanks, Jan
def clean_charges(mol):
rxn_smarts = ['[N+:1]=[*:2]-[O-:3]>>[N:1]-[*:2]=[O:3]']
for smarts in rxn_smarts:
rxn = AllChem.ReactionFromSmarts(smarts)
ps = rxn.RunReactants((mol,))
for x in ps:
mol = x[0]
#rdmolops.SanitizeMol(mol)
return mol
mol = Chem.MolFromSmiles("C[NH+]=C(C)[O-]")
mol = clean_charges(mol)
print Chem.MolToSmiles(mol)
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