Hi RDKitters,
I am seeing some weird behaviour from the adding an atom and a bond to an
EditableMol. It works fine in most cases however for this particular fragment
I'm getting an extra hydrogen being added on for some reason.
>>> mol = Chem.MolFromSmiles('O=C1NC2=C(N1)C(=O)NC(=O)N2')
>>> Chem.Kekulize(mol, clearAromaticFlags = True)
>>> tempMol = Chem.EditableMol(mol)
>>> firstIdx = tempMol.AddAtom(dumAtom)
>>> tempMol.AddBond(8, firstIdx, Chem.BondType.SINGLE)
14
>>> print Chem.MolToSmiles(tempMol.GetMol())
[*][NH]1C(=O)NC2=C(NC(=O)N2)C1=O
So this molecule is not RDKit friendly, I don't really know why this is
happening. I guess some form of conversion of an implicit hydrogen to an
explicit hydrogen...
Is there any way of stopping the magic hydrogen from appearing? Or away of
easily getting rid of it after it's appeared?
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
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