Hi RDKitters, This isn't strictly an RDKit based issue, but I guess someone here will be able to help me. I'm trying to identify the index of atoms in a molecule which have one or more hydrogen bonded to them but are not bonded to a dummy atom ([*]).
>>> mol = Chem.MolFromSmiles('[*]CCC[*]')
>>> patt = Chem.MolFromSmarts('[*H1,H2,H3,H4]!~[#0]')
>>> print mol.GetSubstructMatches(patt)
()
I'd expect this to return (1). But it would appear that I'm in the wrong, as
Pipeline Pilot give the same result. Is there a SMARTS query that will give me
the matches that I want or do I have to go back to iterating over atoms?
Many thanks in advance.
Best,
Nick
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