Another thing to be aware of is that if there are multiple valid
kekulizations that differ only in implicit hydrogen layout, RDKit will
refuse to pick one.
e.g. imidazole: "c1cncn1" will give you a "Can't kekulize mol" error,
whereas "c1c[nH]cn1" and "c1cnc[nH]1" are sanitized without a problem.
Expanding a very small amount on Paolo's answer:
The general rule of thumb is that you should be able to draw a valid
conjugated Kekule structure for the molecule where the ring has 4N+2
electrons.
That works for C1=[S+]SC=N1, which produces the output SMILES c1nc[s+]s1.
-greg
On Mon, Feb 8, 20
Dear Guido,
to be aromatic, that ring system will need a +1 formal charge on one of
the sulfur atoms:
a = Chem.MolFromSmiles("c1ncs[s+]1",sanitize=True)
or
a = Chem.MolFromSmiles("c1nc[s+]s1",sanitize=True)
Best regards,
Paolo
On 08/02/2016 11:19, Wolf-Guido Bolick wrote:
Hi all,
I recent
Hi all,
I recently stumbled over a problem with the kekulization of this structure c1ncss1 .
a = Chem.MolFromSmiles("c1ncss1",sanitize=True)
[11:56:21] Can't kekulize mol
Is it possible to create a sanitized mol-object of this structure?
kind regards,
Guido
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