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.
On Mon, Feb 8, 2016 at 6:43 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 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, 2016 at 12:25 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
>
>> 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 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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