Re: [Rdkit-discuss] SDWriter kekulizes by default

[Michal K. <mic...@gm...>]

Hello Greg,
>>> Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
[14:25:55] Can't kekulize mol

This smiles was generated from ChemSketch. OpenBabel converts it to
O=C1NC=CC1=C1C=C(c2[nH]ccc2)NC1=O which is correctly interpreted by
RDKit (no problems with kekulization).
But IMHO both representations are correct, am I wrong?
Best wishes,
Michal


On 5 December 2013 12:19, Greg Landrum <gre...@gm...> wrote:
> Hi Michal,
>
> On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec <mic...@gm...>
> wrote:
>>
>> Hello,
>> Is it possible to suppress kekulization by SDWriter? I get the
>> following error on a call to SDWriter.write:
>> ValueError: Sanitization error: Can't kekulize mol
>> But some molecules can't be kekulized using RDKit's algorithm, even
>> though they are otherwise 'correct'.
>
>
> hmm, I'd love to see examples of those if you can share them.
>
>>
>> I browsed the sources and it seems that SDWriter calls MolToMolBlock
>> with the default parameter kekulize=True. Can this parameter be
>> exposed in SDWriter?
>
>
> Yep, I'll get it in for the next release.
>
> -greg
>