Hi Yingfeng,
You should use the NeutralisingCompounds on the page Markus linked:
http://www.rdkit.org/docs/Cookbook.html. This version has different SMARTS for
neutralising Tetrazoles.
In the version you linked:
# Tetrazoles
Chem.MolFromSmarts('[n-]'): Chem.MolFromSmarts('n'),
In the cookbook version:
# Tetrazoles
('[n-]','[nH]'),
J
On 19 Dec 2013, at 20:59, Yingfeng Wang <ywang...@gmail.com> wrote:
> The original compound is
> CCCc1nc2ccc(Cl)nc2n1-c1ccc(-c2ccc(-c3ccccc3Cc3nn[n-]n3)cc2)cc1
>
> I used the code at the following link
>
> http://code.google.com/p/rdkit/wiki/NeutralisingCompounds
>
> , and got the neutralized compound
>
> CCCc1nc2ccc(Cl)nc2n1-c1ccc(-c2ccc(-c3ccccc3Cc3nnnn3)cc2)cc1
>
> But it has a problem,
>
> >>> mol =
> >>> Chem.MolFromSmiles("CCCc1nc2ccc(Cl)nc2n1-c1ccc(-c2ccc(-c3ccccc3Cc3nnnn3)cc2)cc1")
> [15:53:43] Can't kekulize mol
>
> Could you please help me to check whether there is a workaround?
>
> Thanks.
>
> Yingfeng
>
>
>
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