Hi Mei,
I do not have an answer to your question about sanifix4.py, but with your
test molecule I do not get a "Can't kekulize mol" problem when
reading/writing it with RDKit. Standard RDKit seems to be doing its job:
In [1]: import rdkit
In [2]: from rdkit import Chem
In [3]: mol = Chem.MolFromSmiles("CCC(N)Cc1cc(=O)[nH]nc1c2ccco2")
In [4]: Chem.MolToSmiles(mol)
Out[4]: 'CCC(N)Cc1cc(=O)[nH]nc1-c1ccco1'
In [5]: Chem.Kekulize(mol)
In [6]: Chem.MolToSmiles(mol)
Out[6]: 'CCC(N)Cc1cc(=O)[nH]nc1-c1ccco1'
In [7]: Chem.MolToSmiles(mol,kekuleSmiles=True)
Out[7]: 'CCC(N)CC1=CC(=O)[NH]N=C1C1=CC=CO1'
In [8]: rdkit.__version__
Out[8]: '2017.03.1'
For your test compound, there is only one valid solution for where the
hydrogens/ double bonds have to be. Can you provide an example where
standard RDKit fails?
Bests,
Christian
*Dr. Christian Kramer*
Computer-Aided Drug Design (CADD) Senior Scientist
F. Hoffmann-La Roche Ltd
Pharma Research and Early Development
Bldg. 092/3.56 C
CH-4070 Basel
Phone +41 61 682 2471
mailto: christian.kra...@roche.com
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On Mon, Oct 9, 2017 at 11:22 PM, Mew Woo <mwo...@mail.com> wrote:
> Hi All,
>
> I have been trying to use sanifix4.py to get around the "Can't kekulize
> mol" problem but without success. I have a library of compounds with
> O=c1cccnn1 fragment unable to kekulize
> (example:CCC(N)Cc1cc(=O)[nH]nc1c2ccco2).
> It has been a few years since this script came ut. I just wonder if anyone
> has further develop this script to enable application to more nitrogen
> aromatics?
>
> Previous discussions:
> http://www.mail-archive.com/rdkit-discuss@lists.
> sourceforge.net/msg01185.html
> http://www.mail-archive.com/rdkit-discuss@lists.
> sourceforge.net/msg01162.html
> http://www.mail-archive.com/rdkit-discuss@lists.
> sourceforge.net/msg01900.html
>
> Regards,
> Mei Woo
>
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