Dear Yingfeng,
The problem is the way the aromatic hetero cycles are encoded. They don't fit
the aromaticity model RDKit is using.
For example that works with RDKit by default:
c1c[nH]cc1
But this does not:
c1cncc1
Try the sanifix4.py routine from James Davidson with your smiles.
http://www.rdkit.org/docs/Cookbook.html
It will fix the problem.
Best,
Markus
On 12/19/2013 09:59 PM, Yingfeng Wang 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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