Hi Yingfeng,
Let me remind you some chemistry basics:
Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it
requires 1 electron to complete octet. Hence it's valency is 1.
Thus it's not a surprise that your smiles is generating an error.
In order to check for get the charge st
John,
Thanks. I meet a couple of problems with the code you suggested.
Input smiles:
[O-][Cl+3]([O-])([O-])O
Output smiles:
O[Cl+3](O)(O)O
First of, the input smiles is not charged, so the neutralizing function is
supposed to do nothing. Could you please help me to know whether there is a
f
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.MolFromSm
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
The original compound is
CCCc1nc2ccc(Cl)nc2n1-c1ccc(-c2ccc(-c3c3Cc3nn[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(-c3c3Cc33)cc2)cc1
But it has a pr
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