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
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-]'):
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.
3 matches
Mail list logo
