Hi Eleanor,
The behavior you describe below is a bug (it's this one:
https://github.com/rdkit/rdkit/issues/334). It had been fixed in the C++
version of the code, but I forgot to fix the older python implementation. I
just made that fix and checked it in, so the github version should yield
the expected behavior.
Thanks for pointing this out.
-greg
On Tue, Oct 14, 2014 at 3:22 PM, Eleanor J Gardiner
e.gardi...@sheffield.ac.uk wrote:
Hi
I'm interested in the number of pi electrons. I have a molecule which has
smiles C=Cc1c1. And
mol = Chem.MolFromSmiles('C=Cc1c1')
for atom in mol.GetAtoms():
npibond = Chem.AtomPairs.Utils.NumPiElectrons(atom)
print npibond
gives
1
1
1
1
1
1
1
1
as expected.
However the molecule comes from a reaction and is coded as
[CH2:3]=[CH:1][c:2]1[cH:5][cH:7][cH:9][cH:8][cH:6]1
Using this in the above gives
3
2
1
1
1
1
1
1
Surely the atom-mapping should not make a difference?
Thanks
Eleanor
--
Dr Eleanor Gardiner
Information School
University of Sheffield
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