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 <
[email protected]> wrote:
> Hi
> I'm interested in the number of pi electrons. I have a molecule which has
> smiles C=Cc1ccccc1. And
>
> mol = Chem.MolFromSmiles('C=Cc1ccccc1')
> 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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