Hi Greg,
My goal when bringing up the example of imidazole was to determine what the
AtomPair pi-electron number was counting, and test my understanding after
reviewing the [original paper](https://pubs.acs.org/doi/10.1021/ci00046a002).
If the AtomPair implementation was counting the number of pi-electron each
atom was contributing, then I thought inputing imidazole would show one and
two for the nitrogens. Once I found that discrepancy I asked the question.
(you could consider that it's really counting the number of orbitals
> involved in pi bonding).
Ah, knowing this the convention now makes interrupting the AtomPairs and
Topological Torsions easier. Maybe this should be documented within the
module itself?
v/r,
Ben
On Mon, Dec 2, 2019 at 4:40 AM Greg Landrum <greg.land...@gmail.com> wrote:
>
> The functions in the AtomPairs module are really intended to be used when
> calculating the Atom Pairs and Topological Torsions fingerprints. For those
> fingerprints the RDKit considers atoms in aromatic rings to have a single
> pi electron (you could consider that it's really counting the number of
> orbitals involved in pi bonding).
>
> Are you looking to calculate the number of electrons in a pi system or
> something like that? Since that's not currently immediately possible
> (though that's fixable), I'm curious why you want to do that.
>
> -greg
>
>
>
> On Fri, Nov 22, 2019 at 5:08 AM Benjamin Datko <
> benjamin.datko....@gmail.com> wrote:
>
>> Hi all,
>>
>> When counting the number of pi-electrons in Imidazole, I would expect a
>> total of 6 pi-electrons, and the contribution of pi-electrons from the
>> nitrogen atoms showing 2 and 1.
>>
>> But both pyScorePair and NumPiElectrons within AtomPairs only show 5
>> pi-electrons, missing the pi-electron from one of the nitrogens. What am
>> I missing?
>>
>> >>> from rdkit import rdBase
>> >>> rdBase.rdkitVersion,rdBase.boostVersion
>>
>> ('2019.03.4', '1_70')
>>
>> >>> from rdkit import Chem
>> >>> from rdkit.Chem.AtomPairs import Pairs
>>
>> >>> m = Chem.MolFromSmiles('C1=CN=CN1')
>> >>> score = Pairs.pyScorePair(m.GetAtomWithIdx(2),m.GetAtomWithIdx(4),3)
>> >>> Pairs.ExplainPairScore(score)
>> (('N', 2, 1), 3, ('N', 2, 1))
>>
>> >>> [Chem.AtomPairs.Utils.NumPiElectrons(atom) for atom in m.GetAtoms()]
>> [1, 1, 1, 1, 1]
>>
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>>
>
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