That's an interesting question...
How about using a charged dummy atom?
In [6]: rxn = AllChem.ReactionFromSmarts('[Fe+2:1]>>[Fe+3:1].[*-1]')
In [7]: ps = rxn.RunReactants((Chem.MolFromSmiles('[Fe+2]'),))
[04:53:52] product 1 has no mapped atoms.
In [8]: Chem.MolToSmiles(ps[0][0])
Out[8]: '[Fe+3]'
In [9]: Chem.MolToSmiles(ps[0][1])
Out[9]: '[*-]'
If you wanted the "electron" to be directly associated with the product
molecule instead of being a separate product, you can use grouping
parentheses:
In [10]: rxn = AllChem.ReactionFromSmarts('[Fe+2:1]>>([Fe+3:1].[*-1])')
In [11]: ps = rxn.RunReactants((Chem.MolFromSmiles('[Fe+2]'),))
In [12]: Chem.MolToSmiles(ps[0][0])
Out[12]: '[*-].[Fe+3]'
Does that help?
-greg
On Thu, Mar 1, 2018 at 12:29 AM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> RDkit Discussion Group,
>
> I am trying to get RDkit to recognize reactants and products in RedOx
> reactions including
> reactions which include explicit electrons using SMILES as patterns. Does
> anyone have any
> suggestions or ideas for how to deal with an explicit electron?
>
> I have tried:
>
> pattern = '[-1]'
> match = mol_object.GetSubstructMatches(pattern)
>
> but this does not work.
>
> I am hesitant to use [H-1], which is read in and is processed, but it
> technically refers to
> hydride which is a legitimate molecule species and is obviously not an
> electron.
>
> I can think of (possibly) another hack involving a large atomic number
> (beyond typical organics),
> but I am wondering if someone has a more intelligent solution, or perhaps
> there is some unusual
> or special SMILES notation that I am not aware of.
>
> Ideas or suggestions are welcome. Thank you.
>
> Regards,
> Jim Metz
> Northwestern University
>
>
>
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