Re: [Rdkit-discuss] changing atomic charges with ReactionFromSmarts

[Chris E. <cge...@gm...>]

Hi Jan

Your code doesn't change the charges because the reaction SMARTS doesn't
tell it to. If you say -

rxn_smarts = ['[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O+0:3]']

- the charges in the product are explicitly defined and you should get the
result you expect.

Best regards,
Chris

On 25 January 2018 at 10:18, Jan Halborg Jensen <jhj...@ch...> wrote:

>
> The following code changes the bond order correctly but does not change
> the charges accordingly
>
> Any idea what I am doing wrong?
>
> Thanks, Jan
>
>
> def clean_charges(mol):
>     rxn_smarts = ['[N+:1]=[*:2]-[O-:3]>>[N:1]-[*:2]=[O:3]']
>
>     for smarts in rxn_smarts:
>         rxn = AllChem.ReactionFromSmarts(smarts)
>         ps = rxn.RunReactants((mol,))
>         for x in ps:
>             mol = x[0]
>
>     #rdmolops.SanitizeMol(mol)
>     return mol
>
> mol = Chem.MolFromSmiles("C[NH+]=C(C)[O-]")
>
> mol = clean_charges(mol)
> print Chem.MolToSmiles(mol)
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