Re: [Rdkit-discuss] Adjusting/neutralising the formal charges on a molecule

[Paolo T. <pao...@gm...>]

Hi Gianmarco,

that's a radical cation, not just a cation, so you'll need to adjust the
number of radical electrons first, then you may neutralize using
Chem.MolStandardize.rdMolStandardize.Uncharger as documented in the RDKit
CookBook:

https://www.rdkit.org/docs/Cookbook.html#neutralizing-molecules

from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize

uc = rdMolStandardize.Uncharger()
Chem.MolToSmiles(uc.uncharge(Chem.MolFromSmiles("[CH+]1C2CCCCC2CC2CCCCC12")))

'C1CCC2CC3CCCCC3CC2C1'


Cheers,
p.


On Fri, Apr 8, 2022 at 4:16 PM Gianmarco Ghiandoni <ghi...@gm...>
wrote:

> Hi all again,
>
> I wonder whether there is a way in RDKit to neutralise the charges of
> compounds such as "[C+]1C2CCCCC2CC2CCCCC12". Specifically, in my case I am
> dealing with only carbon sequences.
>
> Thanks,
> --
> *Gianmarco*
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