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

[Gianmarco G. <ghi...@gm...>]

Hello Paolo,

Thanks a lot for your replies. Looks like I have finally managed to achieve
what I wanted to do!

Have a good weekend,

Giammy

On Fri, 8 Apr 2022 at 15:37, Paolo Tosco <pao...@gm...> wrote:

> 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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>

-- 
*Gianmarco*