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 <ghiandon...@gmail.com> 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* > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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