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 <paolo.tosco.m...@gmail.com> 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 <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 >> > -- *Gianmarco*
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