Hi Max, Third alternative: https://github.com/chembl/ChEMBL_Structure_Pipeline <https://github.com/chembl/ChEMBL_Structure_Pipeline>
parent_molblock, _ = standardizer.get_parent_molblock(o_molblock) This will strip the molecule. Nicolas > On 8 Jun 2020, at 08:19, Pierre-Marie Allard <[email protected]> > wrote: > > Hi Max, > > You can also use MolVS https://molvs.readthedocs.io/en/latest/ > <https://molvs.readthedocs.io/en/latest/> > This should suit most of your needs, > > PM > _________________________________________ > > Pierre-Marie Allard > Research Assistant - Natural Products Chemistry > ISPSO - UniGe - Geneva > [email protected] <mailto:[email protected]> > >> On 8 Jun 2020, at 08:46, Francois Berenger <[email protected] >> <mailto:[email protected]>> wrote: >> >> On 06/06/2020 17:33, Max Pinheiro Jr wrote: >>> Hi RDkit team, >>> I am working on a chemically diverse dataset of smiles strings and I >>> need to do some preprocessing to clean a bit the data before starting >>> the modeling part. So I was looking for some tools or built-in >>> functions in RDkit to make such preprocessing by removing, for >>> instance, solvent (water) molecules and ions. I found the >>> "SaltRemover" module that may solve my problem with removing ions from >>> the database, but I could not find an equivalent module for the case >>> of solvent molecules. Does anyone know a specific tool in RDkit (or >>> any other python program) to make such preprocessing in the smile >>> strings? If so, could you please provide just a simple example of how >>> to do it? I will be really thankful for any help you may provide. >> >> I have used this program several times: >> >> https://github.com/flatkinson/standardiser >> <https://github.com/flatkinson/standardiser> >> >> You can try this: >> ``` >> pip3 install chemo-standardizer >> standardiser -i input.smi -o output_std.smi >> ``` >> >> I believe it uses rdkit under the hood. >> >> Regards, >> F. >> >>> Max Pinheiro Jr >>> --------------------------------------------- >>> Université Aix-Marseille, France >>> Institut de Chimie Radicalaire >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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