Hi Max, You can also use MolVS 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 pierre-marie.all...@unige.ch<mailto:pierre-marie.all...@unige.ch> On 8 Jun 2020, at 08:46, Francois Berenger <mli...@ligand.eu<mailto:mli...@ligand.eu>> 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 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 Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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