Re: [Rdkit-discuss] Removing solvent and ions from dataset

[Pierre-Marie A. <Pie...@un...>]

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
pie...@un...<mailto:pie...@un...>

On 8 Jun 2020, at 08:46, Francois Berenger <ml...@li...<mailto:ml...@li...>> 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
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