FW analysis make easily with rdkit contrib FW package #rdkit #chemoinformatics #memo

Last week I enjoyed RDKit UGM 2022. It was really great and exciting evenif I participated there from online. I hope I could participate RDKIT UGM 2023 locally ;)

As you know RDKit is one of the useful OSS package for chemoinformatician. It has nice community and be developed actively. I respect the community and developer’s effort!

I found new contrib package in rdkit github repo it was “FreeWilson“(FW). The logic of FW analyisis is simple but powerful approach to find the better conbination of R groups.
Original article is shown here. And PatWalter disclosed and described the code and usecase in his repo and blog post.

And fortunately, we can also use FW from rdkit contrib package ;)

Now new version of rdkit(2022.09.1) isn’t available from conda-forge but I could get new version from original repo and FW package could install with pip command.

(base)$ conda activate chemo_py309
(chemo_py309)$ gh repo clone rdkit/rdkit
(chemo_py309)$ cd rdkit/Contrib/FreeWilson
(chemo_py309)$ pip install .

After installation of FW, I run code with sample data. My code (almost same as readme) is uploaded to my gist which is show below.

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By using the package, user can conduct FW analysis really easily. Original repo shows another approach which uses FMCS to get scaffold for the dataset.

Ofcourse FW is not always propose correct combination however it is chance for thinking non additive SAR (e.g https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00525-z)

I felt the package is useful and easy to use. So I would like to apply it in my internal project ;)

Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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