Fast substructure search module of RDKit #rdkit #memo

Recently I posted an example of substructure search with razi, rdkit postgres cartridge. It works well but sometime I would like to conduct SSS faster. And I could get useful information from Greg, yamasakit.

rdSubstructLibrary module can perform fast substructure search! The details are described in rdkit official blog post. https://rdkit.blogspot.com/2018/02/introducing-substructlibrary.html I never tried to use the module so I tested the module and compared to razi with simple structure query. Simple code is below..

https://gist.github.com/iwatobipen/5346eab9025144780da669b4d840b545

In my PC sss with rdSubstructLibrary almost 10 times faster than postgresq-rdkit cartridge.

So I think it is very useful for many chemoinformatitian. However the module can’t store compound ID so if I use the approach to ChEMBL DB, I think I need to make index-ChEMBL ID table for getting compound relative assay data.

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Published by iwatobipen

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

One thought on “Fast substructure search module of RDKit #rdkit #memo

  1. would you please add your blog list for better searching experience. Thank you for your great work

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