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. I never tried to use the module so I tested the module and compared to razi with simple structure query. Simple code is below..

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.


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

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: