Substructure search with SMARTS query against ChEMBLDB #rdkit #razi #pychembldb

Recently I often use razi for making structure search because it is very easy to integrate many workflow written in python.

Today I would like to show how to perform substructure search with SMARTS query in ChEMBL. Because I’m modifying pychembldb to integrate razi for enabling structure search in pychembldb.

To perform substructure seach with SMARTS in razi, SMARTS string should be convert query object with mol_from_smarts method.

So I wrote sample code which search MCS from given compound list and perform search with the MCS. Code is shown below.

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Modified version of pychembldb seems work fine. But sometime it takes long time for retrieving response, it depends on query smarts.

I would like to know way to improve the search speed if there is. Any suggestions comments are greatly appreciated ;)


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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