Extract macro cyclic compounds from ChEMBLDB with rdkit_cartridge #chemoinformatics #RDKit

As you know, RDKit has really useful postgreSQL cartridge. So it’s easy to do substructure or similarity search of query structure from postgresql ChEMBLDB.

But I don’t know how to retrieve only macrocyclic compound from ChEMBLDB with the cartridge.

I searched RDKit mailing list and got good answer! Thanks for the community.

This is the discussion.
https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CACmCNSx57BAhmz-ppLC04XovcCn1CWNM8HTvVWaU3_Ad-EB%2Btw%40mail.gmail.com/#msg36781319

From the discussion, to retrieve macrocyclic compound I need to use SMARTS query like [r{x-y] which x and y means ring-size.

I tried to use the query and uploaded my trial. Here is an my gist. Following example retrieve molecule which has over 12 membered rings.

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It seems works well.

‘::qmol’ is requireed when SMARTS query is used for WHERE clause.

In summary, RDKit psql cartridge is really useful tool for many chemoinformatician. (IMHO)

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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.

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