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.

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)


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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