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..
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.