Hi, I'm working on an application that is trying to do arbitrary
substructure queries across ChEMBL 23. I pretty much followed the
instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres 9.2
instance with RDKit 2016.03.1 all running on a Linux box with 88GB of RAM.

But when running

select count(*) from rdk.mols where m@>'c1cncc2n1ccn2' ;

the query gives back 1775 rows as noted in the page, but takes 2016.182 ms
compared to the 88ms reported on the page.

I realize there are a lot of factors unrelated to RDkit that affect query
performance, but does anybody have suggestions to boost substructure query


Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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