Re: [Rdkit-discuss] SMARTS queries using FP in Postgres Cartridge

[JP <jea...@in...>]

Ugly as it may sound, in this case, it is probably faster to do separate
"like" or postgres regex (i.e. ~) on the SMILES string column (rather than
on the mol) for this.


-
Jean-Paul Ebejer
Early Stage Researcher


On 6 March 2012 11:08, Greg Landrum <gre...@gm...> wrote:

> On Tue, Mar 6, 2012 at 11:53 AM, JP <jea...@in...> wrote:
> > Just for comparison, how large is your test database?
>
> Those queries were from chembl12, so it's a bit over 1 million molecules.
>
> > Do you think I should convert '[!#1;!#6;!#7;!#8;!#9;!#16;!Cl;!Br;!I]' to
> > multiple SMILES queries instead?  Do you figure that would be faster?
>
> Unfortunately not. There just aren't any bits in the fingerprint (as
> currently constructed) that are going to help make this query fast.
>
> -greg
>