Pains matching PubChem 67M structures took under 4 hours.
> Message: 6
> Date: Tue, 15 Mar 2016 10:54:11 -0700
> From: Stefano Forli <[hidden email]>
> Subject: Re: [Open Babel] PAINS filtering
> To: mirix <[hidden email]>,
> "[hidden email]"
> <[hidden email]>
> Message-ID: <[hidden email]>
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> About that, a while ago I had compiled an OB-compatible data file with the three pattern
> classes (L15, L150 and M150) from Raj Gua .
> Dirt cheap implementation with Pybel works fine, but the main issue is timing. Processing
> a Mol2 file with 1000 random molecules from the ZINC database takes about 13 seconds.
> Not bad, but not even fast: to process a pretty large library for virtual screning (e.g,
> ChemBridge library, 1.5M compounds) would take about 5.4 hours.
> I'm not sure if there's a way to speed up the process, but if so, it should be definitely
> Anyway, let me know what would be the best way to share the files, and I'll do it.
>  http://blog.rguha.net/?p=850 >