If you are planning to annotate very large data sets it might be worth looking at Vortex.
http://macinchem.org/reviews/vortex/tut24/scripting_vortex24.php Pains matching PubChem 67M structures took under 4 hours. Chris > > Message: 6 > Date: Tue, 15 Mar 2016 10:54:11 -0700 > From: Stefano Forli <fo...@scripps.edu> > Subject: Re: [Open Babel] PAINS filtering > To: mirix <miromo...@gmail.com>, > "openbabel-discuss@lists.sourceforge.net" > <openbabel-discuss@lists.sourceforge.net> > Message-ID: <56e84c43.4010...@scripps.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > 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 [1]. > > 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 > considered. > > Anyway, let me know what would be the best way to share the files, and I'll > do it. > > Cheers, > > S > > > [1] http://blog.rguha.net/?p=850 > ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
