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 On 03/15/2016 08:21 AM, mirix wrote: > There you go: > > http://pastebin.ca/raw/3401877 <http://pastebin.ca/raw/3401877> > > This comes from here: > > http://blog.rguha.net/?p=850 > > > > > -- > View this message in context: > http://forums.openbabel.org/PAINS-filtering-tp4659223p4659226.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > 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 > -- Stefano Forli, PhD Assistant Professor of Integrative Structural and Computational Biology, Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ 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
