Hi,
There are improved SMARTS for PAINS in RDKit.
https://github.com/rdkit/rdkit/tree/master/Data/Pains
http://rdkit.blogspot.com/2015/08/curating-pains-filters.html
You can also use ODDT to do the filtering
http://oddt.readthedocs.org/en/latest/#oddt-command-line-interface-cli
example #2. (although currently it uses Rajarshi's SMARTS definition). I
have to update those to Greg's revised version.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-03-15 18:54 GMT+01:00 Stefano Forli <fo...@scripps.edu>:
> 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.
> >
> >
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> --
>
> 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/
>
>
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