Re: [Open Babel] : PAINS filtering

2016-03-15 Thread Chris Swain
rom: 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...@scri

Re: [Open Babel] PAINS filtering

2016-03-15 Thread Maciek Wójcikowski
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.

Re: [Open Babel] PAINS filtering

2016-03-15 Thread Stefano Forli
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

Re: [Open Babel] PAINS filtering (mirix)

2016-03-15 Thread Geoffrey Hutchison
> Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php This reminds me that we should integrate the Silicos tools into the main OB distribution. Thanks, -Geoff -- Transform Data into Opportunity.

Re: [Open Babel] PAINS filtering

2016-03-15 Thread mirix
There you go: 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

Re: [Open Babel] PAINS filtering

2016-03-15 Thread Geoffrey Hutchison
> I am able to filter my SDF file using one SMARTS pattern at a time, but I > was wondering if OB provides a simple way of filtering all PAINS in one go. At the moment, no. But if someone posts the set of SMARTS patterns, it’s easy to add this as a filter to plugindefines.txt. -Geoff

Re: [Open Babel] PAINS filtering (mirix)

2016-03-15 Thread Chris Swain
; > > > Today's Topics: > > 1. PAINS filtering (mirix) > > > -- > > Message: 1 > Date: Mon, 14 Mar 2016 08:36:56 -0700 (PDT) > From: mirix <miromo...@gmail.com> > Subject: [Open Babel] PAINS filtering > To: openbabel-discuss@lists.sourceforge.net > M

[Open Babel] PAINS filtering

2016-03-14 Thread mirix
Hello, I have downloaded a subset of the PubChem database in SDF format. On the other hand, I have a file containing SMARTS for about 500 undesirable functionalities. I am able to filter my SDF file using one SMARTS pattern at a time, but I was wondering if OB provides a simple way of filtering