Re: [Open Babel] PAINS filtering (mirix)

Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php Cheers Chris > On 15 Mar 2016, at 12:10, openbabel-discuss-requ...@lists.sourceforge.net > wrote: > > Send OpenBabel-discuss mailing list submissions to > openbabel-discuss@lists.sourceforge.net > > To subscribe or uns

Re: [Open Babel] PAINS filtering

> 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

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 Nab

[Open Babel] Filtering: Ranges, greater than or equal to

Hello, Quick questions on the syntax of the --filter option: - Does it accept greater (or smaller) than OR equal to, for instance "MW>=300"? Well, this is relatively irrelevant. - Does it understand ranges such as "300600"? Best regards, Miro -- View this message in context: http://forums

Re: [Open Babel] PAINS filtering (mirix)

> 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. Acceler

Re: [Open Babel] PAINS filtering

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

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. (altho

Re: [Open Babel] : PAINS filtering

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 Fo