The descriptor "ROTATABLE_BONDS" is used as an example in the online documentation but not actually implemented in the code.
The easiest solution would be this: https://sourceforge.net/p/openbabel/mailman/message/30659149/ Add the following item to /"OBABEL_INSTALLATION_DIRECTORY"/data/plugindefines.txt SmartsDescriptor rotors [!$(*#*)&!D1]-!@[!$(*#*)&!D1] Number of rotatable bonds\n Then you can use the descriptor "rotors" for filtering and other purposed. You may also want to try Filter-It: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html -- Edelmiro Moman, PhD Department of Molecular Medicine Royal College of Surgeons in Ireland POSTAL ADDRESS: L5.08 Trinity Biomedical Sciences Institute - TBSI Trinity College Dublin 152 - 160 Pearse St Dublin 2 IRELAND Phone: +353 (0)1 896 3527 On 5 August 2016 at 05:16, baccilus <destinationsaur...@gmail.com> wrote: > I am using batch files from ZINC and trying to apply Lipinksi filter on it > with openbabel. I am using the official documentation. Although obabel is > able to filter on the basis of MW, HBD and HBA, it seems to failing with > logP and Rotatable bonds. If I include logP and Rotatable bond, it converts > "0" molecules. > Here is an example code that I am using: > > saurabh@saurabh-Inspiron-5521 ~ $ obabel NewcdpsPart2.sdf -O > part2logP-Filter.sdf --filter "logP<=5" > > or this: > > obabel NewcdpsPart2.sdf -O part2logP-Filter.sdf --filter > "ROTATABLE_BONDS<=10" > > This works well: > > obabel NewcdpsPart2.sdf -O part2Filter.sdf --filter "MW<=500 & HBA2<=10 & > HBD<=5" > > I am on Linux and have tried it on Ubuntu 14.04 and 16.04 with same results > Openbabel version 2.3.2 > > > > > > -- > View this message in context: http://forums.openbabel.org/ > Open-Babel-2-3-unable-to-filter-batch-SDF-files-on- > basis-of-logP-and-ROTATABLE-BOND-tp4659418.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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