Thank you so much. Silicos-it solved it for me. But I think it is really odd that they would include a function in the example of official documentation that doesn't actually exist.
On Fri, Aug 5, 2016 at 5:42 PM, mirix [via Open Babel] < ml-node+s957263n4659421...@n4.nabble.com> wrote: > 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 <[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4659421&i=0>> 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/Op >> en-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 >> [hidden email] <http:///user/SendEmail.jtp?type=node&node=4659421&i=1> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > OpenBabel-discuss mailing list > [hidden email] <http:///user/SendEmail.jtp?type=node&node=4659421&i=2> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > http://forums.openbabel.org/Open-Babel-2-3-unable-to- > filter-batch-SDF-files-on-basis-of-logP-and-ROTATABLE- > BOND-tp4659418p4659421.html > To unsubscribe from Open Babel 2.3 unable to filter batch SDF files on > basis of logP and ROTATABLE_BOND, click here > <http://forums.openbabel.org/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4659418&code=ZGVzdGluYXRpb25zYXVyYWJoQGdtYWlsLmNvbXw0NjU5NDE4fDg2Mjk5MTAx> > . > NAML > <http://forums.openbabel.org/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- Saurabh -- 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-tp4659418p4659425.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
