If you can describe the substructures by a SMARTS string, it's fairly easy by customising FP4. Here's the output of FP4 for the arylbromide:
C:\Users\Noel>obabel -:c1(Br)ccc(Br)c1 -ofpt -xf fp4 -xs > Secondary_carbon Alkylbromide 1 molecule converted How to customise?... C:\Users\Noel>obabel -L fp4 One of the fingerprints fp4 SMARTS patterns specified in the file SMARTS_InteLigand.txt PatternFP is definable ...edit SMARTS_InteLigand.txt or copy it to your current directory and edit it then. - Noel On 8 December 2012 13:51, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Hi, > > is it possible with openbabel to classify a molecule based on substructures? > > E.g.: > > 110-dichlorodecane.sdf > alkyl chloride > > 11122334455666-tetradecafluorohexane.sdf > alkyl fluoride > > 111-trimethoxyethane.sdf > orthocarboxylic acid derivative > orthoester > > 13-dibromobenzene.sdf > aryl bromide > aromatic compound > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
