Beg pardon, mea culpa and I tell a lie. It should have been: C:\Users\Noel>obabel -:c1(Br)cc(Br)ccc1 -ofpt -xf fp4 -xs > Arylbromide Aromatic 1 molecule converted
On 8 December 2012 16:41, Noel O'Boyle <baoille...@gmail.com> wrote: > 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
