Thanks Chris, The line you gave seemed to do the trick - after I escaped out the tilde. Is the usage of the tilde to reverse the sense of the filter documented? I would have thought the -v option would be logical.
Sieve seems to do what I want - almost. It looks like it filters using SMARTS - but all my undesirable groups are in SDF format. How do I convert to SMARTS? OpenBabel doesn't seem to do it (although it can filter using them, strangely). I realise I could potentially use SMILES as input but this doesn't work in some cases, e.g. 'C1=CC=CC=C1' is a benzene ring in SMILES format but according to the following link will not match benzene if it's used as a SMARTS string. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html cheers, Doug Quoting Chris Morley <c.mor...@gaseq.co.uk>: > On 08/09/2010 13:17, Douglas Houston wrote: >> Hi, >> >> According to this page: >> >> http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints.html#fingerprints >> >> I can use the -s option with the name of a file, e.g.: >> >> babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf >> >> will write out all the compounds in mymols.sdf that contain the group >> in Substructure.sdf. However, what I'd like is the opposite, i.e. to >> write out everything that doesn't match. I tried using -v instead of >> -s but this didn't work. > > I think the following will do what you want > babel mymols.sdf -s ~Substructure.sdf mymols_filtered.sdf >> >> It would also be nice if I could use a file that contained more than >> one entry, i.e. the file Substructure.sdf could define multiple >> fragments that I don't want in my molecules, rather than having to >> run Babel on each one separately. > > It would have to be decided whether the combination was AND or OR. > What you want is NOT(frag1 OR frag2 OR...) > In the related --filter option there is an implicit AND between tests, > but I think for both the -s filter and its inverse the OR behaviour is > more intuitive. >> >> Would this be doable before the final release? > > It may be, but I am about to go on holiday, so don't hold your breath. > > Thanks for this suggestion. Other suggestions for useful features are > very welcome. > > You could look at the Sieve program, http://www.silicos.be/sieve.html > which is an industrial-strength filtering program, now using OpenBabel. > > Chris > > ------------------------------------------------------------------------------ > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _____________________________________________________ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
