In the development code, -v now can take a file name. For -v and -s the files can contain multiple pattern molecules (which are OR-ed).
Chris On 08/09/2010 17:32, Douglas Houston wrote: > 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 > > > > > > No virus found in this incoming message. > Checked by AVG - www.avg.com > Version: 9.0.851 / Virus Database: 271.1.1/3121 - Release Date: 09/08/10 > 07:07:00 > ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
