Development version is on openbabel. https://github.com/openbabel/openbabel/
-David > On Jul 9, 2014, at 3:10 PM, Stefano Forli <fo...@scripps.edu> wrote: > > Hi, > > thanks for the replies. > > Craig, I think I understood what you meant with the incomplete chiral > description and it > makes sense with the matches returned. > Although, patterns 1 and 2 should not be satisfied in any way, since the > pattern element > "[C@@H]" is not present in the molecule. > > I think this related to what Noel was suggesting (and I suspect it's a bug). > I'm downloading the development version (2.3.2?) from Sourceforge and I'll > test it. > > Thanks, > > > Stefano > >> On 07/09/2014 04:51 AM, Noel O'Boyle wrote: >> Try the development version (bit short on time myself right now). I'm pretty >> sure I >> implemented this. A quick test is: >> >> obabel -:"'F[C@H](Br)Cl" -s "'F[C@@H](Br)Cl" -osmi >> >> ...should be "0 molecules converted" >> >> - Noel >> >> >> On 9 July 2014 00:16, Craig James <cja...@emolecules.com >> <mailto:cja...@emolecules.com>> >> wrote: >> >> On Tue, Jul 8, 2014 at 2:05 PM, Stefano Forli <fo...@scripps.edu >> <mailto:fo...@scripps.edu>> wrote: >> >> Hi all, >> I'm having an issue with SMARTS pattern matching and chirality. >> I'm trying to recognize one specific chiral configuration, but I get >> unexpected >> answers, >> see the following example: >> ------------------------------ >> #!/usr/bin/env python >> import pybel >> ob = pybel.ob >> patterns = [ ('p1' , '[$(*[C@@H])]'), >> ('p2' , 'F[C@@H](Br)Cl'), >> ('p3' , '[$(*[C@H])]'), >> ('p4' , 'F[C@H](Br)Cl'), >> ] >> $ python smartest.py >> Molecule F[C@H](Br)Cl ... >> >> PATTERN p1 : [$(*[C@@H])] => [(1,), (3,), (4,), (5,)] >> PATTERN p2 : F[C@@H](Br)Cl => [(1, 2, 4, 5)] >> PATTERN p3 : [$(*[C@H])] => [(1,), (3,), (4,), (5,)] >> PATTERN p4 : F[C@H](Br)Cl => [(1, 2, 4, 5)] >> >> I would expect patterns p1 and p2 to return no matches, and p3 and p4 >> to succeed. >> >> >> p1 and p3 should match all of the hetero atoms (1,3,4,5), and it does so >> correctly. >> The chiral spec is incomplete, which allows it to match anything. Think >> of it this way: >> >> p1: [$(*[C@@H](*)*)] >> p3: F[C@@H](*)* >> >> Written this way, you can see that p1 and p3 will both match either >> stereo configuration. >> >> >> Although, even carbon chirality is clearly the opposite in the >> molecule and p1, >> p2, the >> script finds matches. >> >> >> It should not match p2. >> >> Craig >> >> >> ------------------------------------------------------------------------------ >> Open source business process management suite built on Java and Eclipse >> Turn processes into business applications with Bonita BPM Community >> Edition >> Quickly connect people, data, and systems into organized workflows >> Winner of BOSSIE, CODIE, OW2 and Gartner awards >> http://p.sf.net/sfu/Bonitasoft >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> <mailto:OpenBabel-discuss@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- > Stefano Forli, PhD > > Staff Scientist > Molecular Graphics Laboratory > Dept. of Integrative Structural > and Computational Biology, MB-112F > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: (858) 784-2055 > fax: (858) 784-2860 > email: fo...@scripps.edu > http://www.scripps.edu/~forli/ > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
