Re: [Joelib-help] stereochemistry in TestSmarts

[Dave R. <dr...@re...>]

Thanks for your quick respose.  However, this doesn't seem to change the
results I get for TestSmarts.

* Joerg K. Wegner <we...@in...> [2004-06-30 10:18 +0200]:
> Hi all,
> 
> As already submitted be Gerd this is a bug in the SMARTS parser. So i 
> opened a bug tracking task and will close it today and check in to CVS.
> 
> > Bugs item #982570, was opened at 2004-06-30 08:09
> > You can respond by visiting:
> > 
> https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
> > Initial Comment:
> > The SMARTS encoder writes Stereo-Up as '\' and
> > Stereo-Down as '/' but the specs says it vise versa.
> > ----------------------------------------------------------------------
> > You can respond by visiting:
> > 
> https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
> 
> If you want a quick fix change line
> -2467- case ('/'):
> with
> -2479- case ('\\'):
> 
> Kind regards, Joerg
> 
> >Hi everyone, I'm new to Joelib and need a little help.
> >
> >I'm having trouble getting the TestSmarts[1] program to recognize
> >stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
> >molecule made with that same SMILES string.  I've tried several releases,
> >including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
> >with no mismatches.
> >
> >I run: 
> >
> >>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
> >
> >where butene.trans.sdf is:
> >  4  3  0  0  1  0            999 V2000
> >    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >  1  2  1  0  0  0  0
> >  2  3  2  0  0  0  0
> >  3  4  1  0  0  0  0
> >M  END
> >$$$$
> >
> >Any suggestions on what I may be doing wrong or what the problem is?
> >
> >  1. 
> >  http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html
> 
> 
> -- 
> Dipl. Chem. Joerg K. Wegner
> Center of Bioinformatics Tuebingen (ZBIT)
> Department of Computer Architecture
> Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
> Phone: (+49/0) 7071 29 78970
> Fax: (+49/0) 7071 29 5091
> E-Mail: mailto:we...@in...
> WWW:    http://www-ra.informatik.uni-tuebingen.de
> --
> Never mistake motion for action.
>                                     (E. Hemingway)
> 
> Never mistake action for meaningful action.
>                                (Hugo Kubinyi,2004)
> 
> 
> 
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-- 
Dave Roe		dr...@re...