Re: [Joelib-help] stereochemistry in TestSmarts

[Joerg K. W. <we...@in...>]

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)