[Joelib-help] stereochemistry in TestSmarts

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

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
-- 
Dave Roe		dr...@re...