I believe your question is answered in
scripts/java/README  - 

 If you get the output "Benzene has 0 atoms", you need to preload the
OpenBabel
 library as follows:
$ LD_PRELOAD=$OB_LIBDIR/libopenbabel.so $JAVA_HOME/bin/java OBTest


Best regards,
Igor

On Wed, 2011-12-21 at 15:12 -0500, BLizzard R wrote:
> 
> 
> Hello
> 
> I just installed OpenBabel 2.3.1 on my windows vista and tried to 
> call OpenBabel 2.3.1 from a java project. 
> 
> When I tested OpenBabel's java sample: OBTest.java, I met the following 
> problem.
> 
> If I put OBTest.class in a same directory with openbabel.jar and DLL files, 
> the sample worked well.
>  
> But if they were not in same directory, it failed to call OpenBabel, output 
> is "Benzene has 0 atoms.".
> 
> I already set PATH and CLASSPATH which included DLL and jar's path.
> 
> Do I need set any other environment variables? 
> Is there anyone has experience on this problem? 
> 
> BTW: I failed to call OpenBabel in Eclipse, got same results.
> I would appreciate your advice.
> 
> Best regards
> Alex
> 
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Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create 
new or port existing apps to sell to consumers worldwide. Explore the 
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev
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