Hi Alireza,

On Wed, Feb 23, 2011 at 12:34 AM, Alireza Kashani
<alireza.kashanip...@gmail.com> wrote:
> I exported all jar files from, cdk/dis/jar into my java classpath

For your use case I recommend to build a single jar from source with:

  ant clean dist-large

Which will create a dist/jar/cdk-1.3.8.jar in the source folder.

Then, you can do on Linux (what operating system are you using?):

$ cp /path/to/cdk/dist/jar/cdk-1.3.8.jar .
$ CLASSPATH=cdk-1.3.8.jar jython

which allows me to do on the Jython command line:

>>> import org.openscience.cdk.Atom

Important all classes with your command

>>> import org.openscience.cdk.*;

does not work for me. Please try to import just the Atom class, which
will tell you if you placed the CDK jars in the right spot.

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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