Some days have passed, and the Debian mirrors have now picked up the CDK package (unstable only so far), allowing you to sudo aptitude install libcdk-java from your favorite local mirror. The details are available from this packages.debian.org/libcdk-java page. The fact that it is listed as contrib is a small mistake; the package is really main material.

Now, also make sure to install BeanShell (sudo aptitude install bsh), which allows you to start scripting the CDK. For example, consider this simple script:

import org.openscience.cdk.Atom;
Atom atom = new Atom("C");
print(atom);

Save this as content of a file simpleExample.bsh, and run the bsh program to run the script. You will have to set the CLASSPATH, so the full command looks like this on my Linux desktop:

CLASSPATH=/usr/share/java/cdk-interfaces.jar:/usr/share/java/cdk-core.jar:/usr/share/java/cdk-data.jar:/usr/share/java/vecmath1.2-1.14.jar bsh simpleExample.bsh

A wrapper script cdkbsh that adds the CLASSPATH seems desirable here :) But you get the point.

Interestingly, BeanShell also comes with a graphical user interface, as well as a command line based scripting environment. Both make perfect set ups for quickly testing some code. The GUI version xbsh looks like (don’t forget to set the CLASSPATH):

cdk  debian