I have found a second bug with cdk under the applet.
For some reason, the problem is with the method Atom.getAtomicNumber(),
which is actually inherited from Element.getAtomicNumber().
This method is always returning 0 when the applet is running.
You can demonstrate this by running the following script against the applet:
If you look at the java console while this is executing you will see the
output as it iterates through all the atoms.
This works fine under the application, but not under the applet.
The selection code *does* work under the applet. You can demonstrate this
with the following commands
Let me know if I can be of further assistance.