How to pass data from Java applet to client side python script?
If you go for JavaScript I'm assuming it would run in a browser and therefore to communicate with anything else it would make HTTP requests (e.g. POST or GET URLs), so the client/server arrangement is unavoidable.
Therefore you would need to turn your Python code into a web application, using something like CherryPy to map URLs to your methods. You could then pass data around using JSON notation.
I have a python script which does various number-crunching jobs and now need to put a graphical front-end on it (a molecular editor in which a user draws a compound to pass to the script) to allow others in the lab to use it more easily.  The available editors are Java applets, standalone Java or written in JavaScript.   
I would greatly appreciate any advice on the best strategy to put the editor and script together.  I really don't want to get into client/server arrangement and envisage a self-contained install on each machine i.e. "client only". Is it better to start off in javascript and pass the output in some way to python and then run the python script from within js.  Or (preferably) is there some way to run applets (or standalone java) within python e.g. in Tkinter or some other GUI and "on-click" take the output from the editor into the python script for the crunching bit. 
Thanks for any pointers - book chapters, useful projects/libraries and links to examples would be great.