One of the only positives that has come out of the swine flu pandemic is a 3 day break that has allowed me to get cracking on the project after a week long hiatus.
With Shobit working on converting .py files into installer setups, I began working on creating the py app itself. The first task being exporting the Blender molecule meshes to Panda. This is achieved using the Chicken Exporter, a python script that converts the .blend files to .egg files forming a common ground between Blender and Panda.
Here's the download link : http://sourceforge.net/projects/chicken-export/
While exporting UV wrapped meshes works perfectly fine, there have been a few problems with armatures, but for all practical purposes, our meshes can be painlessly transfered to Panda.
The first executable shall be posted shortly.