It appears Molecular Workbench is open source as well.
We recommend that the Eclipse IDE be used to get the source code. You can access it through https://svn.concord.org/svn/projects/ using SVN. Once you connect to our SVN server, check out trunk/common/java/simulations/mw/. The source code can also be browsed online.
Question on EJS and Molecular Workbench:
Can EJS be used to view
1. their implementation?
2. their java files be added to library of EJS ?
Question about Molecular Workbench
I don't understand their project enough to comment precisely, but
how to I see the equations that make this work?