GreenGroup/RMG-Py — pull request #85 by rwest (2012-06-20 22:53:28+00:00)
Title: Refactoring of Molecule module and change to how graphs are stored.

Two major things on this branch:

1. a new "molecule" package containing lots of things related to molecules.
2. a change to how graphs are stored (Now storing dict of edges on Vertex and vertices on Edge.)

The second of these was complicated and inevitably introduced some bugs, several of which we have so far found, but an unknown number (perhaps zero!) have not been.
This pull request is to collect debugging efforts so we can merge ASAP, ideally once we have fixed the unit tests!