Cleaned a bit; removed extraneous returns
Removed another extraneous return
Additional extraneous returns...
Added a more informative exception for attempting to replace traj
Moved default protein forcefield ffxml to constructor
deleted default ffxml in abstract BiomoleculeSystemBuilder
Moved local imports to global, made SystemBuilder derive from object.
Restored old driver code to yank.py so that we can compare the two.
modified incorrect method call
Incorporated Patricks changes.