Moved driver code to driver.py, eliminated from yank.py
Fixed imports, argument name for Yank constructor
added code to make systems from mol2 and pdb
moved driver code around, added new systembuilders for PDB and mol2 systems.
Not quite ready, but cleaned up code significantly in base classes. Created SmallMoleculeBuilder abstract class.
Refactored the systembuilder.py file (still in progress, adding tests now and additional file format support)
modified driver.py to work with new constructors in systembuilder.py
currently a minimal working setup, can accept mol2 and and pdb for ligand and receptor, respectively
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
Added lazy creation of traj
Fixed forcefield generation of small molecule; use new function in gaff2xml that handles the gaff_dat file
Added the test that I'm currently using to see if systembuilder works. Should be clearned up a bit but still trying to resolve yank error
Added alchemy tests. will attempt to run
Merge pull request #54 from pgrinaway/new-driver

[WIP] Rewrite driver code, move to driver.py, introduce system builder classes