Created a Molecule class which loads a pdb or the first frame from an
xyz file into graph of a molecule.
Also created a utilities module for generic useful functions
and a wrapper to create a quiet pymol instance.
Deleted unnecessary functions from utilities
A basic molecule class that stores a molecule as a network.
Understands XYZ and PDB files. Has been tested with it's own
unit tester.
A Base class for a simple molecular system representing a molecule
as a networkx graph.  Understands PDB and XYZ files using the pymol
interface, but could easily be modified to add other files that pymol
understands.  tested and passed its own test class also.
Modified the structure of the playground/molecule to
several new classes including parser, analyser, molecularsystem.

Incorporated the protein class as a sub class in the molecule file.

added a testing system which tests the pymol parser and ensures
that the system basically works.
Added two new files
Merge pull request #1 from cjforman/master

Incorporate Chris's molecule stuff