Added 'six' compatibility library dependency to setup.py
Added support for PDB codes, file reading, and filenames.
Made changes based on @rmcgibbo's suggestions.  Updated tests to use PDB code retrieval, switched to simpler test cases for now.
Updated interface based on @peastman suggestions. Started to convert docstrings to numpy format. Updated test with some small PDBs.
Updated command-line interface.
Refined testing.
Increased doctest coverage, converted all public docstrings to numpy format, and refined interfaces with optional values.
Refined tests to only test building, not simulations.
Removed ability to create PDBFixer objects from PdbStructure objects.
Merge pull request #26 from jchodera/master

Add support for specifying PDB codes, filenames, and file objects [ready to merge]