Fix arc.py.  Solves the following exceptions:

/.../mdtraj/formats/arc.pyc in load_arc(filename, top, stride, atom_indices)
     73     mdtraj.ArcTrajectoryFile :  Low level interface to TINKER .arc files
     74     """
---> 75     from mdtraj.trajectory import _parse_topology, Trajectory
     76
     77     # we make it not required in the signature, but required here.  although this

ImportError: No module named trajectory

/.../mdtraj/formats/arc.pyc in load_arc(filename, top, stride, atom_indices)
     87
     88     topology = _parse_topology(top)
---> 89     atom_indices = _cast_indices(atom_indices)
     90     if atom_indices is not None:
     91         topology = topology.subset(atom_indices)

NameError: global name '_cast_indices' is not defined
Update the ARC file parser to account for the (possibility!!) of the periodic
box definition in the 2nd line of each model.  It is not guaranteed to be
present.

The implementation here should introduce a minimal performance regression at
worst, FWIW.  In any case, the ARC format is about as inefficient as they come
and there should not be many large ARC trajectories out there...
Merge branch 'master' of https://github.com/rmcgibbo/mdtraj
Fix the ARC test case.
A number of ARC improvements:

    - Associate .xyz extension with Tinker XYZ format (ARC)

    - Have Tinker XYZ and ARC files create a topology object to use so one does
      not have to be provided. It still uses a provided topology if provided,
      since XYZ and ARC files have no chain, residue, or element information

    - Add test cases for the ARC loader, ARC with PBC information, and make sure
      that ARC files providing their own topology give the same trajectory
      information as a arc file _not_ providing its own trajectory

    - Fix a bug that was causing Travis-CI to fail.  The ARC-related failure
      should be fixed now.

This should now be ready for merge pending the results of CI.
Merge pull request #432 from swails/master

Fix TINKER arc parser (WIP)