Force return in iterload when chunk = 0
Force return in iterload when chunk = 0
Added comment.
Better fix for chunk0, added simple test.
Merge pull request #424 from kyleabeauchamp/chunk2

Chunk2
Silence pending deprication warning
Merge pull request #426 from rmcgibbo/warning

Silence pending deprication warning
Fix reading in an Amber prmtop file as a topology when it has an ATOMIC_NUMBER
section:

/.../mdtraj/formats/prmtop.pyc
in load_prmtop(filename)
    200         if 'ATOMIC_NUMBER' in raw_data:
    201             try:
--> 202                 element = elem.Element.get_by_atomic_number(int(raw_data['ATOMIC_NUMBER'][index]))
    203             except KeyError:
    204                 element = None

AttributeError: type object 'Element' has no attribute 'get_by_atomic_number'
Recognize .parm7 as an Amber prmtop file.  This is the file extension used
typically by Amber programs as well as VMD.  Makes sense to recognize the
extension here as well.
Fix Amber mdcrd parser so it does not rely on whitespace-delimited coordinate
fields. The Amber mdcrd file prints out 10 numbers per line in the format %8.3f.
If a number takes up 8 spaces (i.e., -100.000 <= X <= 1000.000), there will be
no space between that number and the next.  Since the units are Angstroms, this
is equivalent to saying no atom can move more than 10 nm over the course of the
simulation.  These mdcrd files are quite common.
Merge pull request #429 from swails/master

Fix reading in an Amber prmtop file as a topology when it has an ATOMIC_NUMBER section
Merge pull request #430 from swails/parmext

Associate .parm7 extension with Amber prmtop
Merge remote-tracking branch 'origin/master' into fixmdcrd
Add a test case for an Amber mdcrd file.  This is a contrived example taken from
the Amber test suite in which one coordinate was modified to fill all 8 spaces.
Since I never use mdcrd files myself (NetCDF only), and I usually enable
wrapping, I didn't have an example on-hand.
Add atomic numbers to the prmtop to make this a more extensive test.
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
Merge pull request #431 from swails/fixmdcrd

Fix Amber mdcrd parser
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.