Added xyz-reading code from dynamiq r200.
Skeleton of load_xyz, the xyz translator.
Draft of (most of) XYZTranslator.

I think this is about how things should work (still missing implementation
of a few things related to `storage`). Committing and holding until I check
details with JHP.
Merge branch 'master' into xyz_iss1

Bringing current versions of everything into xyz so I can use the correct
data structures to build the XYZTranslator.
Equality tests in TrajFile; rename XYZTranslator.

Renamed module and class to match XYZTranslator.

Added equality functions in TrajFile for integration testing:
* `frames_equal(frame1,frame2)`
* `trajs_equal(traj1, traj2)`
Draft of nose tests for XYZTranslator.

More integration tests than unit tests. Current XYZTranslator is far from
passing tests -- there's my goal for the next day! (or two)
Implement XYZTranslator.guess_fname_format & test.

And yes, it passes the test.
Demostrate problem with nonchemical elements.

We can't build storage in the XYZTranslator due to the use of nonchemical
(arbitrary) elements. I suspect the problem is that mdtraj's
Topology.from_openmm() doesn't load changes to the element database in the
openmm.app.element class. (The test fails with a key error when
mdtraj.element.Element._elements_by_symbol[key] faces a key from the newly
added elements.) Committing this so others can see what's happening and
advise on solutions.
Well, it only took me 4 hours to find this bug...
XYZTranslator up to opening the .nc file.

Still need to fill the .nc file, and read the data back in.
Well, it only took me 4 hours to find this bug...
Changes to get sandbox.py running.

Main important changes are the addition of init_classes() call and setting
self.storage.simulator. I think these were necessary to get things running.

Others might undo my switch from CUDA to CPU, and I switched Alanine_system
to 'auto' mode from 'restore' (since I had nothing to restore).
XYZTranslator.trajfile2trajectory() runs.

Still need to complete the round trip to test, but at least this doesn't
crash for the first half of the trip!
XYZ->netCDF round trip except labels, masses.

Positions and velocities seem to round trip well.
Round trip works for a single trajectory!

NB: this is round tripping from TrajFile to trajectory formats. There's no
guarantee that this will work if we create intermediate files (in
particular, I'm not sure that we can assume that arbitrary element
definitions are written to NetCDF file -- but I'll have to ask JHP how best
to handle that.)
XYZ can generate nc file. Atoms can share elem type.

Still unsure whether the nc file has all the informations, especially
arbitrary element types.
XYZ->netCDF round trip for single trajectory files.

Also added README.md for the xyz_files/ directory and geisslerene000000.xyz
as a test file in XYZ format.
Merge pull request #6 from dwhswenson/xyz_iss1

Single trajectory XYZ<=>netCDF round trip
XYZTranslator converts to/from dirs of xyz trajs.

The .nc file can hold all the trajectories in one file; XYZs use directories
of files.
Polished XYZTranslator and its tests.

Reorganized the code, filled in some docs, made comments clear, improved the
tests significantly. Basically, this is done.