Added atom_indices to legacy loader.
Added np import to test.
Merge pull request #217 from kyleabeauchamp/atom_indices_lh5

Atom indices lh5
hbonds code
add an assert to the test, and fix it for python3
xh donors
check both a1 and a0 against water
Include this function in the documentation, and slight reformatting of the docstring so that the docs come out correctly
Merge pull request #218 from rmcgibbo/hbonds

Identification of hydrogen bonds
Move RMSD onto the trajectory object
Working version of superpose
a couple minor changes
Add comments about the interleaved store
Followed @schwancr's advice, and moved the RMSD to be a function instead of a method on trajectory
Passed err_msg to eq_ in eq().
Centering was taking 10x longer than RMSD calculation
Add the center file
Compute the traces during the centering. Since why not, we have them in cache anyways.
Merge pull request #221 from kyleabeauchamp/eq_msg

Passed err_msg to eq_ in eq().
Expose the fast centering function in cython, so that the trajectory center_coordinates() method can use it