This makes a number of changes:

- numpy is now a hard requirement
- coordinates always has shape (frame, natom, 3)
- you can set coordinates, and it is reshaped to a (frame, natom, 3) ndarray,
  and the first frame's coordinates are assigned to the xx, xy, and xz
  attributes of each atom in the Structure
- did the same thing with the 'box' attribute (which is also always a
  numpy.ndarray now)
- add tests for this new functionality