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
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.
Expose the fast centering function in cython, so that the trajectory center_coordinates() method can use it
Faster centering during superpose
Merge branch 'master' of github.com:rmcgibbo/mdtraj into superpose2
Fix OpenMP pragma
Merge pull request #220 from rmcgibbo/superpose2

add rmsd() and superpose() methods to Trajectory, remove alignment requirement