Added RMSD code re issue #50
Better input tests in wrapper
Merge remote-tracking branch 'upstream/master' into rmsd
Swapped traj1 and traj1
Merge remote-tracking branch 'upstream/master' into rmsd
Fixes for robert
Possibly working alignment.py
Added shape arguments to docstring in alignment
Added QCP and tests; currently broken.
Working alignment, passes tests
atom_distance and contact became distance.  Re issue #63
Merge branch 'rmsd' of git://github.com/kyleabeauchamp/mdtraj into kyleabeauchamp-rmsd
Lots of bugfixes and docstring fixes, better transform api
Ran autopep8 --ignore=E501
Added test for IRMSD
Added tests for IRMSD and transform, changed names
using array ensure
Merge branch 'rmsd' of git://github.com/kyleabeauchamp/mdtraj into kyleabeauchamp-rmsd
merged rmsd