SimTk/msmbuilder — pull request #427 by schwancr (2014-06-18 00:36:24+00:00)
Title: [WIP] Fix for LPRMSD after mdtraj merge

LPRMSD no longer worked when we moved mdtraj into msmbuilder.

It's still necessary because the ```altindices``` behavior is not available in mdtraj (at least to my knowledge).

I attempted to fix it by just appending the old RMSD.TheoData class into lprmsd.py