rmcgibbo/mdtraj — pull request #388 by rmcgibbo (2014-03-14 00:34:23+00:00)
Title: Add LPRMSD to mdtraj

- Currently lprmsd is poorly supported in MSMBuilder. It's in Extras, which means that it's not installed by default and tested by travis-ci. This has resulted in it being broken in the current development version of MSMBuilder (https://github.com/SimTk/msmbuilder/issues/356)

- MSMBuilder's lprsmd currently does two pretty independent tasks -- one is the assignment problem using PermuteIndices and the other is the rotation/superpose thing using AltIndices. According to the C docstring in lprsmd.c, using both options simultaniously is not supported. (https://github.com/SimTk/msmbuilder/blob/master/Extras/LPRMSD/src/lprmsd.c#L337)

I propose that we split the two modes into separate APIs. The first can already be handed by MDTraj's, with the superpose() method from python or with [this method](https://github.com/rmcgibbo/mdtraj/blob/master/MDTraj/rmsd/_rmsd.pyx#L380) which is currently not exposed with a high level python API, but could be.