msmbuilder.metrics.baseclasses.AbstractDistanceMetric.prepare_trajectory

AbstractDistanceMetric.prepare_trajectory(trajectory)

Prepare trajectory on a format that is more conventient to take distances on.

Parameters:

trajecory : msmbuilder.Trajectory

Trajectory to prepare

Returns:

prepared_traj : array-like

the exact form of the prepared_traj is subclass specific, but it should support fancy indexing

Notes

For RMSD, this is going to mean making word-aligned padded arrays (TheoData) suitable for faste calculation, for dihedral-space distances means computing the dihedral angles, etc.