msmbuilder.metrics.RMSD.prepare_trajectory

RMSD.prepare_trajectory(trajectory)

Prepare the trajectory for RMSD calculation.

Preprocessing includes extracting the relevant atoms, centering the frames, and computing the G matrix.

Parameters:

trajectory : msmbuilder.Trajectory

Molecular dynamics trajectory

Returns:

theodata : array_like

A msmbuilder.metrics.TheoData object, which contains some preprocessed calculations for the RMSD calculation