msmbuilder.metrics.RMSD.all_pairwise¶

RMSD.all_pairwise(prepared_traj)¶

Calculate condensed distance metric of all pairwise distances

See scipy.spatial.distance.squareform for information on how to convert the condensed distance matrix to a redundant square matrix

Parameters:

prepared_traj : array_like

Prepared trajectory

Returns:

Y : ndarray

A 1D array containing the distance from each frame to each other frame