msmbuilder.metrics.AtomPairs.many_to_many

AtomPairs.many_to_many(prepared_traj1, prepared_traj2, indices1, indices2)

Get a matrix of distances from each frame in a set to each other frame in a second set.

Calculate a MATRIX of distances from the frames in prepared_traj1 with indices indices1 to the frames in prepared_traj2 with indices indices2, using supplied metric.

Parameters:

prepared_traj1 : ndarray

First prepared trajectory

prepared_traj2 : ndarray

Second prepared trajectory

indices1 : array_like

list of indices in prepared_traj1 to calculate the distances from

indices2 : array_like

list of indices in prepared_traj2 to calculate the distances to

Returns:

distances : ndarray

A 2D array of shape len(indices1) * len(indices2)