msmbuilder.metrics.ContinuousContact.all_pairwise

ContinuousContact.all_pairwise(prepared_traj)

Calculate a condense” distance matrix of all the pairwise distances between each frame with each other frame in prepared_traj

The condensed distance matrix can be converted to the redundant square form if desired

Parameters:

prepared_traj1 : ndarray

Prepared trajectory

Returns:

distances : ndarray

1D vector of length len(pairwise_traj) choose 2 where the i*jth entry contains the distance between prepared_traj[i] and prepared_traj[j]

See also

scipy.spatial.distance.pdist, scipy.spatial.distance.squareform