msmbuilder.metrics.ContinuousContact.prepare_trajectory

ContinuousContact.prepare_trajectory(trajectory)

Prepare a trajectory for distance calculations based on the contact map.

Each frame in the trajectory will be represented by a vector where each entries represents the distance between two residues in the structure. Depending on what contacts you pick to use, this can be a ‘native biased’ picture or not.

Returns:

pairwise_distances : ndarray

1D array of various residue-residue distances