kyleabeauchamp
commented
10 years ago Regarding AtomPairs, I don't think so:
mdtraj.compute_distances?
Returns
-------
distances : np.ndarray, shape=(n_frames, num_pairs), dtype=float
The distance, in each frame, between each pair of atoms.
The continuous contact metric uses mdtraj.compute_contacts to prepare a trajectory, but the problem is that mdtraj function returns both the prepared trajectory and a list of the contacts used.
the prepare_trajectory method should ignore the index list, or at least only return the distances.
AtomPairs may have the same problem?