mdtraj.compute_distances¶

mdtraj.compute_distances(traj, atom_pairs, periodic=True, opt=True)¶

Compute the distances between pairs of atoms in each frame.

Parameters:

traj : Trajectory An mtraj trajectory. atom_pairs : np.ndarray, shape=(num_pairs, 2), dtype=int Each row gives the indices of two atoms involved in the interaction. periodic : bool, default=True If periodic is True and the trajectory contains unitcell information, we will compute distances under the minimum image convention. opt : bool, default=True Use an optimized native library to calculate distances. Our optimized SSE minimum image convention calculation implementation is over 1000x faster than the naive numpy implementation.

Returns:

distances : np.ndarray, shape=(n_frames, num_pairs), dtype=float The distance, in each frame, between each pair of atoms.