mdtraj.compute_displacements¶

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

Compute the displacement vector between pairs of atoms in each frame of a trajectory.

Parameters:

traj : Trajectory Trajectory to compute distances in atom_pairs : np.ndarray, shape[num_pairs, 2], dtype=int Each row gives the indices of two atoms. 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 minimum image convention calculation implementation is over 1000x faster than the naive numpy implementation.

Returns:

displacements : np.ndarray, shape=[n_frames, n_pairs, 3], dtype=float32 The displacememt vector, in each frame, between each pair of atoms.