mdtraj.compute_distances¶
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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.