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
- trajTrajectory
Trajectory to compute distances in
- atom_pairsnp.ndarray, shape[num_pairs, 2], dtype=int
Each row gives the indices of two atoms.
- periodicbool, default=True
If periodic is True and the trajectory contains unitcell information, we will compute distances under the minimum image convention.
- optbool, 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
- displacementsnp.ndarray, shape=[n_frames, n_pairs, 3], dtype=float32
The displacememt vector, in each frame, between each pair of atoms.