mdtraj.compute_angles¶

mdtraj.compute_angles(traj, angle_indices, periodic=True, opt=True)¶

Compute the bond angles between the supplied triplets of indices in each frame of a trajectory.

Parameters:

traj : Trajectory An mdtraj trajectory. angle_indices : np.ndarray, shape=(num_pairs, 2), dtype=int Each row gives the indices of three atoms which together make an angle. periodic : bool, default=True If periodic is True and the trajectory contains unitcell information, we will treat angles that cross periodic images using the minimum image convention. opt : bool, default=True Use an optimized native library to calculate distances. Our optimized SSE angle calculation implementation is 10-20x faster than the (itself optimized) numpy implementation.

Returns:

angles : np.ndarray, shape=[n_frames, n_angles], dtype=float The angles are in radians