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

trajTrajectory

An mdtraj trajectory.

angle_indicesnp.ndarray, shape=(num_angles, 3), dtype=int

Each row gives the indices of three atoms which together make an angle.

periodicbool, 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.

optbool, 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

anglesnp.ndarray, shape=[n_frames, n_angles], dtype=float

The angles are in radians