mdtraj.compute_phi

mdtraj.compute_phi(traj, periodic=True, opt=True)

Calculate the phi torsions of a trajectory.

Parameters

trajTrajectory

Trajectory for which you want dihedrals.

periodicbool, default=True

If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

optbool, default=True

Use an optimized native library to calculate angles.

Returns

indicesnp.ndarray, shape=(n_phi, 4)

The indices of the atoms involved in each of the phi dihedral angles

anglesnp.ndarray, shape=(n_frames, n_phi)

The value of the dihedral angle for each of the angles in each of the frames.