mdtraj.compute_chi2¶

mdtraj.compute_chi2(traj, periodic=True, opt=True)¶

Calculate the chi2 torsions of a trajectory. chi2 is the second side chain torsion angle formed between the corresponding 4 atoms over the CB-CG axis.

Parameters:	traj : Trajectory Trajectory for which you want dihedrals. periodic : bool, 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. opt : bool, default=True Use an optimized native library to calculate angles.
Returns:	indices : np.ndarray, shape=(n_chi, 4) The indices of the atoms involved in each of the chi dihedral angles angles : np.ndarray, shape=(n_frames, n_chi) The value of the dihedral angle for each of the angles in each of the frames.