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
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_chi, 4)

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

anglesnp.ndarray, shape=(n_frames, n_chi)

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