mdtraj.compute_chi3

mdtraj.compute_chi3(traj, periodic=True, opt=True)[source]

Calculate the chi3 torsions of a trajectory. chi3 is the third side chain torsion angle formed between the corresponding 4 atoms over the CG-CD axis (only the residues ARG, GLN, GLU, LYS & MET have these atoms)

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.