mdtraj.compute_chi3¶
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mdtraj.
compute_chi3
(traj, periodic=True, opt=True)¶ 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.