mdtraj.compute_dihedrals¶
- mdtraj.compute_dihedrals(traj, indices, periodic=True, opt=True)[source]¶
Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory.
- Parameters:
traj (Trajectory) – An mtraj trajectory.
indices (np.ndarray, shape=(n_dihedrals, 4), dtype=int) – Each row gives the indices of four atoms which together make a dihedral angle. The angle is between the planes spanned by the first three atoms and the last three atoms, a torsion around the bond between the middle two atoms.
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:
dihedrals – The output array gives, in each frame from the trajectory, each of the n_dihedrals torsion angles. The angles are measured in radians.
- Return type:
np.ndarray, shape=(n_frames, n_dihedrals), dtype=float