Rotates every atom in the AMPAL object.

        Parameters
        ----------
        angle : float
            Angle that AMPAL object will be rotated.
        axis : 3D Vector (tuple, list, numpy.array)
            Axis about which the AMPAL object will be rotated.
        point : 3D Vector (tuple, list, numpy.array), optional
            Point that the axis lies upon. If `None` then the origin is used.
        radians : bool, optional
            True is `angle` is define in radians, False is degrees.
        inc_alt_states : bool, optional
            If true, will rotate atoms in all states i.e. includes
            alternate conformations for sidechains.

def rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True):
        """Rotates every atom in the AMPAL object.

        Parameters
        ----------
        angle : float
            Angle that AMPAL object will be rotated.
        axis : 3D Vector (tuple, list, numpy.array)
            Axis about which the AMPAL object will be rotated.
        point : 3D Vector (tuple, list, numpy.array), optional
            Point that the axis lies upon. If `None` then the origin is used.
        radians : bool, optional
            True is `angle` is define in radians, False is degrees.
        inc_alt_states : bool, optional
            If true, will rotate atoms in all states i.e. includes
            alternate conformations for sidechains.
        """
        q = Quaternion.angle_and_axis(angle=angle, axis=axis, radians=radians)
        for atom in self.get_atoms(inc_alt_states=inc_alt_states):
            atom._vector = q.rotate_vector(v=atom._vector, point=point)
        return