@staticmethod
def _calculate_alpha(radii, cutoff=0.45):
    """Calculate parameter alpha to tune the size of the basins.

        .. math::
            u_{AB} &= \\frac{R_A - R_B}{R_A + R_B} \\\\
            a_{AB} &= \\frac{u_{AB}}{u_{AB}^2 - 1}

        Parameters
        ----------
        radii : np.array(N,)
            Covalent radii of each atoms in the molecule
        cutoff : float, optional
            Cutoff need to be smaller than 0.5 to guarantee monotonous
            transformation.

        Returns
        -------
        np.ndarray(N, N)
            alpha value for each pair of atoms
        """
    u_ab = (radii[:, (None)] - radii) / (radii[:, (None)] + radii)
    alpha = u_ab / (u_ab ** 2 - 1)
    alpha[alpha > cutoff] = cutoff
    alpha[alpha < -cutoff] = -cutoff
    return alpha
