def bonded(self, atom_a, atom_b):
    """
    Check if atom_a is bonded to atom_b given the bonding settings

    Parameters
    ----------
    atom_a, atom_b : Atom objects
        The atoms to be compared
    Returns
    -------
    bonded_bool : bool
        True if the atoms are bonded and False if not
    """
    bonded_bool = atom_a.dist(atom_b, ref=self.bonding) <= self.thresh
    return bonded_bool