Determines the covalent bonds in a molecule.

        Args:
            tol (float): The tol to determine bonds in a structure. See
                CovalentBond.is_bonded.

        Returns:
            List of bonds

def get_covalent_bonds(self, tol=0.2):
        """
        Determines the covalent bonds in a molecule.

        Args:
            tol (float): The tol to determine bonds in a structure. See
                CovalentBond.is_bonded.

        Returns:
            List of bonds
        """
        bonds = []
        for site1, site2 in itertools.combinations(self._sites, 2):
            if CovalentBond.is_bonded(site1, site2, tol):
                bonds.append(CovalentBond(site1, site2))
        return bonds