How to use the parmed.amber.AmberMask function in ParmEd

flat_waters_within_distance = [item for sublist in self.waters_within_distance for item in sublist]
            num_atoms = system.getNumParticles()
            for atom in range(num_atoms):
                if atom in flat_waters_all and atom not in flat_waters_within_distance:
                    system.setParticleMass(atom, 0*unit.daltons)
                else:
                    pass

        if self.freeze_protein:
            #if active freezes protein residues beyond a certain cutoff
            res_list = []
            for traj in self.binding_mode_traj:
                lig_pos = traj.openmm_positions(0)
                structure.positions = lig_pos

                mask = parmed.amber.AmberMask(self.structure,"((:HOH)|(:%s<:%f))&!(:%s)" % ('LIG', self.freeze_protein, 'NA,CL'))
                site_idx = [i for i in mask.Selected()]
                res_list = res_list + site_idx
            res_list = list(set(res_list))
            num_atoms = system.getNumParticles()
            for atom in range(num_atoms):
                if self.freeze_waters > 0:
                    if atom in res_list or atom in flat_waters_within_distance:
                        pass
                    else:
                        system.setParticleMass(atom, 0*unit.daltons)
                else:
                    if atom in res_list:
                        pass
                    else:
                        system.setParticleMass(atom, 0*unit.daltons)

structure : parmed.Structure()
            Structure of the system, used for atom selection.
        selection : str
            AmberMask selection that gets converted to a list of atom indices.

        Returns
        -------
        mask_idx : list of int
            List of atom indices.

        References
        ----------
        .. [amber-syntax] J. Swails, ParmEd Documentation (2015). http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax

        """
        mask = parmed.amber.AmberMask(structure, str(selection))
        mask_idx = [i for i in mask.Selected()]
        return mask_idx

structure : parmed.Structure()
            Structure of the system, used for atom selection.
        selection : str
            AmberMask selection that gets converted to a list of atom indices.

        Returns
        -------
        mask_idx : list of int
            List of atom indices.

        References
        ----------
        .. [amber-syntax] J. Swails, ParmEd Documentation (2015). http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax

        """
        mask = parmed.amber.AmberMask(structure, str(selection))
        mask_idx = [i for i in mask.Selected()]
        return mask_idx

structure : parmed.Structure()
        Structure of the system, used for atom selection.
    selection : str
        AmberMask selection that gets converted to a list of atom indices.

    Returns
    -------
    mask_idx : list of int
        List of atom indices.

    References
    ----------
    .. [amber-syntax] J. Swails, ParmEd Documentation (2015). http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax

    """
    mask = parmed.amber.AmberMask(structure, str(selection))
    mask_idx = [i for i in mask.Selected()]
    return mask_idx

suggest valid residues or atoms.

    Parameters
    ----------
    structure : parmed.Structure
        The structure of the simulated system
    selection : str
        The selection string uses Amber selection syntax to select atoms to be
        restrained/frozen during simulation.
    logger : logging.Logger
        Records information or streams to terminal.

    """

    try:
        mask = parmed.amber.AmberMask(structure, str(selection))
        mask_idx = [i for i in mask.Selected()]
    except:
        mask_idx = []
    if not mask_idx:
        if ':' in selection:
            res_set = set(residue.name for residue in structure.residues)
            logger.error("'{}' was not a valid Amber selection. \n\tValid residue names: {}".format(
                selection, res_set))
        elif '@' in selection:
            atom_set = set(atom.name for atom in structure.atoms)
            logger.error("'{}' was not a valid Amber selection. Valid atoms: {}".format(selection, atom_set))
        return False
    else:
        return True