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

sys.stderr.write('CPEIN generation complete!\n')

if __name__ == '__main__':
    opt = parser.parse_args()

    # List all residues
    if opt.list:
        list_residues()
        sys.exit(0)

    # Describe requested residues
    if opt.descres is not None:
        if len(opt.descres) == 0 or (len(opt.descres) == 1 and
                                     opt.descres[0].upper() == 'ALL'):
            print_residues(residues.titratable_residues,0)
        else:
            opt.descres = process_arglist(opt.descres, str)
            print_residues(opt.descres,1)
        sys.exit(0)

    # Go ahead and make the CPEIN file.
    try:
        main(opt)
    except ParmedError as e:
        sys.exit('%s: %s' % (type(e).__name__, e))
    sys.exit(0)

sys.stderr.write('CEIN generation complete!\n')

if __name__ == '__main__':
    opt = parser.parse_args()

    # List all residues
    if opt.list:
        list_residues()
        sys.exit(0)

    # Describe requested residues
    if opt.descres is not None:
        if len(opt.descres) == 0 or (len(opt.descres) == 1 and
                                     opt.descres[0].upper() == 'ALL'):
            print_residues(residues.titratable_residues,0)
        else:
            opt.descres = process_arglist(opt.descres, str)
            print_residues(opt.descres,1)
        sys.exit(0)

    # Go ahead and make the CEIN file.
    try:
        main(opt)
    except ParmedError as e:
        sys.exit('%s: %s' % (type(e).__name__, e))
    sys.exit(0)

sys.stderr.write('CPIN generation complete!\n')

if __name__ == '__main__':
    opt = parser.parse_args()

    # List all residues
    if opt.list:
        list_residues()
        sys.exit(0)

    # Describe requested residues
    if opt.descres is not None:
        if len(opt.descres) == 0 or (len(opt.descres) == 1 and
                                     opt.descres[0].upper() == 'ALL'):
            print_residues(residues.titratable_residues,0)
        else:
            opt.descres = process_arglist(opt.descres, str)
            print_residues(opt.descres,1)
        sys.exit(0)

    # Go ahead and make the CPIN file.
    try:
        main(opt)
    except ParmedError as e:
        sys.exit('%s: %s' % (type(e).__name__, e))
    sys.exit(0)

def list_residues():
    """ Lists all titratable residues defined in residues.py """
    line = LineBuffer(sys.stdout)
    strarray = []
    for resname in residues.titratable_residues:
        if getattr(residues, resname).typ == "ph":
            strarray.append(resname)
    line.add_words(', '.join(strarray).split(),
                   space_delimited=True)
    line.flush()

raise AmberError('-intdiel must be either 1 or 2 currently')

    # Print warning about old format
    if opt.oldfmt:
        sys.stderr.write('Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
                         '         You should use the new format for simulations with temperatures other than 300.0 Kelvins\n')

    # Set the list of residue names we will be willing to titrate
    titratable_residues = []
    if notresnames is not None:
        for resname in residues.titratable_residues:
            if resname in notresnames: continue
            titratable_residues.append(resname)
    elif resnames is not None:
        for resname in resnames:
            if not resname in residues.titratable_residues:
                raise AmberError('%s is not a titratable residue!' % resname)
            elif not getattr(residues, resname).typ == "ph":
                raise AmberError('%s is not a pH-active titratable residue!' % resname)
            titratable_residues.append(resname)
    else:
        for resname in residues.titratable_residues:
            if getattr(residues, resname).typ == "ph":
                titratable_residues.append(resname)

    solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
                    'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']

    # Filter titratable residues based on min and max pKa
    new_reslist = []
    for res in titratable_residues:
        if getattr(residues, res).pKa < minpka: continue

if resnames is not None and notresnames is not None:
        raise AmberError('Cannot specify -resnames and -notresnames together')

    if opt.intdiel != 1 and opt.intdiel != 2:
        raise AmberError('-intdiel must be either 1 or 2 currently')

    # Set the list of residue names we will be willing to titrate
    titratable_residues = []
    if notresnames is not None:
        for resname in residues.titratable_residues:
            if resname in notresnames: continue
            titratable_residues.append(resname)
    elif resnames is not None:
        for resname in resnames:
            if not resname in residues.titratable_residues:
                raise AmberError('%s is not a titratable residue!' % resname)
            elif not getattr(residues, resname).typ == "redox":
                raise AmberError('%s is not a redox-active titratable residue!' % resname)
            titratable_residues.append(resname)
    else:
        for resname in residues.titratable_residues:
            if getattr(residues, resname).typ == "redox":
                titratable_residues.append(resname)

    solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
                    'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']

    # Filter titratable residues based on min and max pKa
    new_reslist = []
    for res in titratable_residues:
        if getattr(residues, res).Eo < mineo: continue

if opt.intdiel != 1 and opt.intdiel != 2:
        raise AmberError('-intdiel must be either 1 or 2 currently')

    # Set the list of residue names we will be willing to titrate
    titratable_residues = []
    if notresnames is not None:
        for resname in residues.titratable_residues:
            if resname in notresnames: continue
            titratable_residues.append(resname)
    elif resnames is not None:
        for resname in resnames:
            if not resname in residues.titratable_residues:
                raise AmberError('%s is not a titratable residue!' % resname)
            titratable_residues.append(resname)
    else:
        for resname in residues.titratable_residues:
            titratable_residues.append(resname)

    solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
                    'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']

    # Make sure we still have a couple residues
    if len(titratable_residues) == 0:
        raise AmberError('No titratable residues fit your criteria!')

    # Load the topology file
    parm = AmberParm(opt.prmtop)

    # Replace an un-set notresnums with an empty list so we get __contains__()
    if notresnums is None:
        notresnums = []

# Set the list of residue names we will be willing to titrate
    titratable_residues = []
    if notresnames is not None:
        for resname in residues.titratable_residues:
            if resname in notresnames: continue
            titratable_residues.append(resname)
    elif resnames is not None:
        for resname in resnames:
            if not resname in residues.titratable_residues:
                raise AmberError('%s is not a titratable residue!' % resname)
            elif not getattr(residues, resname).typ == "redox":
                raise AmberError('%s is not a redox-active titratable residue!' % resname)
            titratable_residues.append(resname)
    else:
        for resname in residues.titratable_residues:
            if getattr(residues, resname).typ == "redox":
                titratable_residues.append(resname)

    solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
                    'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']

    # Filter titratable residues based on min and max pKa
    new_reslist = []
    for res in titratable_residues:
        if getattr(residues, res).Eo < mineo: continue
        if getattr(residues, res).Eo > maxeo: continue
        new_reslist.append(res)
    titratable_residues = new_reslist
    del new_reslist

    # Make sure we still have a couple residues

if resnames is not None and notresnames is not None:
        raise AmberError('Cannot specify -resnames and -notresnames together')

    if opt.intdiel != 1 and opt.intdiel != 2:
        raise AmberError('-intdiel must be either 1 or 2 currently')

    # Set the list of residue names we will be willing to titrate
    titratable_residues = []
    if notresnames is not None:
        for resname in residues.titratable_residues:
            if resname in notresnames: continue
            titratable_residues.append(resname)
    elif resnames is not None:
        for resname in resnames:
            if not resname in residues.titratable_residues:
                raise AmberError('%s is not a titratable residue!' % resname)
            titratable_residues.append(resname)
    else:
        for resname in residues.titratable_residues:
            titratable_residues.append(resname)

    solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
                    'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']

    # Make sure we still have a couple residues
    if len(titratable_residues) == 0:
        raise AmberError('No titratable residues fit your criteria!')

    # Load the topology file
    parm = AmberParm(opt.prmtop)