How to use the parmed.exceptions.AmberError function in ParmEd

This processes an argument list with an arbitrary number of arguments that
   may or may not be comma-delimited (with any number of spaces)
   """
   # If the argument list is not set, just return None
   if arglist is None:
      return None
   # Otherwise, process the arguments
   processed_args = []
   for arg in arglist:
      # Delete any spaces, split on commas, and add this to processed arg list
      for arg in arg.replace(' ', '').split(','):
         if not arg: continue
         try:
            processed_args.append(argtype(arg))
         except ValueError:
            raise AmberError('Expected type %s for argument. Got %s' %
                             (argtype.__name__, arg))

   return processed_args

# Process the arguments that take multiple args
    resstates = process_arglist(opt.resstates, int)
    resnums = process_arglist(opt.resnums, int)
    notresnums = process_arglist(opt.notresnums, int)
    resnames = process_arglist(opt.resnames, str)
    notresnames = process_arglist(opt.notresnames, str)

    if not opt.igb in (1, 2, 5, 7, 8):
        raise AmberError('-igb must be 1, 2, 5, 7, or 8!')

    if resnums is not None and notresnums is not None:
        raise AmberError('Cannot specify -resnums and -notresnums together')

    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:

# 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 = []

    # If we have a list of residue numbers, check that they're all titratable
    if resnums is not None:
        for resnum in resnums:
            if resnum > parm.ptr('nres'):
                raise AmberError('%s only has %d residues. (%d chosen)' %
                                     (parm, parm.ptr('nres'), resnum))
            if resnum <= 0:
                raise AmberError('Cannot select negative residue numbers.')
            resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
            if not resname in titratable_residues:
                raise AmberError('Residue number %s [%s] is not titratable'
                                     % (resnum, resname))
    else:
        # Select every residue except those in notresnums
        resnums = []
        for resnum in range(1, parm.ptr('nres') + 1):
            if resnum in notresnums: continue
            resnums.append(resnum)

    solvated = False
    first_solvent = 0
    if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
        solvated = True
        for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):

# 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 = []

    # If we have a list of residue numbers, check that they're all titratable
    if resnums is not None:
        for resnum in resnums:
            if resnum > parm.ptr('nres'):
                raise AmberError('%s only has %d residues. (%d chosen)' %
                                     (parm, parm.ptr('nres'), resnum))
            if resnum <= 0:
                raise AmberError('Cannot select negative residue numbers.')
            resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
            if not resname in titratable_residues:
                raise AmberError('Residue number %s [%s] is not titratable'
                                     % (resnum, resname))
    else:
        # Select every residue except those in notresnums
        resnums = []
        for resnum in range(1, parm.ptr('nres') + 1):
            if resnum in notresnums: continue
            resnums.append(resnum)

    solvated = False
    first_solvent = 0
    if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
        solvated = True
        for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):

def main(opt):
    # Check all of the arguments
    if not os.path.exists(opt.prmtop):
        raise AmberError('prmtop file (%s) is missing' % opt.prmtop)

    # Process the arguments that take multiple args
    resstates = process_arglist(opt.resstates, int)
    resnums = process_arglist(opt.resnums, int)
    notresnums = process_arglist(opt.notresnums, int)
    resnames = process_arglist(opt.resnames, str)
    notresnames = process_arglist(opt.notresnames, str)
    minpka = opt.minpka
    maxpka = opt.maxpka

    if not opt.igb in (1, 2, 5, 7, 8):
        raise AmberError('-igb must be 1, 2, 5, 7, or 8!')

    if resnums is not None and notresnums is not None:
        raise AmberError('Cannot specify -resnums and -notresnums together')

    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')

    # 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

def main(opt):
    # Check all of the arguments
    if not os.path.exists(opt.prmtop):
        raise AmberError('prmtop file (%s) is missing' % opt.prmtop)

    # Process the arguments that take multiple args
    resstates = process_arglist(opt.resstates, int)
    resnums = process_arglist(opt.resnums, int)
    notresnums = process_arglist(opt.notresnums, int)
    resnames = process_arglist(opt.resnames, str)
    notresnames = process_arglist(opt.notresnames, str)

    if not opt.igb in (1, 2, 5, 7, 8):
        raise AmberError('-igb must be 1, 2, 5, 7, or 8!')

    if resnums is not None and notresnums is not None:
        raise AmberError('Cannot specify -resnums and -notresnums together')

    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)

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 getattr(residues, res).pKa > maxpka: continue
        new_reslist.append(res)
    titratable_residues = new_reslist
    del new_reslist

    # 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 = []

    # If we have a list of residue numbers, check that they're all titratable
    if resnums is not None:
        for resnum in resnums:
            if resnum > parm.ptr('nres'):
                raise AmberError('%s only has %d residues. (%d chosen)' %
                                     (parm, parm.ptr('nres'), resnum))
            if resnum <= 0:
                raise AmberError('Cannot select negative residue numbers.')

resstates = process_arglist(opt.resstates, int)
    resnums = process_arglist(opt.resnums, int)
    notresnums = process_arglist(opt.notresnums, int)
    resnames = process_arglist(opt.resnames, str)
    notresnames = process_arglist(opt.notresnames, str)
    mineo = opt.mineo
    maxeo = opt.maxeo

    if not opt.igb in (1, 2, 5, 7, 8):
        raise AmberError('-igb must be 1, 2, 5, 7, or 8!')

    if resnums is not None and notresnums is not None:
        raise AmberError('Cannot specify -resnums and -notresnums together')

    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)

# Check all of the arguments
    if not os.path.exists(opt.prmtop):
        raise AmberError('prmtop file (%s) is missing' % opt.prmtop)

    # Process the arguments that take multiple args
    resstates = process_arglist(opt.resstates, int)
    resnums = process_arglist(opt.resnums, int)
    notresnums = process_arglist(opt.notresnums, int)
    resnames = process_arglist(opt.resnames, str)
    notresnames = process_arglist(opt.notresnames, str)

    if not opt.igb in (1, 2, 5, 7, 8):
        raise AmberError('-igb must be 1, 2, 5, 7, or 8!')

    if resnums is not None and notresnums is not None:
        raise AmberError('Cannot specify -resnums and -notresnums together')

    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: