How to use the moltemplate.lttree_styles.AtomStyle2ColNames function in moltemplate

BasicUIParseArgs(argv, settings)

    # Loop over the remaining arguments not processed yet.
    # These arguments are specific to the lttree.py program
    # and are not understood by ttree.py:
    i = 1
    while i < len(argv):
        #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
        if ((argv[i].lower() == '-atomstyle') or
                (argv[i].lower() == '-atom-style') or
                (argv[i].lower() == '-atom_style')):
            if i + 1 >= len(argv):
                raise InputError('Error(' + g_program_name + '): The ' + argv[i] + ' flag should be followed by a LAMMPS\n'
                                 '       atom_style name (or single quoted string containing a space-separated\n'
                                 '       list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
            settings.column_names = AtomStyle2ColNames(argv[i + 1])
            sys.stderr.write('\n    \"' + data_atoms + '\" column format:\n')
            sys.stderr.write(
                '    ' + (' '.join(settings.column_names)) + '\n\n')
            settings.ii_coords = ColNames2Coords(settings.column_names)
            settings.ii_vects = ColNames2Vects(settings.column_names)
            settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(
                settings.column_names)
            del(argv[i:i + 2])
        elif (argv[i].lower() == '-icoord'):
            if i + 1 >= len(argv):
                raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers\n'
                                 '       corresponding to column numbers for coordinates in\n'
                                 '       the \"' + data_atoms + '\" section of a LAMMPS data file.\n')
            ilist = argv[i + 1].split()
            if (len(ilist) % 3) != 0:
                raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers.\n'

each pair of atoms and stores this in the "chargebyatomid" dictionary.

    Input (continued):
       This function requires:
    ...a list of bonded pairs of atoms
        stored in the lines_bonds variable (from the "Data Bond List"
                                       or "Data Bonds AtomId AtomId" sections)
    ...and a list of atom types
        stored in the lines_atoms variable (from the "Data Atoms" section)

    ...and a list of charge-pairs-as-a-function-of-atom-types
        stored in the lines_chargebybond (from the "Data Bonds By Type" section)

    """

    column_names = AtomStyle2ColNames(atom_style)
    i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)

    atomids = []
    atomtypes = []
    atomids2types = {}

    for iv in range(0, len(lines_atoms)):
        line = lines_atoms[iv].strip()
        if '#' in line:
            icomment = line.find('#')
            line = (line[:icomment]).strip()
        if len(line) > 0:
            tokens = ttree_lex.SplitQuotedString(line)
            if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
                sys.stderr.write("\"" + line + "\"\n")
                raise(ttree_lex.InputError(

This function requires:
    ...a list of bonded pairs of atoms
        stored in the lines_bonds variable (from the "Data Bond List"
                                       or "Data Bonds AtomId AtomId" sections)
    ...and a list of atom types
        stored in the lines_atoms variable (from the "Data Atoms" section)
    ...and a list of bond-types-as-a-function-of-atom-types
        stored in the lines_bondsbytype (from the "Data Bonds By Type" section)

    Generated bond_ids (if applicable) are of the form
      prefix + str(number) + suffix
        (where "number" begins at bond_ids_offset+1)

    """

    column_names = AtomStyle2ColNames(atom_style)
    i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)

    atomids = []
    atomtypes = []
    atomids2types = {}

    for iv in range(0, len(lines_atoms)):
        line = lines_atoms[iv].strip()
        if '#' in line:
            icomment = line.find('#')
            line = (line[:icomment]).strip()
        if len(line) > 0:
            tokens = ttree_lex.SplitQuotedString(line)
            if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
                sys.stderr.write("\"" + line + "\"\n")
                raise(ttree_lex.InputError(

#                 '##      are interpreted as direction vectors.             ##\n'
                         #                 '##   3) Use the -icoord \"cx cy cz...\" argument        ##\n'
                         #                 '##      where \"cx cy cz\" is a list of integers        ##\n'
                         #                 '##      indicating the column numbers for the x,y,z   ##\n'
                         #                 '##      coordinates of each atom.                     ##\n'
                         #                 '##   4) Use the -ivect \"cmux cmuy cmuz...\" argument   ##\n'
                         #                 '##      where \"cmux cmuy cmuz...\" is a list of        ##\n'
                         #                 '##      integers indicating the column numbers for    ##\n'
                         #                 '##      the vector that determines the direction of a ##\n'
                         #                 '##      dipole or ellipsoid (ie. a rotateable vector).##\n'
                         #                 '##      (More than one triplet can be specified. The  ##\n'
                         #                 '##       number of entries must be divisible by 3.)   ##\n'
                         '########################################################\n')

        # The default atom_style is "full"
        settings.column_names = AtomStyle2ColNames('full')
        settings.ii_coords = ColNames2Coords(settings.column_names)
        settings.ii_vects = ColNames2Vects(settings.column_names)
        settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(
            settings.column_names)

    return

def GenInteractions_lines(lines_atoms,
                          lines_bonds,
                          lines_nbody,
                          lines_nbodybytype,
                          atom_style,
                          g_bond_pattern,
                          canonical_order,  # function to sort atoms and bonds
                          prefix='',
                          suffix='',
                          report_progress=False,
                          check_undefined=False):

    column_names = AtomStyle2ColNames(atom_style)
    i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)

    atomids_str = []
    atomtypes_str = []

    for iv in range(0, len(lines_atoms)):
        line = lines_atoms[iv].strip()
        if '#' in line:
            icomment = line.find('#')
            line = (line[:icomment]).strip()
        if len(line) > 0:
            tokens = SplitQuotedString(line)
            if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
                raise(InputError('Error not enough columns on line ' +
                                 str(iv + 1) + ' of \"Atoms\" section.'))
            tokens = SplitQuotedString(line)