How to use moltemplate - 10 common examples

'       (even if the simulation is in 2 dimensions)\n')
            settings.iaffinevects = []
            for i in range(0, len(ilist) / 3):
                cols = [int(ilist[3 * i]) + 1,
                        int(ilist[3 * i + 1]) + 1,
                        int(ilist[3 * i + 2]) + 1]
                settings.iaffinevects.append(cols)
            del(argv[i:i + 2])
        elif (argv[i].lower() == '-ivect'):
            if i + 1 >= len(argv):
                raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers\n'
                                 '       corresponding to column numbers for direction vectors 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'
                                 '       This is usually a list of 3 integers, but it can contain more.\n'
                                 '       The number of cooridnate columns must be divisible by 3,\n'
                                 '       (even if the simulation is in 2 dimensions)\n')
            settings.ivects = []
            for i in range(0, len(ilist) / 3):
                cols = [int(ilist[3 * i]) + 1,
                        int(ilist[3 * i + 1]) + 1,
                        int(ilist[3 * i + 2]) + 1]
                settings.ivects.append(cols)
            del(argv[i:i + 2])
        elif ((argv[i].lower() == '-iatomid') or
              (argv[i].lower() == '-iid') or
              (argv[i].lower() == '-iatom-id')):
            if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))):
                raise InputError('Error: ' + argv[i] + ' flag should be followed by an integer\n'
                                 '       (>=1) indicating which column in the \"' +

atom_style_string = atom_style_string.strip()
    if len(atom_style_string) == 0:
        raise InputError('Error: Invalid atom_style\n'
                         '       (The atom_style command was followed by an empty string.)\n')
    atom_style_args = atom_style_string.split()
    atom_style = atom_style_args[0]

    hybrid_args = atom_style_args[1:]
    if (atom_style not in g_style_map):
        if (len(atom_style_args) >= 2):
            # If the atom_style_string includes at least 2 words, then we
            # interpret this as a list of the individual column names
            return atom_style_args
        else:
            raise InputError(
                'Error: Unrecognized atom_style: \"' + atom_style + '\"\n')

    if (atom_style != 'hybrid'):
        return g_style_map[atom_style]
    else:
        column_names = ['atom-ID', 'atom-type', 'x', 'y', 'z']
        if (len(hybrid_args) == 0):
            raise InputError(
                'Error: atom_style hybrid must be followed by a sub_style.\n')
        for sub_style in hybrid_args:
            if (sub_style not in g_style_map):
                raise InputError(
                    'Error: Unrecognized atom_style: \"' + sub_style + '\"\n')
            for cname in g_style_map[sub_style]:
                if cname not in column_names:
                    column_names.append(cname)

'Unrecogized command line argument \"'+argv[i]+'\"\n')
        else:
            i += 1


    if __name__ == "__main__":

        # Instantiate the lexer we will be using.
        #  (The lexer's __init__() function requires an openned file.
        #   Assuming __name__ == "__main__", then the name of that file should
        #   be the last remaining (unprocessed) argument in the argument list.
        #   Otherwise, then name of that file will be determined later by the
        #   python script which imports this module, so we let them handle it.)

        if len(argv) == 1:
            raise InputError('Error: This program requires at least one argument\n'
                             '       the name of a file containing ttree template commands\n')
        elif len(argv) == 2:
            try:
                # Parse text from the file named argv[1]
                settings.lex.infile = argv[1]  
                settings.lex.instream = open(argv[1], 'r')
            except IOError: 
                sys.stderr.write('Error: unable to open file\n'
                                 '       \"'+argv[1]+'\"\n'
                                 '       for reading.\n')
                sys.exit(1)
            del(argv[1:2])

        else:
            # if there are more than 2 remaining arguments,
            problem_args = ['\"'+arg+'\"' for arg in argv[1:]]

lines = text.split('\n')

    for i in range(0, len(lines)):
        line_orig = lines[i]
        ic = line_orig.find('#')
        if ic != -1:
            line = line_orig[:ic]
            comment = ' ' + line_orig[ic:].rstrip('\n')
        else:
            line = line_orig.rstrip('\n')
            comment = ''

        columns = line.split()
        if len(columns) > 0:
            if len(columns) == len(settings.column_names) + 3:
                raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n'
                                 '   within the \"' + data_atoms + '\" section of a LAMMPS data file.\n'
                                 '   Instead please add the appropriate offsets (these offsets\n'
                                 '   should be multiples of the cell size) to the atom coordinates\n'
                                 '   in the data file, and eliminate the extra columns. Then try again.\n'
                                 '   (If you get this message often, email me and I\'ll fix this limitation.)')
            if len(columns) < len(settings.column_names):
                raise InputError('Error: The number of columns in your data file does not\n'
                                 '       match the LAMMPS atom_style you selected.\n'
                                 '       Use the -atomstyle <style> command line argument.\n')
            x0 = [0.0, 0.0, 0.0]
            x = [0.0, 0.0, 0.0]
            # Atomic coordinates transform using "affine" transformations
            # (translations plus rotations [or other linear transformations])
            for cxcycz in settings.ii_coords:
                for d in range(0, 3):
                    x0[d] = float(columns[cxcycz[d]])</style>

elif len(argv) == 2:
            try:
                # Parse text from the file named argv[1]
                settings.lex.infile = argv[1]  
                settings.lex.instream = open(argv[1], 'r')
            except IOError: 
                sys.stderr.write('Error: unable to open file\n'
                                 '       \"'+argv[1]+'\"\n'
                                 '       for reading.\n')
                sys.exit(1)
            del(argv[1:2])

        else:
            # if there are more than 2 remaining arguments,
            problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
            raise InputError('Syntax Error('+__file__+'):\n\n'
                             '       Problem with argument list.\n'
                             '       The remaining arguments are:\n\n'
                             '         '+(' '.join(problem_args))+'\n\n'
                             '       (The actual problem may be earlier in the argument list.\n'

comment = ' ' + line_orig[ic:].rstrip('\n')
        else:
            line = line_orig.rstrip('\n')
            comment = ''

        columns = line.split()
        if len(columns) > 0:
            if len(columns) == len(settings.column_names) + 3:
                raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n'
                                 '   within the \"' + data_atoms + '\" section of a LAMMPS data file.\n'
                                 '   Instead please add the appropriate offsets (these offsets\n'
                                 '   should be multiples of the cell size) to the atom coordinates\n'
                                 '   in the data file, and eliminate the extra columns. Then try again.\n'
                                 '   (If you get this message often, email me and I\'ll fix this limitation.)')
            if len(columns) < len(settings.column_names):
                raise InputError('Error: The number of columns in your data file does not\n'
                                 '       match the LAMMPS atom_style you selected.\n'
                                 '       Use the -atomstyle <style> command line argument.\n')
            x0 = [0.0, 0.0, 0.0]
            x = [0.0, 0.0, 0.0]
            # Atomic coordinates transform using "affine" transformations
            # (translations plus rotations [or other linear transformations])
            for cxcycz in settings.ii_coords:
                for d in range(0, 3):
                    x0[d] = float(columns[cxcycz[d]])
                    AffineTransform(x, matrix, x0)  # x = matrix * x0 + b
                for d in range(0, 3):  # ("b" is part of "matrix")
                    columns[cxcycz[d]] = str(x[d])
            # Dipole moments and other direction-vectors
            # are not effected by translational movement
            for cxcycz in settings.ii_vects:
                for d in range(0, 3):</style>

def AtomStyle2ColNames(atom_style_string):

    atom_style_string = atom_style_string.strip()
    if len(atom_style_string) == 0:
        raise InputError('Error(dump2data): Invalid atom_style\n'
                         '       (The atom_style command was followed by an empty string.)\n')
    atom_style_args = atom_style_string.split()
    atom_style = atom_style_args[0]

    hybrid_args = atom_style_args[1:]

    if (atom_style not in g_style_map):
        if (len(atom_style_args) >= 2):
            # If the atom_style_string includes at least 2 words, then we
            # interpret this as a list of the individual column names
            return atom_style_args
        else:
            raise InputError(
                'Error(dump2data): Unrecognized atom_style: \"' + atom_style + '\"\n')

    if (atom_style != 'hybrid'):

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'

def CommandsToMatrix(text,  # text containing affine transformation commands
                         src_loc=OSrcLoc(),   # for debugging
                         xcm=None):  # position of center of object
        Mdest = [[1.0, 0.0, 0.0, 0.0], [
            0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]
        M = [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]
        Mtmp = [[1.0, 0.0, 0.0, 0.0], [
            0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]

        transform_commands = text.split(').')
        for transform_str in transform_commands:
            if transform_str.find('move(') == 0:
                i_paren_close = transform_str.find(')')
                if i_paren_close == -1:
                    i_paren_close = len(transform_str)
                args = transform_str[5:i_paren_close].split(',')
                if (len(args) != 3):
                    raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n'

# (with the original variable names present)
        WriteFiles(files_content, suffix=".template", write_to_stdout=False)

        # Write the files with the variables substituted by values
        sys.stderr.write(' done\nbuilding and rendering templates...')
        files_content = defaultdict(list)
        ExecCommands(g_static_commands, files_content, settings, True)
        ExecCommands(g_instance_commands, files_content, settings, True)
        sys.stderr.write(' done\nwriting rendered templates...\n')
        WriteFiles(files_content)

        # Now write the variable bindings/assignments table.
        sys.stderr.write('writing \"ttree_assignments.txt\" file...')
        open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
        WriteVarBindingsFile(g_objectdefs)
        WriteVarBindingsFile(g_objects)
        sys.stderr.write(' done\n')

    except (ValueError, InputError) as err:
        sys.stderr.write('\n\n'+str(err)+'\n')
        sys.exit(-1)