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#!/usr/bin/python
# -*- coding: utf-8 -*-
#------------------------------------------------------------------------------
#$Author: andrius $
#$Revision: 5703 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/scripts/cif_printout_Python $
#$Date: 2017-11-02 17:43:23 +0200 (Kt, 02 lapkr. 2017) $
#$Id: cif_printout_Python 5703 2017-11-02 15:43:23Z andrius $
#------------------------------------------------------------------------------
#*
#* Parse CIF file and print out the structure generated by CIF parser.
#**
import argparse
import pprint
import sys
from pycodcif import parse, CifParserException
def version():
import os
from os.path import realpath,dirname
from subprocess import call
directory = os.path.dirname(os.path.realpath(__file__))
call( "{}/cod-tools-version".format(directory) )
sys.exit()
parser = argparse.ArgumentParser(description='Parse CIF file and print out '
'the structure generated by '
'the CIF parser')
parser.add_argument("--do-not-unprefix-text",
dest='do_not_unprefix_text',
action='store_const', const=1)
parser.add_argument("--do-not-unfold-text",
dest='do_not_unfold_text',
action='store_const', const=1)
parser.add_argument("--fix-errors",
dest='fix_errors',
action='store_const', const=1)
parser.add_argument("--fix-duplicate-tags-with-same-values",
dest='fix_duplicate_tags_with_same_values',
action='store_const', const=1)
parser.add_argument("--fix-duplicate-tags-with-empty-values",
dest='fix_duplicate_tags_with_empty_values',
action='store_const', const=1)
parser.add_argument("--fix-data-header",
dest='fix_data_header',
action='store_const', const=1)
parser.add_argument("--fix-datablock-names",
dest='fix_datablock_names',
action='store_const', const=1)
parser.add_argument("--fix-string-quotes",
dest='fix_string_quotes',
action='store_const', const=1)
parser.add_argument("--fix-missing-closing-double-quote",
dest='fix_missing_closing_double_quote',
action='store_const', const=1)
parser.add_argument("--fix-missing-closing-single-quote",
dest='fix_missing_closing_single_quote',
action='store_const', const=1)
parser.add_argument("--fix-ctrl-z",
dest='fix_ctrl_z',
action='store_const', const=1)
parser.add_argument("--allow-uqstring-brackets",
dest='allow_uqstring_brackets',
action='store_const', const=1)
parser.add_argument("--version", dest='version',
action='store_const', const=1)
parser.add_argument("files", nargs='*')
options = vars(parser.parse_args(args=sys.argv[1:]))
for key in options.keys():
if not options[key]:
options.pop(key)
files = options.pop('files',[])
if not files:
files = ['-']
if 'version' in options.keys():
version()
for filename in files:
try:
data, errcount, _ = parse(filename, options)
pprint.PrettyPrinter().pprint(data)
print len(data[0]['tags'][0])
sys.stderr.write("{} error(s) detected\n".format(errcount))
except CifParserException:
sys.exit(1)
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