1#!/usr/bin/env python 

2# -*- coding: utf-8 -*- 

3# 

4# Copyright (c) 2017, the cclib development team 

5# 

6# This file is part of cclib (http://cclib.github.io) and is distributed under 

7# the terms of the BSD 3-Clause License. 

8 

9import argparse 

10import logging 

11import os.path 

12import sys 

13 

14from cclib.parser import ccData 

15from cclib.io import ccopen 

16from cclib.io import ccwrite 

17 

18 

19def main(): 

20 

21 parser = argparse.ArgumentParser() 

22 

23 parser.add_argument('outputtype', 

24 choices=('json', 'cjson', 'cml', 'xyz', 'molden', 'wfx'), 

25 help='the output format to write (json/cjson are identical)') 

26 parser.add_argument('compchemlogfile', 

27 nargs='+', 

28 help='one or more computational chemistry output files to parse and convert') 

29 

30 parser.add_argument('-v', '--verbose', 

31 action='store_true', 

32 help='more verbose parsing output (only errors by default)') 

33 

34 parser.add_argument('-g', '--ghost', 

35 type=str, 

36 default=None, 

37 help='Symbol to use for ghost atoms') 

38 

39 parser.add_argument('-t', '--terse', 

40 action='store_true', 

41 help='CJSON by default is not indented for readability, saves space (indented for readability\'s sake)') 

42 

43 parser.add_argument('-u', '--future', 

44 action='store_true', 

45 help='use experimental features (currently optdone_as_list)') 

46 

47 parser.add_argument('-i', '--index', 

48 type=int, 

49 default=None, 

50 help='optional zero-based index for which structure to extract') 

51 

52 args = parser.parse_args() 

53 

54 outputtype = args.outputtype 

55 filenames = args.compchemlogfile 

56 verbose = args.verbose 

57 terse = args.terse 

58 future = args.future 

59 index = args.index 

60 ghost = args.ghost 

61 

62 for filename in filenames: 

63 

64 # We might want to use this option in the near future. 

65 ccopen_kwargs = dict() 

66 if future: 

67 ccopen_kwargs['future'] = True 

68 

69 print("Attempting to parse {}".format(filename)) 

70 log = ccopen(filename, **ccopen_kwargs) 

71 

72 if not log: 

73 print("Cannot figure out what type of computational chemistry output file '{}' is.".format(filename)) 

74 print("Report this to the cclib development team if you think this is an error.") 

75 sys.exit() 

76 

77 if verbose: 

78 log.logger.setLevel(logging.INFO) 

79 else: 

80 log.logger.setLevel(logging.ERROR) 

81 data = log.parse() 

82 

83 print("cclib can parse the following attributes from {}:".format(filename)) 

84 hasattrs = [' {}'.format(attr) for attr in ccData._attrlist if hasattr(data, attr)] 

85 print('\n'.join(hasattrs)) 

86 

87 # Write out to disk. 

88 outputdest = '.'.join([os.path.splitext(os.path.basename(filename))[0], outputtype]) 

89 ccwrite_kwargs = dict() 

90 if future: 

91 ccwrite_kwargs['future'] = True 

92 if ghost: 

93 ccwrite_kwargs['ghost'] = ghost 

94 # For XYZ files, write the last geometry unless otherwise 

95 # specified. 

96 if not index: 

97 index = -1 

98 ccwrite_kwargs['jobfilename'] = filename 

99 

100 # The argument terse presently is only applicable to 

101 # CJSON/JSON formats 

102 ccwrite(data, outputtype, outputdest, indices=index, terse=terse, 

103 **ccwrite_kwargs) 

104 

105 

106if __name__ == "__main__": 

107 main()