1#!/usr/bin/env python 

2# -*- coding: utf-8 -*- 

3# 

4# Copyright (c) 2019, 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"""Script for writing data tables from computational chemistry files.""" 

9 

10import argparse 

11import os.path 

12import sys 

13 

14from cclib.io import ccopen 

15from cclib.io import ccframe 

16from cclib.parser.utils import find_package 

17 

18_has_pandas = find_package("pandas") 

19if _has_pandas: 

20 import pandas as pd 

21 

22 

23def process_logfiles(filenames, output, identifier): 

24 df = ccframe([ccopen(path) for path in filenames]) 

25 if output is not None: 

26 outputtype = os.path.splitext(os.path.basename(output))[1][1:] 

27 if not outputtype: 

28 raise RuntimeWarning( 

29 "The output type could not be determined from the given path, " 

30 "not writing DataFrame to disk" 

31 ) 

32 

33 if outputtype in {'csv'}: 

34 df.to_csv(output, mode='w') 

35 elif outputtype in {'h5', 'hdf', 'hdf5'}: 

36 df.to_hdf(output, mode='w', key=identifier) 

37 elif outputtype in {'json'}: 

38 df.to_json(output) 

39 elif outputtype in {'pickle', 'pkl'}: 

40 df.to_pickle(output) 

41 elif outputtype in {'xlsx'}: 

42 writer = pd.ExcelWriter(output, mode='w') 

43 # This overwrites previous sheets 

44 # (see https://stackoverflow.com/a/42375263/4039050) 

45 df.to_excel(writer, sheet_name=identifier) 

46 writer.save() 

47 else: 

48 print(df) 

49 

50 

51def main(): 

52 parser = argparse.ArgumentParser() 

53 parser.add_argument('-O', '--output', 

54 help=('the output document to write, including an ' 

55 'extension supported by pandas ' 

56 '(csv, h5/hdf/hdf5, json, pickle/pkl, xlsx)')) 

57 parser.add_argument('compchemlogfiles', metavar='compchemlogfile', 

58 nargs='+', 

59 help=('one or more computational chemistry output ' 

60 'files to parse and convert')) 

61 parser.add_argument('--identifier', 

62 default='logfiles', 

63 help=('name of sheet which will contain DataFrame, if ' 

64 'writing to an Excel file, or identifier for ' 

65 'the group in HDFStore, if writing a HDF file')) 

66 parser.add_argument('-f', '--force', action='store_true', 

67 help=('overwrite output file in case it already exists')) 

68 args = parser.parse_args() 

69 if args.output is not None and not args.force and os.path.exists(args.output): 

70 parser.exit(1, 'failure: exiting to avoid overwriting existing file "{}"\n'.format(args.output)) 

71 

72 process_logfiles(args.compchemlogfiles, args.output, args.identifier) 

73 

74 

75if __name__ == "__main__": 

76 main()