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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Script for writing data tables from computational chemistry files."""
import argparse
import os.path
import sys
from cclib.io import ccopen
from cclib.io import ccframe
from cclib.parser.utils import find_package
_has_pandas = find_package("pandas")
if _has_pandas:
import pandas as pd
def process_logfiles(filenames, output, identifier):
df = ccframe([ccopen(path) for path in filenames])
if output is not None:
outputtype = os.path.splitext(os.path.basename(output))[1][1:]
if not outputtype:
raise RuntimeWarning(
"The output type could not be determined from the given path, "
"not writing DataFrame to disk"
)
if outputtype in {'csv'}:
df.to_csv(output)
elif outputtype in {'h5', 'hdf', 'hdf5'}:
df.to_hdf(output, key=identifier)
elif outputtype in {'json'}:
df.to_json(output)
elif outputtype in {'pickle', 'pkl'}:
df.to_pickle(output)
elif outputtype in {'xlsx'}:
writer = pd.ExcelWriter(output)
# This overwrites previous sheets
# (see https://stackoverflow.com/a/42375263/4039050)
df.to_excel(writer, sheet_name=identifier)
writer.save()
else:
print(df)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-O', '--output',
help=('the output document to write, including an '
'extension supported by pandas '
'(csv, h5/hdf/hdf5, json, pickle/pkl, xlsx)'))
parser.add_argument('compchemlogfiles', metavar='compchemlogfile',
nargs='+',
help=('one or more computational chemistry output '
'files to parse and convert'))
parser.add_argument('--identifier',
default='logfiles',
help=('name of sheet which will contain DataFrame, if '
'writing to an Excel file, or identifier for '
'the group in HDFStore, if writing a HDF file'))
args = parser.parse_args()
process_logfiles(args.compchemlogfiles, args.output, args.identifier)
if __name__ == "__main__":
main()
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