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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, 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 loading data from computational chemistry files."""
from __future__ import print_function
import glob
import logging
import os.path
import sys
from functools import partial
from pprint import pprint
import numpy
from cclib.parser import ccData
from cclib.io import ccread, URL_PATTERN
# Set up options for pretty-printing output.
if sys.version_info < (3, 4):
pprint = partial(pprint, width=120)
else:
pprint = partial(pprint, width=120, compact=True)
numpy.set_printoptions(linewidth=120)
def ccget():
"""Parse files with cclib based on command line arguments."""
import argparse
parser = argparse.ArgumentParser()
parser.add_argument(
"attribute_or_compchemlogfile", nargs="+",
help="one or more attributes to be parsed from one ore more logfiles",
)
group = parser.add_mutually_exclusive_group()
group.add_argument(
"--list", "-l",
action="store_true",
help="print a list of attributes available in each file",
)
group.add_argument(
"--json", "-j",
action="store_true",
help="the given logfile is in CJSON format",
)
group.add_argument(
"--multi", "-m",
action="store_true",
help="parse multiple input files as one input stream",
)
parser.add_argument(
"--verbose", "-v",
action="store_true",
help="more verbose parsing output (only errors by default)",
)
parser.add_argument(
"--future", "-u",
action="store_true",
help="use experimental features (currently optdone_as_list)",
)
parser.add_argument(
"--full", "-f",
action="store_true",
help="toggle full print behaviour for attributes",
)
args = parser.parse_args()
arglist = args.attribute_or_compchemlogfile
showattr = args.list
cjsonfile = args.json
multifile = args.multi
verbose = args.verbose
future = args.future
full = args.full
# Toggle full print behaviour for numpy arrays.
if full:
numpy.set_printoptions(threshold=numpy.nan)
# We need at least one attribute and the filename, so two arguments, or
# just one filename if we want to list attributes that can be extracted.
# In multifile mode, we generally want at least two filenames, so the
# expected number of arguments is a bit different.
if not multifile:
correct_number = (not showattr and len(arglist) > 1) or (showattr and len(arglist) > 0)
else:
correct_number = (not showattr and len(arglist) > 2) or (showattr and len(arglist) > 1)
if not correct_number:
print("The number of arguments does not seem to be correct.")
parser.print_usage()
parser.exit(1)
# Figure out which are the attribute names and which are the filenames or links.
# Note that in Linux, the shell expands wild cards, but not so in Windows,
# so try to do that here using glob.
attrnames = []
filenames = []
for arg in arglist:
if arg in ccData._attrlist:
attrnames.append(arg)
elif URL_PATTERN.match(arg) or os.path.isfile(arg):
filenames.append(arg)
else:
wildcardmatches = glob.glob(arg)
if wildcardmatches:
filenames.extend(wildcardmatches)
else:
print("%s is neither a filename nor an attribute name." % arg)
parser.print_usage()
parser.exit(1)
# Since there is some ambiguity to the correct number of arguments, check
# that there is at least one filename (or two in multifile mode), and also
# at least one attribute to parse if the -l option was not passed.
if len(filenames) == 0:
print("No logfiles given")
parser.exit(1)
if multifile and len(filenames) == 1:
print("Expecting at least two logfiles in multifile mode")
parser.exit(1)
if not showattr and len(attrnames) == 0:
print("No attributes given")
parser.exit(1)
# This should be sufficient to correctly handle multiple files, that is to
# run the loop below only once with all logfiles in the variable `filename`.
# Although, perhaps it would be clearer to abstract the contents of the loop
# into another function.
if multifile:
filenames = [filenames]
# Now parse each file and print out the requested attributes.
for filename in filenames:
if multifile:
name = ", ".join(filename[:-1]) + " and " + filename[-1]
else:
name = filename
# The keyword dictionary are not used so much. but could be useful for
# passing options downstream. For example, we might use --future for
# triggering experimental or alternative behavior (as with optdone).
kwargs = {}
if verbose:
kwargs['verbose'] = True
kwargs['loglevel'] = logging.INFO
else:
kwargs['verbose'] = False
kwargs['loglevel'] = logging.ERROR
if future:
kwargs['future'] = True
if cjsonfile:
kwargs['cjson'] = True
print("Attempting to read %s" % name)
data = ccread(filename, **kwargs)
if data is None:
print("Cannot figure out the format of '%s'" % name)
print("Report this to the cclib development team if you think it is an error.")
print("\n" + parser.format_usage())
parser.exit(1)
if showattr:
print("cclib can parse the following attributes from %s:" % name)
if cjsonfile:
for key in data:
print(key)
break
for attr in data._attrlist:
if hasattr(data, attr):
print(" %s" % attr)
else:
invalid = False
for attr in attrnames:
if cjsonfile:
if attr in data:
print("%s:\n%s" % (attr, data[attr]))
continue
else:
if hasattr(data, attr):
print(attr)
attr_val = getattr(data, attr)
# List of attributes to be printed with new lines
if attr in data._listsofarrays and full:
for val in attr_val:
pprint(val)
else:
pprint(attr_val)
continue
print("Could not parse %s from this file." % attr)
invalid = True
if invalid:
parser.print_help()
if __name__ == "__main__":
ccget()
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