/usr/bin/cclib-get is in cclib 1.3.1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | #!/usr/bin/python
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You should have
# received a copy of the license along with cclib. You can also access
# the full license online at http://www.gnu.org/copyleft/lgpl.html.
"""Script for loading data from computational chemistry files."""
from __future__ import print_function
import getopt
import glob
import logging
import os
import sys
from cclib.parser import ccData
from cclib.parser import ccread
MSG_USAGE = """\
Usage: ccget <attribute> [<attribute>] <compchemlogfile> [<compchemlogfile>]
Try ccget --help for more information\
"""
MSG_USAGE_LONG = """\
Usage: ccget <attribute> [<attribute>] <compchemlogfile> [<compchemlogfile>]
where <attribute> is one of the attributes to be parsed by cclib
from each of the compchemlogfiles.
For a list of attributes available in a file, use --list (or -l):
ccget --list <compchemlogfile>
To parse multiple files as one input stream, use --multi (or -m):
ccget --multi <attr> [<attr>] <cclogfile> <cclogfile> [<cclogfile>]
Additional options:
-v or --verbose: more verbose parsing output (only errors by default)
-u or --future: use experimental features (currently optdone_as_list)\
"""
# These are the options ccget accepts and their one letter versions.
OPTS_LONG = ["help", "list", "multi", "verbose", "future"]
OPTS_SHORT = "hlmvu"
def ccget():
"""Parse files with cclib based on command line arguments."""
# Parse the arguments and pass them to ccget, but print help information
# and exit if it fails.
try:
optlist, arglist = getopt.getopt(sys.argv[1:], OPTS_SHORT, OPTS_LONG)
except getopt.GetoptError:
print(MSG_USAGE_LONG)
sys.exit(1)
future = False
showattr = False
multifile = False
verbose = False
for opt, arg in optlist:
if opt in ("-h", "--help"):
print(MSG_USAGE_LONG)
sys.exit()
if opt in ("-l", "--list"):
showattr = True
if opt in ("-m", "--multi"):
multifile = True
if opt in ("-v", "--verbose"):
verbose = True
if opt in ("-u", "--future"):
future = True
# 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.")
print(MSG_USAGE)
sys.exit(1)
# Figure out which are the attribute names and which are the filenames.
# 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 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)
print(MSG_USAGE)
sys.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")
sys.exit(1)
if multifile and len(filenames) == 1:
print("Expecting at least two logfiles in multifile mode")
sys.exit(1)
if not showattr and len(attrnames) == 0:
print("No attributes given")
sys.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
print("Attempting to read %s" % name)
data = ccread(filename, **kwargs)
if data == 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" + MSG_USAGE)
sys.exit()
if showattr:
print("cclib can parse the following attributes from %s:" % name)
for attr in data._attrlist:
if hasattr(data, attr):
print(" %s" % attr)
else:
invalid = False
for attr in attrnames:
if hasattr(data, attr):
print("%s:\n%s" % (attr, getattr(data, attr)))
else:
print("Could not parse %s from this file." % attr)
invalid = True
if invalid:
print(MSG_USAGE_LONG)
if __name__ == "__main__":
ccget()
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