From fc27d8bfc3fc978d6a9a6b2dd644eb93e532f957 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Thu, 21 May 2020 11:53:03 -0700 Subject: [PATCH] Fix bugs in invocation and options. Add non-command-arguments. Restore --quiet option. --- propka/lib.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/propka/lib.py b/propka/lib.py index 31b2880..fc2da5a 100644 --- a/propka/lib.py +++ b/propka/lib.py @@ -210,17 +210,21 @@ def build_parser(parser=None): "ligand bond orders")) group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true", help="Keep protons in input file", default=False) + group.add_argument("-q", "--quiet", action="store_const", const="WARNING", + dest="log_level", help="supress non-warning messages") group.add_argument("--protonate-all", dest="protonate_all", action="store_true", help="Protonate all atoms (will not influence pKa calculation)", default=False) return parser -def loadOptions(*args): +def loadOptions(args): """ Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked. + Arguments: + args: list of arguments Returns: argparse namespace """ @@ -235,7 +239,7 @@ def loadOptions(*args): # command line options = parser.parse_args() else: - options = parser.parse_args(list(args)) + options = parser.parse_args(args) # adding specified filenames to arguments options.filenames.append(options.input_pdb)