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Fix bugs in invocation and options.

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Add non-command-arguments.
Restore --quiet option.
This commit is contained in:
Nathan Baker
2020-05-21 11:53:03 -07:00
parent 393f5cee50
commit fc27d8bfc3
1 changed files with 6 additions and 2 deletions
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8
propka/lib.py
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@@ -210,17 +210,21 @@ def build_parser(parser=None):
"ligand bond orders")) "ligand bond orders"))
group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true", group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False) 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", group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)", help="Protonate all atoms (will not influence pKa calculation)",
default=False) default=False)
return parser return parser
def loadOptions(*args): def loadOptions(args):
""" """
Load the arguments parser with options. Note that verbosity is set as soon Load the arguments parser with options. Note that verbosity is set as soon
as this function is invoked. as this function is invoked.
Arguments:
args: list of arguments
Returns: Returns:
argparse namespace argparse namespace
""" """
@@ -235,7 +239,7 @@ def loadOptions(*args):
# command line # command line
options = parser.parse_args() options = parser.parse_args()
else: else:
options = parser.parse_args(list(args)) options = parser.parse_args(args)
# adding specified filenames to arguments # adding specified filenames to arguments
options.filenames.append(options.input_pdb) options.filenames.append(options.input_pdb)