diff options
Diffstat (limited to 'plip/plipcmd.py')
| -rw-r--r-- | plip/plipcmd.py | 13 |
1 files changed, 7 insertions, 6 deletions
diff --git a/plip/plipcmd.py b/plip/plipcmd.py index e4c0815..f7dffab 100644 --- a/plip/plipcmd.py +++ b/plip/plipcmd.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python3 +#! /usr/bin/env python """ Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files. plipcmd.py - Main script for PLIP command line execution. @@ -166,7 +166,7 @@ def run_analysis(inputstructs, inputpdbids): logger.info(f'finished analysis, find the result files in {config.BASEPATH}') -if __name__ == '__main__': +def main(): """Parse command line arguments and start main script for analysis.""" parser = ArgumentParser(prog="PLIP", description=description) pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file @@ -178,7 +178,7 @@ if __name__ == '__main__': outputgroup.add_argument("-O", "--stdout", dest="stdout", action="store_true", default=False, help="Write to stdout instead of file") parser.add_argument("--rawstring", dest="use_raw_string", default=False, action="store_true", - help="Use Python raw strings for stdout and stdin") + help="Use Python raw strings for stdin") parser.add_argument("-v", "--verbose", dest="verbose", default=False, help="Turn on verbose mode", action="store_true") parser.add_argument("-q", "--quiet", dest="quiet", default=False, help="Turn on quiet mode", action="store_true") @@ -240,9 +240,7 @@ if __name__ == '__main__': for t in thresholds: parser.add_argument('--%s' % t.name, dest=t.name, type=lambda val: threshold_limiter(parser, val), help=argparse.SUPPRESS) - arguments = parser.parse_args() - # configure log levels config.VERBOSE = True if arguments.verbose else False config.QUIET = True if arguments.quiet else False @@ -255,7 +253,6 @@ if __name__ == '__main__': logger.setLevel(logging.CRITICAL) else: logger.setLevel(config.DEFAULT_LOG_LEVEL) - config.MAXTHREADS = arguments.maxthreads config.XML = arguments.xml config.TXT = arguments.txt @@ -308,3 +305,7 @@ if __name__ == '__main__': parser.error("The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle") expanded_path = tilde_expansion(arguments.input) if arguments.input is not None else None run_analysis(expanded_path, arguments.pdbid) # Start main script + + +if __name__ == '__main__': + main() |