From b334659db44942ca1457af4752751b1281da4948 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Tue, 7 Jul 2020 20:48:27 +0530
Subject: using PLIP v2.1.3

---
 plip/plipcmd.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'plip/plipcmd.py')

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()
-- 
cgit v1.2.3