separate parser from main code. Update public and pilot docs to hopef…

…ully be nice.

apps/pilot/jadolfbr/copy_top_each_strategy.py

@@ -12,9 +12,7 @@
 
 
 
-
-
-if __name__ == "__main__":
+def get_parser():
     parser = ArgumentParser()
     parser.add_argument("-n",
                         help = "Number of models to copy. DEFAULT = 2",
@@ -32,7 +30,11 @@
                         help = "The type of strategies we are interested in",
                         default = ["delta_unsats_per_1000_dSASA", "dG_top_Ptotal"],
                         nargs = '*')
+    return parser
+
+if __name__ == "__main__":
 
+    parser = get_parser()
     options = parser.parse_args()
 
 

apps/pilot/jadolfbr/glycan_basic_LCM_protocol.py

@@ -4,15 +4,15 @@
 from argparse import ArgumentParser
 
 from rosetta import *
+from pyrosetta import *
 from rosetta.protocols.carbohydrates import LinkageConformerMover
 from rosetta.protocols.carbohydrates import SimpleGlycosylateMover
 from rosetta.core.pose import parse_resnum
 
-rosetta.init("-include_sugars -write_pdb_link_records")
+init("-include_sugars -write_pdb_link_records")
 
 
-
-if __name__ == "__main__":
+def get_parser():
     parser = ArgumentParser("This is a sample demonstration of the LinkageConformerMover in PyRosetta.  "
                             "For more, use GlycanRelax, which uses the LCM. ")
 
@@ -36,7 +36,12 @@
                         default = 75,
                         help = "Total number of cycles to attempt using the LCM")
 
+    return parser
+
+if __name__ == "__main__":
+
 
+    parser = get_parser()
     options = parser.parse_args()
 
 

apps/pilot/jadolfbr/nnk_scorefxn.py

@@ -14,8 +14,7 @@
 NNKSortIndex = namedtuple('NNKSortIndex', 'antibody antigen sort')
 _sorts_ = ['S1', 'S2', 'S3']
 
-if __name__ == "__main__":
-
+def get_parser():
     parser = ArgumentParser("This app scores putitative broadly neutralizing antibodies based on pre-processed NNK sorting data")
 
     parser.add_argument('--nnk_dir', '-d', default = "sort_data",         help = "Full or relative path to pre-processed NNK data")
@@ -60,6 +59,12 @@
     parser.add_argument('--prefix', default = "", help = "Any prefix for output data.")
 
     parser.add_argument('--include_cdrs', default = ['L1','L2','L3','H1','H2'], nargs="*", help = "CDRs to include.  By default we skip H3")
+
+    return parser
+
+if __name__ == "__main__":
+
+    parser = get_parser()
     options = parser.parse_args()
 
 

apps/public/antibody_benchmark_utils/RunRosettaBenchmarksMPI.py

@@ -5,6 +5,10 @@
 
 ##Main to RunRosetta.
 
+def get_parser():
+    run_rosetta = RunRosettaBenchmarks()
+    return run_rosetta.parser
+
 if __name__ == "__main__":
     run_rosetta = RunRosettaBenchmarks()
     run_rosetta.run()