Update utils/parsing.py

utils/parsing.py

@@ -24,10 +24,14 @@ def parse_guidance_args():
     parser.add_argument("--motifs", type=str, required=False)
     parser.add_argument("--weights", type=float, nargs='+', required=False)
     parser.add_argument("--output_file", type=str, default='moo_outputs.txt')
-    parser.add_argument("--motif_penalty", action='store_true')
+    parser.add_argument("--specificity", default=False)
     parser.add_argument("--objectives", nargs="+", type=str, required=False, default=None,
-        choices=["Hemolysis","Non-Fouling","Solubility","Half-Life","Affinity","Motif","Specificity"],  
+        choices=["Hemolysis","Non-Fouling","Solubility", "Permeability", "Half-Life","Affinity","OffTarget","Motif","Specificity"],  
     )
+    parser.add_argument("--fixed_positions", type=str, default=None)
+    parser.add_argument("--cyclic", action='store_true')
+    parser.add_argument("--starting_sequence", type=str, default=None)
+    parser.add_argument("--offtarget", type=str, default=None)
     
     args = parser.parse_args()
     return args