changed to run the processor on molecule not system.

changed file writer to deferred file writer

added cli to write file if desired

changed function names for internal use

made bond_type a global variable and removed function

corrected error in sphere generation

moved system merging to martinize2

bin/martinize2

@@ -48,7 +48,7 @@ from vermouth.map_input import (
     generate_all_self_mappings,
     combine_mappings,
 )
-from vermouth.rcsu.contact_map import GenerateContactMap
+from vermouth.rcsu.contact_map import GenerateContactMap, read_go_map
 from vermouth.rcsu.go_pipeline import GoPipeline
 from vermouth.gmx.topology import write_gmx_topology
 
@@ -550,8 +550,7 @@ def entry():
         const=None,
         type=Path,
         help="Use Martini Go model. Accepts either an input file from the server, "
-             "or just provide the flag to calculate as part of Martinize. Can be slow for large proteins "
-             "(> 1500 residues)"
+             "or just provide the flag to calculate as part of Martinize."
     )
     go_group.add_argument(
         "-go-eps",
@@ -582,6 +581,13 @@ def entry():
         help=("Minimum graph distance (similar sequence distance) below which"
               "contacts are removed. "),
     )
+    go_group.add_argument(
+        "-go-write-file",
+        dest="go_write_file",
+        action="store_false",
+        default=True,
+        help=("Write out contact map to file if calculating as part of Martinize2.")
+    )
 
     water_group = parser.add_argument_group("Apply water bias.")
     water_group.add_argument(
@@ -830,7 +836,7 @@ def entry():
     """
     Sort out the use of the go model:
     
-    go_file = True: calculate contact map
+    go = True: apply go model
     go_file = str: parse contact map 
     bool(go_file) = False: no go
     """
@@ -839,9 +845,8 @@ def entry():
     if args.go is None:
         go = True
     else:
-        if Path(args.go).is_file():
-            go_file = args.go
-            go = True
+        go_file = args.go
+        go = True
 
     if args.to_ff.startswith("elnedyn"):
         # FIXME: This type of thing should be added to the FF itself.
@@ -985,13 +990,14 @@ def entry():
         vermouth.AddCysteinBridgesThreshold(args.cystein_bridge).run_system(system)
 
     if go:
+        system = vermouth.MergeAllMolecules().run_system(system)
         # need this here because have to get contact map at atomistic resolution
         if go_file is None:
             LOGGER.info("Generating Go model contact map.", type="step")
-            GenerateContactMap().run_system(system)
+            GenerateContactMap(write_file=args.go_write_file).run_system(system)
         else:
             LOGGER.info("Reading Go model contact map.", type="step")
-            GenerateContactMap(path=go_file).run_system(system)
+            read_go_map(system=system, path=go_file)
 
 
     # Run martinize on the system.