Merge pull request #634 from marrink-lab/custom-molname

Custom molname

bin/martinize2

@@ -323,6 +323,14 @@ def entry():
              "if instead all chains in the input file should be merged.\n"
              "Can be given multiple times for different groups of chains to merge.",
     )
+    file_group.add_argument(
+        "-name",
+        dest="molname",
+        type=str,
+        default="molecule",
+        help="Name for the output molecule. If not specified, will default to 'molecule_{0..n}' for the number of"
+             " molecules in your system."
+    )
     file_group.add_argument(
         "-resid",
         dest="resid_handling",
@@ -551,12 +559,6 @@ def entry():
         default=9.414,
         help=("The strength of the Go model structural bias in kJ/mol."),
     )
-    go_group.add_argument(
-        "-go-moltype",
-        dest="govs_moltype",
-        default="molecule_0",
-        help=("Set the name of the molecule when using " "Virtual Sites GoMartini."),
-    )
     go_group.add_argument(
         "-go-low",
         dest="go_low",
@@ -987,11 +989,12 @@ def entry():
 
     # Generate the Go model if required
     if args.go:
+        go_name_prefix = args.molname
         LOGGER.info("Reading Go model contact map.", type="step")
         go_map = read_go_map(args.go)
         LOGGER.info("Generating the Go model.", type="step")
         GoPipeline.run_system(system,
-                              moltype=args.govs_moltype,
+                              moltype=go_name_prefix,
                               contact_map=go_map,
                               cutoff_short=args.go_low,
                               cutoff_long=args.go_up,
@@ -1019,7 +1022,7 @@ def entry():
                 raise argparse.ArgumentError(chain_merging,
                                              message=("Multiple conflicting merging arguments given. "
                                                       "Either specify -merge all or -merge A,B,C (+)."))
-        vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp).run_system(system)
+        vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp, molname=args.molname).run_system(system)
         defines = ()
 
     # Apply a rubber band elastic network is required.

vermouth/processors/name_moltype.py

@@ -58,9 +58,10 @@ class NameMolType(Processor):
         the molecule.
     """
     # TODO: See issue #35
-    def __init__(self, deduplicate=True, meta_key='moltype'):
+    def __init__(self, deduplicate=True, meta_key='moltype', molname='molecule'):
         self.deduplicate = deduplicate
         self.meta_key = meta_key
+        self.molname = molname
         super().__init__()
 
     def run_system(self, system):
@@ -85,8 +86,8 @@ def _name_with_deduplication(self, system):
                 group_id += 1
                 representatives.append((group_id, molecule))
                 match_id = group_id
-            molecule.meta[self.meta_key] = 'molecule_{}'.format(match_id)
+            molecule.meta[self.meta_key] = '{}_{}'.format(self.molname, match_id)
 
     def _name_without_deduplication(self, system):
         for molecule_id, molecule in enumerate(system.molecules):
-            molecule.meta[self.meta_key] = 'molecule_{}'.format(molecule_id)
+            molecule.meta[self.meta_key] = '{}_{}'.format(self.molname, molecule_id)

vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command

@@ -8,3 +8,4 @@ martinize2
 -go ../map.map 
 -noscfix
 -cys none
+-name molecule_0

vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command

@@ -10,3 +10,4 @@ martinize2
 -water-bias-eps E:-.5 C:1.0 H:-1.0
 -noscfix
 -cys none
+-name molecule_0