fix some more issues

bin/martinize2

@@ -549,7 +549,7 @@ def entry():
         "-go-eps",
         dest="go_eps",
         type=float,
-        default=0.0,
+        default=9.414,
         help=("The strength of the Go model structural bias in kJ/mol."),
     )
     go_group.add_argument(

vermouth/rcsu/contact_map.py

@@ -36,15 +36,27 @@ def read_go_map(file_path):
         lines = _file.readlines()
 
     contacts = []
+    OV=0
+    rCSU=0
     for line in lines:
         tokens = line.strip().split()
         if len(tokens) == 0:
             continue
 
         if tokens[0] == "R" and len(tokens) == 18:
-            contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8]))
+            # this is a bad place to filter but follows
+            # the old script
+            if tokens[11] == "1":
+                # this is a OV contact we take it
+                contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8]))
+                OV+=1
+            if tokens[11] == "0" and tokens[14] == "1":
+                # this is a rCSU contact we take it
+                contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8]))
+                rCSU+=1
 
     if len(contacts) == 0:
         raise IOError("You contact map is empty. Are you sure it has the right formatting?")
 
+    print(len(contacts), OV, rCSU)
     return contacts

vermouth/rcsu/go_structure_bias.py

@@ -184,6 +184,8 @@ def contact_selector(self, molecule):
                                                                resid=resIDB,
                                                                chain=chainB,
                                                                prefix=self.moltype))
+                    if (atype_b, atype_a, dist) in contact_matrix:
+                        continue
                     # generate backbone backbone exclusions
                     # perhaps one day can be it's own function
                     excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"})
@@ -218,7 +220,7 @@ def compute_go_interaction(self, contacts):
             contact_bias = NonbondParam(atoms=(atype_a, atype_b),
                                         sigma=sigma,
                                         epsilon=self.go_eps,
-                                        meta={"comment": ["go bond"]})
+                                        meta={"comment": [f"go bond {dist}"]})
             self.system.gmx_topology_params["nonbond_params"].append(contact_bias)
 
     def run_molecule(self, molecule):