better check for consistent molecule names

src/multiego/ensemble.py

@@ -260,9 +260,9 @@ def initialize_molecular_contacts(contact_matrix, path, ensemble_molecules_idx_s
             # for intra-domain
             if args.multi_epsilon is not None:
                 temp_epsi_intra = args.multi_epsilon[contact_matrix["molecule_idx_ai_temp"].to_numpy(dtype=int)[0] - 1]
-                contact_matrix.loc[
-                    (contact_matrix["same_chain"]) & (contact_matrix["intra_domain"]), "epsilon_0"
-                ] = temp_epsi_intra
+                contact_matrix.loc[(contact_matrix["same_chain"]) & (contact_matrix["intra_domain"]), "epsilon_0"] = (
+                    temp_epsi_intra
+                )
                 if name[0] == "intramat":
                     print(f"		-Intra-domain epsilon {temp_epsi_intra}")
             else:
@@ -272,9 +272,9 @@ def initialize_molecular_contacts(contact_matrix, path, ensemble_molecules_idx_s
                 temp_epsi_inter_dom = args.multi_epsilon_inter_domain[
                     contact_matrix["molecule_idx_ai_temp"].to_numpy(dtype=int)[0] - 1
                 ]
-                contact_matrix.loc[
-                    (contact_matrix["same_chain"]) & (~contact_matrix["intra_domain"]), "epsilon_0"
-                ] = temp_epsi_inter_dom
+                contact_matrix.loc[(contact_matrix["same_chain"]) & (~contact_matrix["intra_domain"]), "epsilon_0"] = (
+                    temp_epsi_inter_dom
+                )
                 if name[0] == "intramat":
                     print(f"		-Inter-domain epsilon {temp_epsi_inter_dom}")
             else:
@@ -296,9 +296,9 @@ def initialize_molecular_contacts(contact_matrix, path, ensemble_molecules_idx_s
             if name[0] == "intramat":
                 print(f"		-Intra-domain epsilon {args.epsilon}")
             # for inter-domain
-            contact_matrix.loc[
-                (contact_matrix["same_chain"]) & (~contact_matrix["intra_domain"]), "epsilon_0"
-            ] = args.inter_domain_epsilon
+            contact_matrix.loc[(contact_matrix["same_chain"]) & (~contact_matrix["intra_domain"]), "epsilon_0"] = (
+                args.inter_domain_epsilon
+            )
             if name[0] == "intramat":
                 print(f"		-Inter-domain epsilon {args.inter_domain_epsilon}")
             # for inter-molecular
@@ -488,6 +488,7 @@ def init_meGO_ensemble(args):
         return ensemble
 
     reference_set = set(ensemble["topology_dataframe"]["name"].to_list())
+    unique_ref_molecule_names = topology_dataframe["molecule_name"].unique()
 
     # now we process the train contact matrices
     train_contact_matrices = {}
@@ -513,6 +514,10 @@ def init_meGO_ensemble(args):
             _,
             _,
         ) = initialize_topology(topology, custom_dict, args)
+        # check that the molecules defined have a reference
+        unique_temp_molecule_names = temp_topology_dataframe["molecule_name"].unique()
+        check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
+
         train_topology_dataframe = pd.concat(
             [train_topology_dataframe, temp_topology_dataframe],
             axis=0,
@@ -584,6 +589,9 @@ def init_meGO_ensemble(args):
             _,
             _,
         ) = initialize_topology(topology, custom_dict, args)
+        # check that the molecules defined have a reference
+        unique_temp_molecule_names = temp_topology_dataframe["molecule_name"].unique()
+        check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
         check_topology_dataframe = pd.concat(
             [check_topology_dataframe, temp_topology_dataframe],
             axis=0,
@@ -1323,6 +1331,16 @@ def do_apply_check_rules(meGO_ensemble, meGO_LJ, check_dataset, symmetries, para
     return meGO_LJ
 
 
+def check_molecule_names(ref_list, tmp_list):
+    # Check if all unique entries in temp_topology_dataframe are in other_dataframe
+    missing_molecules = [molecule for molecule in tmp_list if molecule not in ref_list]
+
+    if missing_molecules:
+        raise ValueError(
+            f"The following molecule(s) from a train dataset {missing_molecules} are not found in the reference dataset  {ref_list}"
+        )
+
+
 def consistency_checks(meGO_LJ):
     """
     Perform consistency checks on LJ parameters.