Update core/evolution/evolution.py

core/evolution/evolution.py

@@ -163,25 +163,32 @@ class MolecularEvolution:
         sample_smiles = []
         
         if survivors:
-            if self.config.maximize_cn:
-                # sort by highest CN
-                sorted_survivors = sorted(survivors, key=lambda m: m.cn, reverse=True)
+            is_final_gen = (gen == self.config.generations)
+        
+            if is_final_gen:
+                # FINAL generation → show top 5 survivors
+                if self.config.maximize_cn:
+                    sorted_survivors = sorted(survivors, key=lambda m: m.cn, reverse=True)
+                else:
+                    sorted_survivors = sorted(survivors, key=lambda m: m.cn_error)
+        
+                chosen = sorted_survivors[:5]
+        
             else:
-                # sort by lowest CN error (closest to target)
-                sorted_survivors = sorted(survivors, key=lambda m: m.cn_error)
+                # EARLY generations → show rejected molecules
+                survivor_smiles = set(m.smiles for m in survivors)
+                rejected = [m for m in population if m.smiles not in survivor_smiles]
         
-            top5 = sorted_survivors[:5]
+                chosen = rejected[:5]  # show up to 5 rejected ones
         
-            sample_smiles = [m.smiles for m in top5]
+            sample_smiles = [m.smiles for m in chosen]
+            sample_smiles = list(dict.fromkeys(sample_smiles))  # remove duplicates
         
-            # remove duplicates just in case
-            sample_smiles = list(dict.fromkeys(sample_smiles))
-    
             self.history.append({
                 "generation": gen,
                 "smiles": sample_smiles
             })
-            
+
             
             offspring = self._generate_offspring(survivors)