changes using model

Gen_PartialSMILES2.py

@@ -274,7 +274,10 @@ model.to(device)
 model.eval()
 budget_generation = 10
 batch_size = 512
-scaf_smi = "[*]c1ccccc1"
+parser.add_argument("--scaffold", type=str, default="[*]c1ccccc1")
+
+scaf_smi = args.scaffold
+
 if len(scaf_smi) > 0:
     if "[*]" not in scaf_smi:
         raise ValueError("Scaffold does not contain attachment point")

src/ui/handlers.py

@@ -8,6 +8,7 @@ for the drug discovery application UI components.
 from ..molecules.analysis import analyze_molecule_image_only, validate_smiles_realtime, get_molecule_properties_for_hover
 from ..molecules.variations import generate_chemical_series_variations, generate_molecule_images
 from ..ai.services import respond, handle_structure_chat, parse_ai_structures
+from ..molecules.generated_variations import generate_variations_from_model
 
 
 class VariationHandlers:
@@ -24,7 +25,7 @@ class VariationHandlers:
         print(f"SMILES: {smiles}")
         print(f"Num variations: {num_variations}")
         
-        variations = generate_chemical_series_variations(smiles)
+        variations = generate_variations_from_model(smiles, num_variations)
         print(f"Generated {len(variations)} variations")
         
         self.current_variations = variations[:num_variations]