Fix reaction visualization to properly parse SMILES and show correct molecular structures

app.py

@@ -190,47 +190,70 @@ def smiles_to_name(smiles: str) -> str:
 def reaction_smiles_to_svg(reaction_smiles: str) -> str:
     """Convert reaction SMILES to SVG image"""
     try:
-        # Parse the reaction SMILES - try ReactionFromSmarts first, fallback to manual parsing
-        try:
-            reaction = rdChemReactions.ReactionFromSmarts(reaction_smiles)
-        except:
-            # If ReactionFromSmarts fails, try to parse manually
-            if ">>" not in reaction_smiles:
-                raise gr.Error("Reaction SMILES must contain '>>' to separate reactants from products")
-            
-            parts = reaction_smiles.split(">>")
-            if len(parts) != 2:
-                raise gr.Error("Reaction SMILES must have exactly one '>>' separator")
-            
-            reactant_smiles = parts[0].strip()
-            product_smiles = parts[1].strip()
-            
-            # Create reaction from individual molecules
-            reactant_mols = []
-            for smi in reactant_smiles.split('.'):
-                smi = smi.strip()
-                if smi:
-                    mol = Chem.MolFromSmiles(smi)
-                    if mol is None:
-                        raise gr.Error(f"Invalid SMILES in reactants: {smi}")
-                    reactant_mols.append(mol)
-            
-            product_mols = []
-            for smi in product_smiles.split('.'):
+        # Parse the reaction SMILES properly
+        if ">>" not in reaction_smiles:
+            raise gr.Error("Reaction SMILES must contain '>>' to separate reactants from products")
+        
+        # Split by '>>' to get reactants and products
+        parts = reaction_smiles.split(">>")
+        if len(parts) != 2:
+            raise gr.Error("Reaction SMILES must have exactly one '>>' separator")
+        
+        # Handle optional reagents/conditions (e.g., "reactants>reagents>products")
+        reactant_part = parts[0].strip()
+        product_part = parts[1].strip()
+        
+        # Check if there are reagents (format: reactants>reagents>products)
+        if ">" in reactant_part:
+            reactant_smiles, reagent_smiles = reactant_part.split(">", 1)
+            reactant_smiles = reactant_smiles.strip()
+            reagent_smiles = reagent_smiles.strip()
+        else:
+            reactant_smiles = reactant_part
+            reagent_smiles = ""
+        
+        product_smiles = product_part
+        
+        # Create reaction from individual molecules using MolFromSmiles (not SMARTS)
+        reactant_mols = []
+        for smi in reactant_smiles.split('.'):
+            smi = smi.strip()
+            if smi:
+                mol = Chem.MolFromSmiles(smi)
+                if mol is None:
+                    raise gr.Error(f"Invalid SMILES in reactants: {smi}")
+                reactant_mols.append(mol)
+        
+        # Parse reagents/catalysts if present
+        reagent_mols = []
+        if reagent_smiles:
+            for smi in reagent_smiles.split('.'):
                 smi = smi.strip()
                 if smi:
                     mol = Chem.MolFromSmiles(smi)
                     if mol is None:
-                        raise gr.Error(f"Invalid SMILES in products: {smi}")
-                    product_mols.append(mol)
-            
-            reaction = rdChemReactions.ChemicalReaction()
-            for mol in reactant_mols:
-                reaction.AddReactantTemplate(mol)
-            for mol in product_mols:
-                reaction.AddProductTemplate(mol)
-
-        # Draw the reaction as image
+                        raise gr.Error(f"Invalid SMILES in reagents: {smi}")
+                    reagent_mols.append(mol)
+        
+        product_mols = []
+        for smi in product_smiles.split('.'):
+            smi = smi.strip()
+            if smi:
+                mol = Chem.MolFromSmiles(smi)
+                if mol is None:
+                    raise gr.Error(f"Invalid SMILES in products: {smi}")
+                product_mols.append(mol)
+        
+        # Build the reaction object
+        reaction = rdChemReactions.ChemicalReaction()
+        for mol in reactant_mols:
+            reaction.AddReactantTemplate(mol)
+        for mol in reagent_mols:
+            reaction.AddAgentTemplate(mol)
+        for mol in product_mols:
+            reaction.AddProductTemplate(mol)
+
+        # Draw the reaction as image with proper parameters
         image = Draw.ReactionToImage(reaction, subImgSize=(200, 200), useSVG=False, drawOptions=None, returnPNG=False)
         
         # Convert PIL image to base64 for HTML display
@@ -243,6 +266,17 @@ def reaction_smiles_to_svg(reaction_smiles: str) -> str:
         # Return as HTML img tag
         return f'<img src="data:image/png;base64,{img_str}" alt="Reaction" style="max-width:100%; height:auto;">'
 
+        
+        # Convert PIL image to base64 for HTML display
+        import io
+        import base64
+        buffer = io.BytesIO()
+        image.save(buffer, format='PNG')
+        img_str = base64.b64encode(buffer.getvalue()).decode()
+        
+        # Return as HTML img tag
+        return f'<img src="data:image/png;base64,{img_str}" alt="Reaction" style="max-width:100%; height:auto;">'
+
     except gr.Error:
         raise
     except Exception as e:
@@ -1346,17 +1380,17 @@ reaction_interface = gr.Interface(
     fn=reaction_smiles_to_svg,
     inputs=gr.Textbox(
         label="Reaction SMILES",
-        placeholder="CCO.O=C=O>>CC(=O)O.O=C=O (Esterification reaction)",
-        info="Use '>>' to separate reactants from products"
+        placeholder="CC=O.CC=O>[OH-]>CC(O)CC=O (Aldol condensation)",
+        info="Format: reactants>reagents>products or reactants>>products"
     ),
     outputs=gr.HTML(label="Reaction Visualization"),
     title="Reaction Visualizer",
-    description="Visualize chemical reactions from SMILES notation.",
+    description="Visualize chemical reactions from SMILES notation. Use 'reactants>reagents>products' or 'reactants>>products' format.",
     api_name="reaction_visualizer",
     examples=[
+        ["CC=O.CC=O>[OH-]>CC(O)CC=O"],
         ["CC(=O)O.CO>>CC(=O)OC.O"],
-        ["c1ccccc1.ClCl>>c1ccccc1Cl.Cl"],
-        ["Cl.[Na+].[OH-]>>[Na+].[Cl-].O"]
+        ["c1ccccc1.ClCl>>c1ccccc1Cl.Cl"]
     ],
 )