fix: fix broken pubchem api temporarily

app.py

@@ -50,14 +50,60 @@ def retrieve_smiles_tool(compound_name: str) -> str | None:
     Args:
         compound_name: The compound name to retrieve the SMILES from described in natural language.
     """
-
-    compounds = get_compounds(compound_name, namespace='name')
-
-    if compounds:
+    
+    # Common chemical name mappings as fallback
+    common_smiles = {
+        "ethane": "CC",
+        "methane": "C", 
+        "propane": "CCC",
+        "butane": "CCCC",
+        "benzene": "c1ccccc1",
+        "toluene": "Cc1ccccc1",
+        "water": "O",
+        "ethanol": "CCO",
+        "methanol": "CO"
+    }
+    
+    try:
+        compounds = get_compounds(compound_name, namespace='name')
+        
+        if not compounds:
+            # Try lowercase fallback for common compounds
+            if compound_name.lower() in common_smiles:
+                print(f"PubChem search failed, using known SMILES for {compound_name}")
+                return common_smiles[compound_name.lower()]
+            
+            print(f"No compounds found for {compound_name}.")
+            return None
+        
         compound = compounds[0]
-        return compound.isomeric_smiles
-    else:
-        print(f"No compounds found for {compound_name}.")
+        
+        # Workaround for PubChemPy issue #101 - extract SMILES from record properties
+        smiles_props = [i for i in compound.to_dict().get("record").get("props") if i["urn"]["label"] == "SMILES"]
+        
+        if smiles_props:
+            # Prefer "Absolute" SMILES (isomeric), fall back to "Connectivity" (canonical)
+            for prop in smiles_props:
+                if prop["urn"]["name"] == "Absolute":
+                    return prop["value"]["sval"]
+            
+            # If no Absolute found, use the first SMILES available
+            return smiles_props[0]["value"]["sval"]
+        else:
+            # Fall back to common compounds if no SMILES found
+            if compound_name.lower() in common_smiles:
+                print(f"No SMILES found in PubChem, using fallback for {compound_name}")
+                return common_smiles[compound_name.lower()]
+            return None
+            
+    except Exception as e:
+        print(f"PubChem API error for {compound_name}: {e}")
+        
+        # Fallback to common compounds
+        if compound_name.lower() in common_smiles:
+            print(f"Using fallback SMILES for {compound_name}")
+            return common_smiles[compound_name.lower()]
+        
         return None
 
 @tool
@@ -383,15 +429,22 @@ def qsartoolbox_get_property_value_tool(smiles:str, qsartoolbox_qsar_model: str)
             "VEGA - Adipose tissue - blood model (INERIS)"
     """
 
-    qsar_model_guid = next(x for x in possible_qsar_guids if qsartoolbox_qsar_model == x["value"])["key"]
-
-    results = jaqpot.qsartoolbox_qsar_model_predict_sync(smiles, qsar_model_guid)
-    result = next((x for x in results if x["Value"] != ''), None)
+    try:
+        qsar_model_guid = next(x for x in possible_qsar_guids if qsartoolbox_qsar_model == x["value"])["key"]
+        
+        print(f"Attempting QSAR prediction for SMILES: {smiles} using model: {qsartoolbox_qsar_model}")
+        results = jaqpot.qsartoolbox_qsar_model_predict_sync(smiles, qsar_model_guid)
+        result = next((x for x in results if x["Value"] != ''), None)
 
-    if(result != None):
-        return result
-    else:
-        return None
+        if(result != None):
+            return result
+        else:
+            return "No prediction results available for this compound with the selected model."
+            
+    except Exception as e:
+        error_msg = f"QSAR prediction failed: {str(e)}"
+        print(error_msg)
+        return error_msg
 
 final_answer = FinalAnswerTool()