Add 3D SDF file download to molecule viewer

app.py

@@ -50,8 +50,8 @@ def name_to_smiles(name: str) -> str:
         raise gr.Error(f"Error converting name to SMILES: {str(e)}")
 
 
-def name_to_3d_molecule(name: str) -> str:
-    """Convert chemical name to 3D molecule visualization"""
+def name_to_3d_molecule(name: str) -> tuple:
+    """Convert chemical name to 3D molecule SDF file and 2D visualization"""
     try:
         # Convert name to SMILES
         smiles = cirpy.resolve(name, 'smiles')
@@ -74,8 +74,17 @@ def name_to_3d_molecule(name: str) -> str:
         # Optimize geometry
         AllChem.MMFFOptimizeMolecule(mol)
 
-        # Generate 2D image as fallback and show SMILES
-        img = Draw.MolToImage(mol, size=(400, 400))
+        # Save to SDF file
+        import tempfile
+        import os
+        sdf_file = tempfile.NamedTemporaryFile(mode='w', suffix='.sdf', delete=False)
+        writer = Chem.SDWriter(sdf_file.name)
+        writer.write(mol)
+        writer.close()
+        
+        # Generate 2D image for preview
+        mol_2d = Chem.MolFromSmiles(smiles)  # Get 2D version
+        img = Draw.MolToImage(mol_2d, size=(400, 400))
         
         # Convert image to base64
         import io
@@ -85,22 +94,23 @@ def name_to_3d_molecule(name: str) -> str:
         img_str = base64.b64encode(buffered.getvalue()).decode()
         
         # Get SMILES string
-        canonical_smiles = Chem.MolToSmiles(mol)
+        canonical_smiles = Chem.MolToSmiles(mol_2d)
 
-        # Create HTML with 2D image and molecule info
+        # Create HTML with 2D image and download info
         html_content = f"""
         <div style="text-align: center; padding: 20px;">
             <h3>{name}</h3>
             <p><strong>SMILES:</strong> {canonical_smiles}</p>
             <img src="data:image/png;base64,{img_str}" style="max-width: 100%; border: 1px solid #ddd; border-radius: 8px; padding: 10px; background: white;">
-            <p style="margin-top: 10px; color: #666;">2D Structure Visualization</p>
+            <p style="margin-top: 10px; color: #666;">2D Structure Preview</p>
+            <p style="margin-top: 10px; color: #28a745; font-weight: bold;">✓ 3D SDF file ready for download below</p>
         </div>
         """
 
-        return html_content
+        return html_content, sdf_file.name
 
     except Exception as e:
-        raise gr.Error(f"Error creating 3D molecule: {str(e)}")
+        raise gr.Error(f"Error creating molecule: {str(e)}")
 
 
 smiles_interface = gr.Interface(
@@ -147,9 +157,12 @@ tpsa_interface = gr.Interface(
 molecule_3d_interface = gr.Interface(
     fn=name_to_3d_molecule,
     inputs=gr.Textbox(label="Chemical Name", placeholder="e.g., benzene, aspirin, caffeine"),
-    outputs=gr.HTML(label="Molecule Viewer"),
+    outputs=[
+        gr.HTML(label="Molecule Viewer"),
+        gr.File(label="Download 3D SDF File")
+    ],
     api_name="name_to_molecule",
-    description="Convert a chemical name to a molecule visualization with SMILES.",
+    description="Convert a chemical name to a 2D visualization and download 3D SDF file with coordinates.",
     cache_examples=False,
 )