Fix File component schema bug - use Textbox for SDF content instead

app.py

@@ -51,7 +51,7 @@ def name_to_smiles(name: str) -> str:
 
 
 def name_to_3d_molecule(name: str) -> tuple:
-    """Convert chemical name to 3D molecule SDF file and 2D visualization"""
+    """Convert chemical name to 3D molecule SDF and 2D visualization"""
     try:
         # Convert name to SMILES
         smiles = cirpy.resolve(name, 'smiles')
@@ -74,13 +74,8 @@ def name_to_3d_molecule(name: str) -> tuple:
         # Optimize geometry
         AllChem.MMFFOptimizeMolecule(mol)
 
-        # 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 SDF content
+        sdf_content = Chem.MolToMolBlock(mol)
         
         # Generate 2D image for preview
         mol_2d = Chem.MolFromSmiles(smiles)  # Get 2D version
@@ -96,7 +91,7 @@ def name_to_3d_molecule(name: str) -> tuple:
         # Get SMILES string
         canonical_smiles = Chem.MolToSmiles(mol_2d)
 
-        # Create HTML with 2D image and download info
+        # Create HTML with 2D image and SDF content
         html_content = f"""
         <div style="text-align: center; padding: 20px;">
             <h3>{name}</h3>
@@ -105,16 +100,16 @@ def name_to_3d_molecule(name: str) -> tuple:
             <p style="margin-top: 10px; color: #666;">2D Structure Preview</p>
             <div style="margin-top: 20px; padding: 15px; background-color: #d4edda; border: 2px solid #28a745; border-radius: 8px;">
                 <p style="color: #155724; font-size: 16px; font-weight: bold; margin: 0;">
-                    ✓ 3D SDF File Generated Successfully!
+                    ✓ 3D SDF Content Ready!
                 </p>
                 <p style="color: #155724; margin: 5px 0 0 0;">
-                    Scroll down to download the 3D SDF file with optimized coordinates
+                    Copy the SDF content below and save as .sdf file
                 </p>
             </div>
         </div>
         """
 
-        return html_content, sdf_file.name
+        return html_content, sdf_content
 
     except Exception as e:
         raise gr.Error(f"Error creating molecule: {str(e)}")
@@ -166,10 +161,10 @@ molecule_3d_interface = gr.Interface(
     inputs=gr.Textbox(label="Chemical Name", placeholder="e.g., benzene, aspirin, caffeine, glucose"),
     outputs=[
         gr.HTML(label="2D Preview"),
-        gr.File(label="📥 Download 3D SDF File (with optimized 3D coordinates)")
+        gr.Textbox(label="3D SDF Content (copy and save as .sdf file)", lines=20, max_lines=30)
     ],
     api_name="name_to_molecule",
-    description="Get 2D structure preview and download 3D SDF file with optimized molecular coordinates. The SDF file can be opened in PyMOL, Avogadro, ChimeraX, or other molecular viewers.",
+    description="Get 2D structure preview and 3D SDF content. Copy the SDF text and save as .sdf file to open in PyMOL, Avogadro, ChimeraX, or other molecular viewers.",
     cache_examples=False,
 )