Use matplotlib with 4 viewing angles for reliable orbital visualization

app.py

@@ -253,35 +253,102 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
                 if not Path(cube_file).exists():
                     continue
                 
-                # Read cube file content
-                cube_data = Path(cube_file).read_text()
+                # Read cube file and parse
+                x, y, z, values = parse_cube_file(cube_file)
                 
-                # Get molecular structure
-                mol_block = Chem.MolToMolBlock(mol_3d)
+                # Create matplotlib figure with 4 viewing angles
+                fig = plt.figure(figsize=(16, 12))
                 
-                # Create py3Dmol viewer using the Python library
-                import py3Dmol
+                # Get atom positions
+                atom_coords = []
+                atom_symbols = []
+                for atom in mol_3d.GetAtoms():
+                    pos = mol_3d.GetConformer().GetAtomPosition(atom.GetIdx())
+                    atom_coords.append([pos.x, pos.y, pos.z])
+                    atom_symbols.append(atom.GetSymbol())
+                atom_coords = np.array(atom_coords)
                 
-                view = py3Dmol.view(width=800, height=600)
+                # Create 3D mesh grid
+                X, Y, Z = np.meshgrid(x, y, z, indexing='ij')
                 
-                # Add molecular structure
-                view.addModel(mol_block, "sdf")
-                view.setStyle({'stick': {'radius': 0.15}, 'sphere': {'scale': 0.3}})
+                # Sample points for orbital lobes
+                iso_val = 0.02
+                pos_mask = values > iso_val
+                neg_mask = values < -iso_val
                 
-                # Add orbital isosurfaces from cube data
-                view.addVolumetricData(cube_data, "cube", {'isoval': 0.02, 'color': "blue", 'alpha': 0.75})
-                view.addVolumetricData(cube_data, "cube", {'isoval': -0.02, 'color': "red", 'alpha': 0.75})
+                # Get positive and negative points
+                pos_points = None
+                neg_points = None
+                if np.any(pos_mask):
+                    pos_points = np.column_stack((X[pos_mask], Y[pos_mask], Z[pos_mask]))
+                    if len(pos_points) > 2000:
+                        sample_idx = np.random.choice(len(pos_points), 2000, replace=False)
+                        pos_points = pos_points[sample_idx]
                 
-                view.zoomTo()
+                if np.any(neg_mask):
+                    neg_points = np.column_stack((X[neg_mask], Y[neg_mask], Z[neg_mask]))
+                    if len(neg_points) > 2000:
+                        sample_idx = np.random.choice(len(neg_points), 2000, replace=False)
+                        neg_points = neg_points[sample_idx]
                 
-                # Generate standalone HTML
-                viewer_html = view._make_html()
+                # Create 4 subplots with different angles
+                viewing_angles = [
+                    (30, 45, 'Front-Right'),
+                    (30, 135, 'Front-Left'),
+                    (30, 225, 'Back-Left'),
+                    (30, 315, 'Back-Right')
+                ]
+                
+                for idx, (elev, azim, view_name) in enumerate(viewing_angles):
+                    ax = fig.add_subplot(2, 2, idx + 1, projection='3d')
+                    
+                    # Plot atoms
+                    for coord, symbol in zip(atom_coords, atom_symbols):
+                        if symbol == 'C':
+                            color, size = 'black', 200
+                        elif symbol == 'O':
+                            color, size = 'red', 250
+                        elif symbol == 'N':
+                            color, size = 'blue', 250
+                        elif symbol == 'H':
+                            color, size = 'lightgray', 100
+                        else:
+                            color, size = 'purple', 150
+                        ax.scatter(*coord, c=color, s=size, alpha=0.9, edgecolors='white', linewidth=1.5)
+                        ax.text(*coord, f'  {symbol}', fontsize=10, fontweight='bold')
+                    
+                    # Plot orbital lobes
+                    if pos_points is not None:
+                        ax.scatter(pos_points[:, 0], pos_points[:, 1], pos_points[:, 2], 
+                                 c='blue', alpha=0.4, s=3, label='Positive (+)')
+                    
+                    if neg_points is not None:
+                        ax.scatter(neg_points[:, 0], neg_points[:, 1], neg_points[:, 2], 
+                                 c='red', alpha=0.4, s=3, label='Negative (-)')
+                    
+                    ax.set_xlabel('X (Å)', fontsize=10, fontweight='bold')
+                    ax.set_ylabel('Y (Å)', fontsize=10, fontweight='bold')
+                    ax.set_zlabel('Z (Å)', fontsize=10, fontweight='bold')
+                    ax.set_title(f'{view_name} View', fontsize=12, fontweight='bold')
+                    ax.view_init(elev=elev, azim=azim)
+                    ax.legend(loc='upper right', fontsize=9)
+                    ax.grid(True, alpha=0.3)
+                
+                plt.suptitle(f'{label} Orbital - Multiple Views', fontsize=16, fontweight='bold', y=0.98)
+                plt.tight_layout()
+                
+                # Convert to base64 image
+                buf = io.BytesIO()
+                plt.savefig(buf, format='png', dpi=150, bbox_inches='tight', facecolor='white')
+                buf.seek(0)
+                img_base64 = base64.b64encode(buf.read()).decode('utf-8')
+                plt.close(fig)
                 
                 html_sections.append(
-                    f"<div style='margin: 20px 0; padding: 10px; border: 1px solid #ddd; border-radius: 5px;'>"
-                    f"<h3>{label} Orbital (Interactive 3D)</h3>"
-                    f"<p><small>Blue = positive orbital lobe, Red = negative orbital lobe. Use mouse to rotate, scroll to zoom.</small></p>"
-                    f"<div style='width: 100%; height: 600px;'>{viewer_html}</div>"
+                    f"<div style='margin: 20px 0; padding: 15px; background: white; border: 2px solid #ddd; border-radius: 8px;'>"
+                    f"<h3 style='color: #333; margin-top: 0;'>{label} Orbital Visualization</h3>"
+                    f"<img src='data:image/png;base64,{img_base64}' style='max-width: 100%; height: auto; border-radius: 4px;'/>"
+                    f"<p style='margin-bottom: 0; color: #666;'><small><strong>Blue</strong> = positive orbital lobe | <strong>Red</strong> = negative orbital lobe | Four different viewing angles shown</small></p>"
                     f"</div>"
                 )
 

force_rebuild.txt

@@ -1,2 +1,2 @@
 # Force rebuild
-2025-11-08 v12
+2025-11-08 v13