Switch from Volume to Isosurface for better orbital visualization rendering

app.py

@@ -249,58 +249,92 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
                 # Parse cube file
                 x, y, z, values = parse_cube_file(cube_file)
                 
-                # Create plotly figure for volume rendering
-                fig = go.Figure(data=go.Volume(
-                    x=x,
-                    y=y,
-                    z=z,
+                # Create 3D meshgrid
+                X, Y, Z = np.meshgrid(x, y, z, indexing='ij')
+                
+                # Create plotly figure with isosurface
+                fig = go.Figure()
+                
+                # Add positive isosurface (blue)
+                fig.add_trace(go.Isosurface(
+                    x=X.flatten(),
+                    y=Y.flatten(),
+                    z=Z.flatten(),
                     value=values.flatten(),
-                    isomin=-0.02,
-                    isomax=0.02,
-                    opacity=0.1,
-                    surface_count=2,
-                    colorscale='RdBu',
-                    reversescale=True
+                    isomin=0.02,
+                    isomax=values.max(),
+                    surface_count=1,
+                    colorscale=[[0, 'blue'], [1, 'blue']],
+                    showscale=False,
+                    caps=dict(x_show=False, y_show=False, z_show=False),
+                    opacity=0.7,
+                    name='Positive'
+                ))
+                
+                # Add negative isosurface (red)
+                fig.add_trace(go.Isosurface(
+                    x=X.flatten(),
+                    y=Y.flatten(),
+                    z=Z.flatten(),
+                    value=values.flatten(),
+                    isomin=values.min(),
+                    isomax=-0.02,
+                    surface_count=1,
+                    colorscale=[[0, 'red'], [1, 'red']],
+                    showscale=False,
+                    caps=dict(x_show=False, y_show=False, z_show=False),
+                    opacity=0.7,
+                    name='Negative'
                 ))
                 
                 # Add molecular structure
                 atom_x, atom_y, atom_z = [], [], []
                 atom_colors = []
+                atom_text = []
                 for atom in mol_3d.GetAtoms():
                     pos = mol_3d.GetConformer().GetAtomPosition(atom.GetIdx())
                     atom_x.append(pos.x)
                     atom_y.append(pos.y)
                     atom_z.append(pos.z)
+                    atom_text.append(atom.GetSymbol())
                     # Color by atom type
                     if atom.GetSymbol() == 'C':
-                        atom_colors.append('black')
+                        atom_colors.append('gray')
                     elif atom.GetSymbol() == 'N':
-                        atom_colors.append('blue')
+                        atom_colors.append('darkblue')
                     elif atom.GetSymbol() == 'O':
-                        atom_colors.append('red')
+                        atom_colors.append('darkred')
                     elif atom.GetSymbol() == 'H':
-                        atom_colors.append('white')
+                        atom_colors.append('lightgray')
                     else:
-                        atom_colors.append('gray')
+                        atom_colors.append('purple')
                 
                 fig.add_trace(go.Scatter3d(
                     x=atom_x, y=atom_y, z=atom_z,
-                    mode='markers',
-                    marker=dict(size=8, color=atom_colors),
+                    mode='markers+text',
+                    marker=dict(size=10, color=atom_colors, line=dict(width=1, color='white')),
+                    text=atom_text,
+                    textposition='top center',
+                    textfont=dict(size=8),
                     name='Atoms'
                 ))
                 
                 fig.update_layout(
-                    title=f'{label} Orbital',
-                    width=800,
+                    title=dict(text=f'{label} Orbital', x=0.5, xanchor='center'),
+                    width=700,
                     height=600,
                     scene=dict(
                         xaxis_title='X (Å)',
                         yaxis_title='Y (Å)',
                         zaxis_title='Z (Å)',
-                        aspectmode='data'
+                        aspectmode='data',
+                        camera=dict(
+                            eye=dict(x=1.5, y=1.5, z=1.5)
+                        )
                     ),
-                    margin=dict(l=0, r=0, t=40, b=0)
+                    margin=dict(l=0, r=0, t=40, b=0),
+                    showlegend=True,
+                    legend=dict(x=0.02, y=0.98)
                 )
                 
                 # Generate HTML with config
@@ -308,10 +342,10 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
                 config = {
                     'displayModeBar': True,
                     'displaylogo': False,
-                    'modeBarButtonsToRemove': ['toImage']
+                    'responsive': True
                 }
                 plot_html = pio.to_html(fig, full_html=False, include_plotlyjs='cdn', config=config)
-                html_sections.append(f"<div style='margin: 20px 0;'><h3>{label}</h3>{plot_html}</div>")
+                html_sections.append(f"<div style='margin: 20px 0; padding: 10px; border: 1px solid #ddd; border-radius: 5px;'>{plot_html}</div>")
 
             if not html_sections:
                 return "<p>Could not prepare HOMO/LUMO visualizations.</p>"

force_rebuild.txt

@@ -1,2 +1,2 @@
 # Force rebuild
-2025-11-08 v8
+2025-11-08 v9