Update app.py

app.py

@@ -33,11 +33,12 @@ import warnings
 warnings.filterwarnings('ignore')
 
 # --- Page Configuration ---
+# CORRECTED: Removed the 'theme' argument to prevent errors and rely on custom CSS.
 st.set_page_config(
     page_title="AI Drug Discovery Pipeline",
     page_icon="🔬",
     layout="wide",
-    initial_sidebar_state="collapsed"
+    initial_sidebar_state="collapsed", 
 )
 
 # Custom CSS for a professional, dark theme
@@ -156,8 +157,7 @@ def visualize_protein_3d(pdb_data: str, title="Protein 3D Structure"):
     if not pdb_data:
         return None, "Cannot generate 3D view: No PDB data provided."
     try:
-        js_url = 'https://cdn.jsdelivr.net/npm/[email protected]/build/3Dmol.js'
-        viewer = py3Dmol.view(width='100%', height=600, js=js_url)
+        viewer = py3Dmol.view(width='100%', height=600)
         viewer.setBackgroundColor('#1C1C1C') 
         viewer.addModel(pdb_data, "pdb")
         viewer.setStyle({'cartoon': {'color': 'spectrum', 'thickness': 0.8}})
@@ -448,15 +448,15 @@ def visualize_molecule_2d_3d(smiles: str, name: str):
         svg_2d = svg_2d.replace('fill:black', 'fill:white')
         svg_2d = svg_2d.replace('stroke:#000000', 'stroke:#FFFFFF')
         svg_2d = svg_2d.replace('fill:#000000', 'fill:#FFFFFF')
-        svg_2d = svg_2d.replace('stroke:#000', 'stroke:#FFF')
+        svg_2d = svg_2d.replace('stroke:#000', 'stroke="#FFF"')
         svg_2d = svg_2d.replace('fill:#000', 'fill="#FFF"')
         svg_2d = svg_2d.replace('stroke="rgb(0,0,0)"', 'stroke="rgb(255,255,255)"')
         svg_2d = svg_2d.replace('fill="rgb(0,0,0)"', 'fill="rgb(255,255,255)"')
         svg_2d = svg_2d.replace('stroke:rgb(0,0,0)', 'stroke:rgb(255,255,255)')
         svg_2d = svg_2d.replace('fill:rgb(0,0,0)', 'fill:rgb(255,255,255)')
         svg_2d = svg_2d.replace('color="black"', 'color="white"')
-        svg_2d = svg_2d.replace('color:#000000', 'color:#FFFFFF')
-        svg_2d = svg_2d.replace('color:#000', 'color:#FFF')
+        svg_2d = svg_2d.replace('color:#000000', 'color="#FFFFFF"')
+        svg_2d = svg_2d.replace('color:#000', 'color="#FFF"')
         
         # Aggressive regex-based fixes for all text elements
         # Remove any existing fill attributes from text elements and add white fill
@@ -487,8 +487,7 @@ def visualize_molecule_2d_3d(smiles: str, name: str):
         AllChem.MMFFOptimizeMolecule(mol_3d)
         sdf_data = Chem.MolToMolBlock(mol_3d)
 
-        js_url = 'https://cdn.jsdelivr.net/npm/[email protected]/build/3Dmol.js'
-        viewer = py3Dmol.view(width=400, height=300, js=js_url)
+        viewer = py3Dmol.view(width=400, height=300)
         viewer.setBackgroundColor('#1C1C1C') 
         viewer.addModel(sdf_data, "sdf")
         viewer.setStyle({'stick': {}, 'sphere': {'scale': 0.25}})
@@ -520,8 +519,7 @@ def visualize_protein_ligand_interaction(pdb_data: str, pdb_id: str, ligand_resn
         return None, "Cannot generate interaction view: No PDB data provided."
     
     try:
-        js_url = 'https://cdn.jsdelivr.net/npm/[email protected]/build/3Dmol.js'
-        viewer = py3Dmol.view(width='100%', height=650, js=js_url)
+        viewer = py3Dmol.view(width='100%', height=650)
         viewer.setBackgroundColor('#1C1C1C')
         
         # Add the protein structure
@@ -795,7 +793,8 @@ with tab1:
         with p1_tabs[0]:
             st.subheader(f"3D Structure for PDB ID: {pdb_id_input}")
             if res1.get('protein_view'):
-                st.html(res1['protein_view'])
+                # CORRECTED: Use st.markdown with unsafe_allow_html=True to render the component.
+                st.markdown(res1['protein_view'], unsafe_allow_html=True)
             else:
                 st.warning("Could not display 3D structure. Check PDB ID and logs.")
         
@@ -879,7 +878,8 @@ with tab2:
         with p2_tabs[1]:
             st.subheader(f"Simulated Interaction for PDB {p2_pdb_id} with Ligand {p2_ligand_resn}")
             if res2.get('interaction_view'):
-                st.html(res2['interaction_view'])
+                # CORRECTED: Use st.markdown with unsafe_allow_html=True to render the component.
+                st.markdown(res2['interaction_view'], unsafe_allow_html=True)
             else:
                 st.warning("Could not display interaction view. Check inputs and logs.")
                 
@@ -941,7 +941,8 @@ with tab3:
         
         st.subheader("2D & 3D Molecular Structures")
         for name, visual_html in res3.get('visuals', {}).items():
-            st.html(visual_html)
+            # CORRECTED: Use st.markdown with unsafe_allow_html=True to render the component.
+            st.markdown(visual_html, unsafe_allow_html=True)
 
 
 # --- Phase 4: Pre-clinical & RWE ---
@@ -1002,5 +1003,4 @@ with tab4:
             st.dataframe(res4.get('reg_df', pd.DataFrame()), use_container_width=True, hide_index=True)
             
             st.subheader("Ethical AI Framework")
-            st.dataframe(res4.get('eth_df', pd.DataFrame()), use_container_width=True, hide_index=True)
-
+            st.dataframe(res4.get('eth_df', pd.DataFrame()), use_container_width=True, hide_index=True)