Update app.py

app.py

@@ -58,7 +58,7 @@ def inject_bfactors_and_save(pdb_file, scores_list, component_indices):
 
     return output_paths
 
-#--render the structure images
+# Render structure with py3Dmol and inject script tag manually
 def render_structure(pdb_path):
     with open(pdb_path, 'r') as f:
         pdb_data = f.read()
@@ -66,16 +66,25 @@ def render_structure(pdb_path):
     view.addModel(pdb_data, 'pdb')
     view.setStyle({'cartoon': {'color': 'bfactor'}})
     view.zoomTo()
-    
-    # Safely embed viewer + required 3Dmol.js script
-    viewer_html = view._make_html()
-    full_html = (
-        '<script src="https://3Dmol.org/build/3Dmol.js"></script>\n'
-        + viewer_html
+
+    # Combine viewer HTML with explicit 3Dmol.js script
+    html = (
+        '<script src="https://3Dmol.org/build/3Dmol.js"></script>'
+        + view._make_html()
     )
-    return full_html
+    return html
 
+# Gradio interface logic
+def process(seq, pdb_file, component_string):
+    try:
+        components = [int(c.strip()) for c in component_string.split(",") if c.strip().isdigit()]
+    except:
+        return [], "<p style='color:red'>Error: Invalid component list. Use comma-separated integers.</p>"
 
+    scores_list = compute_scaled_pca_scores(seq, components)
+    pdb_paths = inject_bfactors_and_save(pdb_file, scores_list, components)
+    html_view = render_structure(pdb_paths[0]) if pdb_paths else ""
+    return pdb_paths, html_view
 
 # Gradio UI
 demo = gr.Interface(
@@ -87,9 +96,10 @@ demo = gr.Interface(
     ],
     outputs=[
         gr.File(label="Download PDBs with PCA Projections", file_types=[".pdb"], file_count="multiple"),
-        gr.HTML(label="Interactive Structure Viewer (first PC only)")
+        gr.HTML(label="Interactive Structure Viewer (first PCA component only)")
     ],
     title="ESM-1b PCA Component Projection with Interactive 3D Structure"
 )
 
 demo.launch()
+