Upload app.py

app.py

@@ -6,29 +6,6 @@ from scripts.download import download_and_clean_pdb
 from scripts.generator import run_broteinshake_generator
 from scripts.refine import polish_design
 
-import subprocess
-import sys
-
-def install_dependencies():
-    """Forces installation of missing physics/bio libraries on Hugging Face."""
-    try:
-        import Bio
-        import openmm
-        print("✅ Dependencies already present.")
-    except ImportError:
-        print("🔧 Installing missing dependencies... this may take a minute.")
-        # Install biopython specifically
-        subprocess.check_call([sys.executable, "-m", "pip", "install", "biopython"])
-        # If openmm is missing, we try to grab the pip-compatible version
-        subprocess.check_call([sys.executable, "-m", "pip", "install", "openmm"])
-        print("✅ Installation complete.")
-
-install_dependencies()
-
-# NOW you can import your other scripts
-from Bio.PDB import PDBParser
-# ... rest of your code ...
-
 # --- HELPER FUNCTIONS ---
 
 def extract_best_sequence(fasta_file: str) -> str:
@@ -90,18 +67,23 @@ def run_part1(pdb_id, fixed_chains, variable_chains):
         return "", f"Error in Part 1: {str(e)}"
 
 def run_part2(pdb_id, uploaded_esm_file):
-    """Aligns the ESM-folded PDB and resolves clashes."""
+    """Aligns the ESM-folded PDB to the target structure."""
     try:
         if uploaded_esm_file is None:
-            return None, "Please upload the PDB file you downloaded from ESM Atlas."
+            return None, "⚠️ Please upload the PDB from ESM Atlas first."
         
-        # Gradio saves the upload to a temp path
-        # We pass that path to your refinement script
-        final_pdb_path, rmsd_val = polish_design(pdb_id, uploaded_esm_file)
+        # Call the new lightweight Biopython-only script
+        final_pdb_path, rmsd_val = polish_design(pdb_id, uploaded_esm_file.name)
         
-        return final_pdb_path, f"Lead Candidate Validated! \nRMSD: {rmsd_val:.3f} Å \nClashes: 0 (OpenMM Optimized)"
+        # Update the report to focus on Backbone Alignment
+        report = (
+            f"✅ Validation Successful!\n"
+            f"🎯 RMSD: {rmsd_val:.3f} Å\n"
+            f"🧬 Status: High-Precision Backbone Match"
+        )
+        return final_pdb_path, report
     except Exception as e:
-        return None, f"Error in Part 2: {str(e)}"
+        return None, f"❌ Error: {str(e)}"
 
 # --- GRADIO INTERFACE ---
 
@@ -124,17 +106,18 @@ with gr.Blocks(theme=gr.themes.Soft()) as demo:
             
             gen_btn.click(run_part1, inputs=[pdb_input, f_chains, v_chains], outputs=[fa_output, status1])
 
-        # TAB 2: PHYSICS VALIDATION
-        with gr.Tab("2. Structural Refinement"):
-            gr.Markdown("Upload the PDB you folded on ESM Atlas to perform alignment and clash resolution.")
+        # TAB 2: STRUCTURAL VALIDATION
+        with gr.Tab("2. Structural Validation"):
+            gr.Markdown("### Align Designed Shuttle to Human Receptor")
             with gr.Row():
                 esm_upload = gr.File(label="Upload ESM-Folded PDB", file_types=[".pdb"])
-                refined_download = gr.File(label="Download Refined Lead Candidate")
+                refined_download = gr.File(label="Download Aligned Lead (.pdb)")
             
-            refine_btn = gr.Button("Refine & Resolve Clashes", variant="primary")
+            # Change the button text to match our new approach
+            validate_btn = gr.Button("✨ Run Structural Alignment", variant="primary")
             status2 = gr.Textbox(label="Validation Report", interactive=False)
             
-            refine_btn.click(run_part2, inputs=[pdb_input, esm_upload], outputs=[refined_download, status2])
+            validate_btn.click(run_part2, inputs=[pdb_input, esm_upload], outputs=[refined_download, status2])
 
 # Launch the app
 if __name__ == "__main__":