Update inference_app.py

inference_app.py

@@ -155,8 +155,27 @@ def predict (input_sequence, input_ligand, input_protein):
         [10,10,10],
     )
     os.system("pdb_rplresname -UNL:LIG /usr/src/app/docking_pose.pdb > /usr/src/app/docking_pose_renamed.pdb")
-    os.system("cat {input_protein.name} /usr/src/app/docking_pose_renamed.pdb > /usr/src/app/output.pdb")
+    parser = PDB.PDBParser(QUIET=True)
     
+    # Parse the PDB files
+    structure1 = parser.get_structure('Structure1', input_protein.name)
+    structure2 = parser.get_structure('Structure2', "/usr/src/app/docking_pose_renamed.pdb")
+    
+    # Create a new structure for the combined output
+    combined_structure = PDB.Structure.Structure('Combined_Structure')
+    
+    # Add models from the first structure
+    for model in structure1:
+        combined_structure.add(model)
+    
+    # Add models from the second structure
+    for model in structure2:
+        combined_structure.add(model)
+    
+    # Save the combined structure to the output file
+    io = PDB.PDBIO()
+    io.set_structure(combined_structure)
+    io.save("/usr/src/app/output.pdb")    
     #os.system(f"pdb_merge {input_protein.name} /usr/src/app/docking_pose_renamed.pdb > /usr/src/app/output.pdb")
     end_time = time.time()
     run_time = end_time - start_time