Update inference_app.py

inference_app.py

@@ -28,11 +28,6 @@ from enspara import geometry
 from sklearn.cluster import DBSCAN
 import pandas as pd
 
-os.system("pwd")
-
-os.system("ls")
-
-os.system("touch ligand.sdf")
 
 def run_smina(
     ligand_path, protein_path, out_path, pocket_center, pocket_size, num_poses=1, exhaustiveness=1
@@ -151,36 +146,14 @@ def predict (input_sequence, input_ligand, input_protein):
     output_text = run_smina(
         "/usr/src/app/ligand.pdbqt",
         "/usr/src/app/receptor.pdbqt",
-        "/usr/src/app/docking_pose.pdb",
+        "/usr/src/app/docking_pose.sdf",
         pocket_center,
         [10,10,10],
     )
-    os.system("pdb_rplresname -UNL:LIG /usr/src/app/docking_pose.pdb > /usr/src/app/docking_pose_renamed.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
-    return "/usr/src/app/output.pdb", run_time
+    return ["/usr/src/app/output.pdb","/usr/src/app/docking_pose.sdf"], run_time
 
 with gr.Blocks() as app:
 
@@ -229,6 +202,11 @@ with gr.Blocks() as app:
       "resname": "LIG",
       "style": "stick",
       "color": "greenCarbon",
+    },
+         {
+      "model": 1,
+      "style": "stick",
+      "color": "greenCarbon",
     }
         
   ]