Update inference_app.py

inference_app.py

@@ -94,10 +94,10 @@ def predict (input_sequence, input_ligand, input_protein):
     AllChem.EmbedMolecule(m2)
     AllChem.MMFFOptimizeMolecule(m2)
     
-    Chem.SDWriter("ligand.sdf").write(m2)
+    Chem.SDWriter("/usr/src/app/ligand.sdf").write(m2)
 
-    os.system(f"obabel {input_protein.name} -xr -O receptor.pdbqt")
-    os.system("obabel -isdf ligand.sdf -O ligand.pdbqt")
+    os.system(f"obabel {input_protein.name} -xr -O /usr/src/app/receptor.pdbqt")
+    os.system("obabel -isdf /usr/src/app/ligand.sdf -O l/usr/src/app/ligand.pdbqt")
     #Find pocket
     pdb = md.load('receptor.pdb')
     # run ligsite
@@ -133,24 +133,24 @@ def predict (input_sequence, input_ligand, input_protein):
     
     pocket_top = md.Topology.from_dataframe(top_df, np.array([]))
     pocket_trj = md.Trajectory(xyz=densest_cluster_points, topology=pocket_top)
-    pocket_trj.save('./pockets_dense.pdb')
+    pocket_trj.save('/usr/src/app/pockets_dense.pdb')
     
     parser = PDBParser()
-    struc = parser.get_structure("X", "pockets_dense.pdb")
+    struc = parser.get_structure("X", "/usr/src/app/pockets_dense.pdb")
     coords = [x.coord for x in struc.get_atoms()]
     pocket_center = np.mean(coords, axis=0)
     output_text = run_smina(
-        "ligand.pdbqt",
-        "receptor.pdbqt",
-        "docking_pose.pdb",
+        "/usr/src/app/ligand.pdbqt",
+        "/usr/src/app/receptor.pdbqt",
+        "/usr/src/app/docking_pose.pdb",
         pocket_center,
         [10,10,10],
     )
-    os.system("pdb_rplresname -UNL:LIG docked_pose.pdb")
-    os.system("pdb_merge receptor.pdb docked_pose.pdb > output.pdb")
+    os.system("pdb_rplresname -UNL:LIG /usr/src/app/docking_pose.pdb")
+    os.system("pdb_merge /usr/src/app/receptor.pdb /usr/src/app/docking_pose.pdb > /usr/src/app/output.pdb")
     end_time = time.time()
     run_time = end_time - start_time
-    return "output.pdb", run_time
+    return "/usr/src/app/output.pdb", run_time
 
 with gr.Blocks() as app: