Update inference_app.py

inference_app.py

@@ -18,7 +18,6 @@ def generate_input_conformer(
     addHs: bool = False,
     minimize_maxIters: int = -1,
 ) -> Chem.Mol:
-
     _mol = Chem.MolFromSmiles(ligand_smiles)
     # need to add Hs to generate sensible conformers
     _mol = Chem.AddHs(_mol)
@@ -55,24 +54,19 @@ def generate_input_conformer(
 
 
 def optimize_coordinate(points, bound_buffer=15, dmin=6.05):
-
     bounds = list(
         zip(
             np.average(points, axis=0) - [bound_buffer]*3,
             np.average(points, axis=0) + [bound_buffer]*3
             )
         )
-
     # Define the constraint function (ensure dmin distance)
     con = NonlinearConstraint(lambda x: np.min(np.linalg.norm(points - x, axis=1)), dmin, 8)
-
     # Define the objective function (minimize pairwise distance)
     def objective(x):
         return np.sum(np.linalg.norm(points - x, axis=1))
-
     # Perform differential evolution to find the optimal coordinate
     result = differential_evolution(objective, bounds, constraints=con)
-
     return result.x, result.fun
 
 
@@ -96,12 +90,12 @@ def optimize_decoy_coordinate(points, bound_buffer=15, dmin=6.05, decoy_min=4.0,
 
 def add_decoy_atom(structure, decoy_pos):
     decoy = AtomArrayStack(length=1, depth=1)
-    decoy.coord = np.ones_like(struct.coord) * decoy_pos
+    decoy.coord = np.ones_like(decoy.coord) * decoy_pos
     decoy.chain_id = ["q"]
     decoy.element = ["C"]
     decoy.atom_name = ["C"]
     decoy.res_name = ["GLY"]
-    return structure + struct
+    return structure + decoy
 
 
 def set_protein_to_new_coord_plus_decoy_atom(input_pdb_file, new_coord, decoy_coord, output_file):