[bugfix] unidock pipeline option

dptech-corp · Apr 16, 2024 · a5e23d6 · a5e23d6
1 parent 5b98771
commit a5e23d6
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/unidock_tools/src/unidock_tools/application/proteinprep.py b/unidock_tools/src/unidock_tools/application/proteinprep.py
@@ -16,7 +16,7 @@ def parse_covalent_residue_atom_info(covalent_residue_atom_info_str: str) -> Lis
             residue_info_list.append((chain_id, residue_name, int(residue_number), atom_name))
         return residue_info_list
 
-    protein_pdbqt_file_name = receptor_preprocessor(
+    protein_pdbqt_file_name, protein_grid_prefix = receptor_preprocessor(
         protein_pdb_file_name=args['protein_pdb'],
         kept_ligand_resname_list=args['kept_ligand_resname_list'],
         prepared_hydrogen=args['prepared_hydrogen'],

diff --git a/unidock_tools/src/unidock_tools/application/unidock_pipeline.py b/unidock_tools/src/unidock_tools/application/unidock_pipeline.py
@@ -242,6 +242,11 @@ def main(args: dict):
         exit(1)
     logging.info(f"[UniDock Pipeline] {len(ligands)} ligands found.")
 
+    if args['scoring_function'] == 'ad4':
+        generate_ad4_grids = True
+    else:
+        generate_ad4_grids = False
+
     logging.info("[UniDock Pipeline] Start")
     start_time = time.time()
     def parse_covalent_residue_atom_info(covalent_residue_atom_info_str: str) -> List[List[Tuple[str, str, int, str]]]:
@@ -266,7 +271,7 @@ def parse_covalent_residue_atom_info(covalent_residue_atom_info_str: str) -> Lis
         prepared_hydrogen=args.get("prepared_hydrogen", True),
         preserve_original_resname=args.get("preserve_original_resname", True),
         covalent_residue_atom_info_list=parse_covalent_residue_atom_info(args.get("covalent_residue_atom_info")) if args.get("covalent_residue_atom_info") is not None else None,
-        generate_ad4_grids=args.get("generate_ad4_grids", False),
+        generate_ad4_grids=generate_ad4_grids,
         workdir=workdir
     )
     logging.info("[UniDock Pipeline] Start docking")