fix:tool app add default args

.github/workflows/ci_test_tools.yml

@@ -25,8 +25,9 @@ jobs:
         pip install flake8
 
     - name: Run flake8 formating
+      working-directory: ./unidock_tools
       run: |
-        flake8 unidock_tools/unidock_tools --exit-zero
+        flake8 src --exit-zero
 
   pyright:
     continue-on-error: true
@@ -48,7 +49,7 @@ jobs:
       id: pyright_check
       working-directory: ./unidock_tools
       run: |
-        pyright
+        pyright src
 
   tests:
     if: ${{ always() }}
@@ -84,10 +85,12 @@ jobs:
         pip install .
 
     - name: run unit-test
+      working-directory: ./unidock_tools
       run: |
         pip install pytest pytest-cov
-        pytest unidock_tools/tests/ut -vv --cov --cov-report term
+        pytest tests/ut -vv --cov --cov-report term
 
     - name: run application e2e test
+      working-directory: ./unidock_tools
       run: |
-        pytest unidock_tools/tests/applications -vv --cov --cov-report term
+        pytest tests/applications -vv --cov --cov-report term

.gitignore

@@ -18,5 +18,4 @@ unidock/example/screening_test/unidock_root
 unidock/example/screening_test/test_dock
 unidock_tools/dist
 unidock_tools/dist/*
-unidock_tools/unidock_tools.egg-info
-unidock_tools/unidock_tools.egg-info/*
+*.egg-info

unidock_tools/src/unidock_tools/application/mcdock.py

@@ -11,6 +11,41 @@
 from .unidock_pipeline import UniDock
 
 
+DEFAULT_ARGS = {
+    "receptor": None,
+    "ligands": None,
+    "ligand_index": None,
+    "gen_conf": False,
+    "max_num_confs_per_ligand": 200,
+    "min_rmsd": 0.3,
+    "center_x": None,
+    "center_y": None,
+    "center_z": None,
+    "size_x": 22.5,
+    "size_y": 22.5,
+    "size_z": 22.5,
+    "workdir": "mcdock_workdir",
+    "savedir": "mcdock_results",
+    "batch_size": 1200,
+    "scoring_function_rigid_docking": "vina",
+    "search_mode_rigid_docking": "",
+    "exhaustiveness_rigid_docking": 128,
+    "max_step_rigid_docking": 20,
+    "num_modes_rigid_docking": 3,
+    "refine_step_rigid_docking": 3,
+    "topn_rigid_docking": 100,
+    "scoring_function_local_refine": "vina",
+    "search_mode_local_refine": "",
+    "exhaustiveness_local_refine": 512,
+    "max_step_local_refine": 40,
+    "num_modes_local_refine": 1,
+    "refine_step_local_refine": 3,
+    "topn_local_refine": 1,
+    "seed": 181129,
+    "debug": False,
+}
+
+
 class MultiConfDock(UniDock):
     def __init__(self,
                  receptor: Path,
@@ -69,6 +104,7 @@ def generate_conformation(self,
 
 
 def main(args: dict):
+    args = {**DEFAULT_ARGS, **args}
     if args["debug"]:
         logging.getLogger().setLevel("DEBUG")
 
@@ -154,7 +190,7 @@ def get_parser() -> argparse.ArgumentParser:
                         help="Receptor file in pdbqt format.")
     parser.add_argument("-l", "--ligands", type=lambda s: s.split(','), default=None,
                         help="Ligand file in sdf format. Specify multiple files separated by commas.")
-    parser.add_argument("-i", "--ligand_index", type=str, default="",
+    parser.add_argument("-i", "--ligand_index", type=str, default=None,
                         help="A text file containing the path of ligand files in sdf format.")
 
     parser.add_argument("-g", "--gen_conf", action="store_true",
@@ -181,8 +217,8 @@ def get_parser() -> argparse.ArgumentParser:
                         help="Working directory. Default: 'MultiConfDock'.")
     parser.add_argument("-sd", "--savedir", type=str, default="mcdock_results",
                         help="Save directory. Default: 'MultiConfDock-Result'.")
-    parser.add_argument("-bs", "--batch_size", type=int, default=20,
-                        help="Batch size for docking. Default: 20.")
+    parser.add_argument("-bs", "--batch_size", type=int, default=1200,
+                        help="Batch size for docking. Default: 1200.")
 
     parser.add_argument("-sf_rd", "--scoring_function_rigid_docking",
                         type=str, default="vina",
@@ -200,7 +236,7 @@ def get_parser() -> argparse.ArgumentParser:
                         type=int, default=3,
                         help="Number of modes used in rigid docking. Default: 3.")
     parser.add_argument("-rs_rd", "--refine_step_rigid_docking",
-                        type=int, default=5,
+                        type=int, default=3,
                         help="Refine step used in rigid docking. Default: 3.")
     parser.add_argument("-topn_rd", "--topn_rigid_docking",
                         type=int, default=100,
@@ -222,8 +258,8 @@ def get_parser() -> argparse.ArgumentParser:
                         type=int, default=1,
                         help="Number of modes used in local refine. Default: 1.")
     parser.add_argument("-rs_lr", "--refine_step_local_refine",
-                        type=int, default=5,
-                        help="Refine step used in local refine. Default: 5.")
+                        type=int, default=3,
+                        help="Refine step used in local refine. Default: 3.")
     parser.add_argument("-topn_lr", "--topn_local_refine",
                         type=int, default=1,
                         help="Top N results used in local refine. Default: 1.")

unidock_tools/src/unidock_tools/application/unidock_pipeline.py

@@ -16,6 +16,34 @@
 from .base import Base
 
 
+DEFAULT_ARGS = {
+    "receptor": None,
+    "ligands": None,
+    "ligand_index": None,
+    "center_x": None,
+    "center_y": None,
+    "center_z": None,
+    "size_x": 22.5,
+    "size_y": 22.5,
+    "size_z": 22.5,
+    "workdir": "docking_workdir",
+    "savedir": "docking_results",
+    "batch_size": 1200,
+    "scoring_function": "vina",
+    "search_mode": "",
+    "exhaustiveness": 128,
+    "max_step": 20,
+    "num_modes": 3,
+    "refine_step": 3,
+    "energy_range": 3.0,
+    "topn": 100,
+    "score_only": False,
+    "local_only": False,
+    "seed": 181129,
+    "debug": False,
+}
+
+
 class UniDock(Base):
     def __init__(self,
                  receptor: Path,
@@ -177,17 +205,18 @@ def save_results(self, save_dir: Union[str, os.PathLike] = ""):
 
 
 def main(args: dict):
+    args = {**DEFAULT_ARGS, **args}
     workdir = Path(args["workdir"]).resolve()
     savedir = Path(args["savedir"]).resolve()
 
     ligands = []
-    if args["ligands"]:
+    if args.get("ligands"):
         for lig in args["ligands"]:
             if not Path(lig).exists():
                 logging.error(f"Cannot find {lig}")
                 continue
             ligands.append(Path(lig).resolve())
-    if args["ligand_index"]:
+    if args.get("ligand_index"):
         with open(args["ligand_index"], "r") as f:
             index_content = f.read()
         index_lines1 = [Path(line.strip()).resolve() for line in index_content.split("\n") 
@@ -243,7 +272,7 @@ def get_parser() -> argparse.ArgumentParser:
                         help="Receptor file in pdbqt format.")
     parser.add_argument("-l", "--ligands", type=lambda s: s.split(','), default=None,
                         help="Ligand file in sdf format. Specify multiple files separated by commas.")
-    parser.add_argument("-i", "--ligand_index", type=str, default="",
+    parser.add_argument("-i", "--ligand_index", type=str, default=None,
                         help="A text file containing the path of ligand files in sdf format.")
 
     parser.add_argument("-cx", "--center_x", type=float, required=True,