readd ad4 tests (#122)

Author: dp-yuanyn

unidock_tools/tests/applications/test_unidock.py

@@ -79,24 +79,24 @@ def test_unidock_pipeline_ligand_index(receptor, ligand, pocket):
     shutil.rmtree(results_dir, ignore_errors=True)
 
 
-# def test_unidock_pipeline_scoring_ad4(receptor, ligand, pocket):
-#     results_dir = "unidock_results_ad4"
-#     cmd = f"unidocktools unidock_pipeline -r {receptor} -l {ligand} -sd {results_dir} \
-#             -cx {pocket['center_x']} -cy {pocket['center_y']} -cz {pocket['center_z']} \
-#             -sx {pocket['size_x']} -sy {pocket['size_y']} -sz {pocket['size_z']} \
-#             -sf ad4 -nm 1 --seed 181129"
-#     print(cmd)
-#     resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
-#     print(resp.stdout)
-#     assert resp.returncode == 0, f"run unidock pipeline app err:\n{resp.stderr}"
-
-#     result_file = os.path.join(results_dir, Path(ligand).name)
-#     assert os.path.exists(result_file), f"docking result file not found"
-
-#     score_list = read_scores(result_file, "docking_score")
-#     score = score_list[0]
-#     assert -20 <= score <= 0, f"Uni-Dock score not in range: {score}"
-#     shutil.rmtree(results_dir, ignore_errors=True)
+def test_unidock_pipeline_scoring_ad4(receptor, ligand, pocket):
+    results_dir = "unidock_results_ad4"
+    cmd = f"unidocktools unidock_pipeline -r {receptor} -l {ligand} -sd {results_dir} \
+            -cx {pocket['center_x']} -cy {pocket['center_y']} -cz {pocket['center_z']} \
+            -sx {pocket['size_x']} -sy {pocket['size_y']} -sz {pocket['size_z']} \
+            -sf ad4 -nm 1 --seed 181129"
+    print(cmd)
+    resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
+    print(resp.stdout)
+    assert resp.returncode == 0, f"run unidock pipeline app err:\n{resp.stderr}"
+
+    result_file = os.path.join(results_dir, Path(ligand).name)
+    assert os.path.exists(result_file), f"docking result file not found"
+
+    score_list = read_scores(result_file, "docking_score")
+    score = score_list[0]
+    assert -20 <= score <= 0, f"Uni-Dock score not in range: {score}"
+    shutil.rmtree(results_dir, ignore_errors=True)
 
 
 def test_unidock_pipeline_multi_pose(receptor, ligand, pocket):

unidock_tools/tests/ut/dock/test_run_unidock.py

@@ -55,32 +55,32 @@ def test_run_unidock_vina(receptor, ligand, pocket):
     shutil.rmtree(workdir, ignore_errors=True)
 
 
-# def test_run_unidock_ad4(receptor, ligand, pocket):
-#     from unidock_tools.modules.docking import run_unidock
-
-#     workdir = Path(f"./tmp+{uuid.uuid4()}")
-#     workdir.mkdir(parents=True, exist_ok=True)
-
-#     result_ligands, scores_list = run_unidock(
-#         receptor=receptor,
-#         ligands=[ligand],
-#         output_dir=workdir,
-#         center_x=pocket[0],
-#         center_y=pocket[1],
-#         center_z=pocket[2],
-#         size_x=pocket[3],
-#         size_y=pocket[4],
-#         size_z=pocket[5],
-#         scoring="ad4",
-#         num_modes=5,
-#         energy_range=6.0,
-#         seed=181129,
-#     )
-
-#     result_ligand = result_ligands[0]
-#     assert os.path.exists(result_ligand)
-
-#     scores = scores_list[0]
-#     assert len(scores) == 5
-
-#     shutil.rmtree(workdir, ignore_errors=True)
+def test_run_unidock_ad4(receptor, ligand, pocket):
+    from unidock_tools.modules.docking import run_unidock
+
+    workdir = Path(f"./tmp+{uuid.uuid4()}")
+    workdir.mkdir(parents=True, exist_ok=True)
+
+    result_ligands, scores_list = run_unidock(
+        receptor=receptor,
+        ligands=[ligand],
+        output_dir=workdir,
+        center_x=pocket[0],
+        center_y=pocket[1],
+        center_z=pocket[2],
+        size_x=pocket[3],
+        size_y=pocket[4],
+        size_z=pocket[5],
+        scoring="ad4",
+        num_modes=5,
+        energy_range=6.0,
+        seed=181129,
+    )
+
+    result_ligand = result_ligands[0]
+    assert os.path.exists(result_ligand)
+
+    scores = scores_list[0]
+    assert len(scores) == 5
+
+    shutil.rmtree(workdir, ignore_errors=True)