Merge pull request #39 from keisuke-yanagisawa/yaml_default

Refactor Default Value Handling in Configuration Files

Author: keisuke-yanagisawa

script/alignresenv.py

@@ -56,7 +56,7 @@ def selector(a: Atom):
 
     sup = SuperImposer()
     tmppdb = Path(tempfile.mkstemp(suffix=".pdb")[1])
-    with uPDB.PDBIOhelper(str(tmppdb)) as pdbio:
+    with uPDB.PDBIOhelper(tmppdb) as pdbio:
         for model in tqdm(struct, desc="[align res. env.]", disable=not verbose):
 
             # print(struct, i)

script/test_generate_msmd_system.py

@@ -63,11 +63,11 @@ def test_create_frcmod(self):
 
     def test_invalid_atomtype(self):
         with self.assertRaises(ValueError):
-            _create_frcmod(self.mol2file, "INVALID")  # type: ignore
+            _create_frcmod(self.mol2file, Path("INVALID"))  # type: ignore
 
     def test_mol2file_does_not_exist(self):
         with self.assertRaises(FileNotFoundError):
-            _create_frcmod("INVALID", self.atomtype)  # type: ignore
+            _create_frcmod(Path("INVALID"), self.atomtype)  # type: ignore
 
     def test_invalid_mol2file(self):
         with self.assertRaises(ValueError):

script/utilities/Bio/PDB.py

@@ -137,7 +137,7 @@ class PDBIOhelper:
     これは1つずつモデルを保存していきます。
     """
 
-    def __init__(self, path: str):
+    def __init__(self, path: Path):
         self.path = expandpath(path)
         self.open()
 
@@ -449,7 +449,7 @@ def concatenate_structures(structs: List[Structure]) -> Structure:
 
     with tempfile.NamedTemporaryFile("w") as f:
 
-        out_helper = PDBIOhelper(f.name)
+        out_helper = PDBIOhelper(Path(f.name))
         for struct in structs:
             out_helper.save(struct)
         out_helper.close()

script/utilities/Bio/test_PDB.py

@@ -30,7 +30,7 @@ def test_pdb_io_helper(self):
         reader = PDB.MultiModelPDBReader(str(self.pdbfile))
         models = [model for model in reader]
         tmp_output_pdb = Path(tempfile.mkstemp(suffix=".pdb")[1])
-        writer = PDB.PDBIOhelper(str(tmp_output_pdb))
+        writer = PDB.PDBIOhelper(tmp_output_pdb)
         for model in models:
             writer.save(model)
         writer.close()  # This is important, otherwise the unittest will hang up

script/utilities/util.py

@@ -7,8 +7,17 @@
 import yaml
 
 from .logger import logger
+import collections.abc
 
 
+def update_dict(d: dict, u: dict):
+    for k, v in u.items():
+        if isinstance(v, collections.abc.Mapping):
+            d[k] = update_dict(d.get(k, {}), v) # type: ignore
+        else:
+            d[k] = v
+    return d
+
 def getabsolutepath(path: Path) -> Path:
     """
     Get absolute path from relative path
@@ -67,29 +76,6 @@ def expand_index(ind_info: Union[str, int]):
     return ret
 
 
-def set_default(setting: dict) -> None:
-    """
-    Set default values (in place) for some fields in setting
-    """
-    if "multiprocessing" not in setting["general"]:
-        setting["general"]["multiprocessing"] = -1
-    if "valid_dist" not in setting["map"]:
-        setting["map"]["valid_dist"] = 5
-    if "threshold" not in setting["probe_profile"]:
-        setting["probe_profile"]["threshold"] = 0.001
-    if "env_dist" not in setting["probe_profile"]:
-        setting["probe_profile"]["resenv"]["env_dist"] = 4
-
-    if "dt" not in setting["exprorer_msmd"]["general"]:
-        setting["exprorer_msmd"]["general"]["dt"] = 0.002
-    if "temperature" not in setting["exprorer_msmd"]["general"]:
-        setting["exprorer_msmd"]["general"]["temperature"] = 300
-    if "pressure" not in setting["exprorer_msmd"]["general"]:
-        setting["exprorer_msmd"]["general"]["pressure"] = 1.0
-    if "num_process_per_gpu" not in setting["general"]:
-        setting["general"]["num_process_per_gpu"] = 1
-
-
 def ensure_compatibility_v1_1(setting: dict):
     """
     Ensure compatibility with exprorer_msmd v1.1
@@ -110,6 +96,38 @@ def ensure_compatibility_v1_1(setting: dict):
 
 
 def parse_yaml(yamlpath: Path) -> dict:
+    setting: dict = {
+        "general": {
+            "workdir": Path(""),
+            "multiprocessing": -1,
+            "num_process_per_gpu": 1,
+        },
+        "input": {
+            "protein": {
+                "pdb": Path(""),
+            },
+            "probe": {
+                "cid": "",
+            },
+        },
+        "exprorer_msmd": {
+            "general": {
+                "dt": 0.002,
+                "temperature": 300,
+                "pressure": 1.0,
+            },
+        },
+        "map": {
+            "snapshot": "",
+            "valid_dist": 5.0,
+        },
+        "probe_profile": {
+            "threshold": 0.001,
+            "resenv": {
+                "env_dist": 4.0,
+            },
+        },
+    }
     YAML_PATH = getabsolutepath(yamlpath)
     YAML_DIR_PATH = YAML_PATH.parent
     if not YAML_PATH.exists():
@@ -119,10 +137,11 @@ def parse_yaml(yamlpath: Path) -> dict:
     if not os.path.splitext(YAML_PATH)[1][1:] == "yaml":
         raise ValueError("YAML file must have .yaml extension: %s" % YAML_PATH)
     with YAML_PATH.open() as fin:
-        setting: dict = yaml.safe_load(fin)  # type: ignore
+        yaml_dict: dict = yaml.safe_load(fin) # type: ignore
+        if yaml_dict is not None:
+            update_dict(setting, yaml_dict)
 
     ensure_compatibility_v1_1(setting)
-    set_default(setting)
 
     if "mol2" not in setting["input"]["probe"] or setting["input"]["probe"]["mol2"] is None:
         setting["input"]["probe"]["mol2"] = setting["input"]["probe"]["cid"] + ".mol2"
@@ -169,9 +188,8 @@ def parse_yaml(yamlpath: Path) -> dict:
     )
     setting["input"]["probe"]["mol2"] = Path(setting["input"]["probe"]["mol2"])
 
-    if setting["input"]["protein"]["ssbond"] is None:
+    if "ssbond" not in setting["input"]["protein"] or setting["input"]["protein"]["ssbond"] is None:
         setting["input"]["protein"]["ssbond"] = []
 
     setting["general"]["yaml"] = YAML_PATH
-
     return setting