stjames 0.0.55__tar.gz → 0.0.57__tar.gz

{stjames-0.0.55/stjames.egg-info → stjames-0.0.57}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.55
+Version: 0.0.57
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.55 → stjames-0.0.57}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.55"
+version = "0.0.57"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.55 → stjames-0.0.57}/stjames/pdb.py

@@ -36,10 +36,10 @@ class PDBWater(BaseModel):
 
     model_config = ConfigDict(extra=EXTRA)
 
-    name: str | None
-    full_name: str | None
+    name: str | None = None
+    full_name: str | None = None
     atoms: dict[int, PDBAtom] = {}
-    internal_id: str | None
+    internal_id: str | None = None
     polymer: str
 
 
@@ -48,7 +48,7 @@ class PDBResidue(BaseModel):
 
     model_config = ConfigDict(extra=EXTRA)
 
-    name: str | None
+    name: str | None = None
     full_name: str | None = None
     atoms: dict[int, PDBAtom] = {}
     number: int
@@ -62,7 +62,7 @@ class PDBPolymer(BaseModel):
     internal_id: str
     helices: list[list[str]] = []
     residues: dict[str, PDBResidue] = {}
-    sequence: str | None
+    sequence: str | None = None
     strands: list[list[str]] = []
 
 
@@ -105,10 +105,10 @@ class PDBAssembly(BaseModel):
     model_config = ConfigDict(extra=EXTRA)
 
     transformations: list[PDBTransformations]
-    software: str | None
-    buried_surface_area: float | None
-    surface_area: float | None
-    delta_energy: float | None
+    software: str | None = None
+    buried_surface_area: float | None = None
+    surface_area: float | None = None
+    delta_energy: float | None = None
     id: int
 
 
@@ -152,10 +152,10 @@ class PDBExperiment(BaseModel):
 
     model_config = ConfigDict(extra=EXTRA)
 
-    expression_system: str | None
+    expression_system: str | None = None
     missing_residues: list[PDBMissingResidue] = []
-    source_organism: str | None
-    technique: str | None
+    source_organism: str | None = None
+    technique: str | None = None
 
 
 class PDBDescription(BaseModel):
@@ -163,11 +163,11 @@ class PDBDescription(BaseModel):
 
     model_config = ConfigDict(extra=EXTRA)
 
-    code: str | None
-    title: str | None
+    code: str | None = None
+    title: str | None = None
     authors: list[str] = []
-    classification: str | None
-    deposition_date: str | None
+    classification: str | None = None
+    deposition_date: str | None = None
     keywords: list[str] = []
 
     @field_validator("deposition_date", mode="before")
@@ -179,7 +179,7 @@ class PDBDescription(BaseModel):
         if isinstance(v, date):
             return v.isoformat()
 
-        return str(date)
+        return str(v)
 
 
 class PDB(BaseModel):

{stjames-0.0.55 → stjames-0.0.57/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.55
+Version: 0.0.57
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames