stjames 0.0.56__tar.gz → 0.0.58__tar.gz

{stjames-0.0.56/stjames.egg-info → stjames-0.0.58}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.56
+Version: 0.0.58
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.56 → stjames-0.0.58}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.56"
+version = "0.0.58"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.56 → stjames-0.0.58}/stjames/atomium_stjames/mmcif.py

@@ -399,12 +399,12 @@ def update_models_list(mmcif_dict: dict[str, Any], data_dict: dict[str, Any]) ->
     # sequences = make_sequences(mmcif_dict)
     secondary_structure = make_secondary_structure(mmcif_dict)
     aniso = make_aniso(mmcif_dict)
-    model: dict[str, Any] = {"polymer": {}, "non-polymer": {}, "water": {}, "branched": {}}
+    model: dict[str, Any] = {"polymer": {}, "non_polymer": {}, "water": {}, "branched": {}}
     model_num = mmcif_dict["atom_site"][0]["pdbx_PDB_model_num"]
     for atom in mmcif_dict["atom_site"]:
         if atom["pdbx_PDB_model_num"] != model_num:
             data_dict["models"].append(model)
-            model = {"polymer": {}, "non-polymer": {}, "water": {}, "branched": {}}
+            model = {"polymer": {}, "non_polymer": {}, "water": {}, "branched": {}}
             model_num = atom["pdbx_PDB_model_num"]
         mol_type = types[entities[atom["label_asym_id"]]]
         if mol_type == "polymer" or mol_type == "branched":
@@ -501,13 +501,13 @@ def add_atom_to_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict
 
 
 def add_atom_to_non_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict[str, Any], mol_type: str, names: dict[str, Any]) -> None:
-    """Takes an MMCIF atom dictionary, converts it, and adds it to a non-polymer
+    """Takes an MMCIF atom dictionary, converts it, and adds it to a non_polymer
     dictionary.
 
     :param dict atom: the .mmcif dictionary to read.
     :param dict aniso: lookup dictionary for anisotropy information.
     :param dict model: the model to update.
-    :param str mol_type: non-polymer or water.
+    :param str mol_type: non_polymer or water.
     :param dict names: the lookup dictionary for full name information."""
 
     mol_id = make_residue_id(atom)

{stjames-0.0.56 → stjames-0.0.58}/stjames/atomium_stjames/pdb.py

@@ -145,7 +145,7 @@ def update_models_list(pdb_dict: dict[str, Any], data_dict: dict[str, Any]) -> N
     for model_lines in pdb_dict["MODEL"]:
         aniso = make_aniso(model_lines)
         last_ter = get_last_ter_line(model_lines)
-        model: dict[str, Any] = {"polymer": {}, "non-polymer": {}, "water": {}}
+        model: dict[str, Any] = {"polymer": {}, "non_polymer": {}, "water": {}}
         for index, line in enumerate(model_lines):
             if line[:6] in ["ATOM  ", "HETATM"]:
                 chain_id = line[21] if index < last_ter else id_from_line(line)
@@ -512,7 +512,7 @@ def add_atom_to_non_polymer(line: str, model: dict[Any, Any], res_id: str, aniso
     :param str res_id: the molecule ID to add to.
     :param dict aniso_dict: lookup dictionary for anisotropy information."""
 
-    key = "water" if line[17:20] in ["HOH", "DOD"] else "non-polymer"
+    key = "water" if line[17:20] in ["HOH", "DOD"] else "non_polymer"
     try:
         model[key][res_id]["atoms"][int(line[6:11])] = atom_line_to_dict(line, aniso_dict)
     except Exception:

{stjames-0.0.56 → stjames-0.0.58}/stjames/pdb.py

@@ -84,7 +84,7 @@ class PDBModel(BaseModel):
     model_config = ConfigDict(extra=EXTRA)
 
     polymer: dict[str, PDBPolymer] = {}
-    non_polymer: dict[str, PDBNonPolymer] = Field(alias="non-polymer", default_factory=dict)
+    non_polymer: dict[str, PDBNonPolymer] = {}
     branched: dict[str, Any] = {}
     water: dict[str, PDBWater] = {}
 
@@ -179,7 +179,7 @@ class PDBDescription(BaseModel):
         if isinstance(v, date):
             return v.isoformat()
 
-        return str(date)
+        return str(v)
 
 
 class PDB(BaseModel):

{stjames-0.0.56 → stjames-0.0.58/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.56
+Version: 0.0.58
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames