stjames 0.0.50__tar.gz → 0.0.52__tar.gz

{stjames-0.0.50/stjames.egg-info → stjames-0.0.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.50
+Version: 0.0.52
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.50 → stjames-0.0.52}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.50"
+version = "0.0.52"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.50 → stjames-0.0.52}/stjames/pdb.py

@@ -4,7 +4,7 @@ from typing import Any, Literal
 
 import atomium  # type: ignore [import-untyped]
 from atomium.pdb import pdb_dict_to_data_dict, pdb_string_to_pdb_dict  # type: ignore [import-untyped]
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 from stjames.types import Matrix3x3, Vector3D
 
@@ -166,9 +166,17 @@ class PDBDescription(BaseModel):
     title: str | None
     authors: list[str] = []
     classification: str | None
-    deposition_date: date | None
+    deposition_date: str | None
     keywords: list[str] = []
 
+    @field_validator("deposition_date", mode="before")
+    @classmethod
+    def date_to_string(cls, v: str | date | None) -> str | None:
+        if v is None:
+            return v
+
+        return str(date)
+
 
 class PDB(BaseModel):
     """A PDB formatted file."""

{stjames-0.0.50 → stjames-0.0.52}/stjames/workflows/docking.py

@@ -1,25 +1,25 @@
 """Docking workflow."""
 
-from typing import Self
+from typing import Annotated
 
-from pydantic import BaseModel, ConfigDict, field_validator, model_validator
+from pydantic import AfterValidator, ConfigDict, field_validator
 
-from ..molecule import Molecule
+from ..base import Base, round_float
 from ..pdb import PDB
-from ..types import Vector3D
+from ..types import UUID, Vector3D
 from .workflow import Workflow
 
 
-class Score(BaseModel):
+class Score(Base):
     """
     Pose with its score.
 
     :param pose: conformation of the ligand when docked
-    :param score: score of the pose
+    :param score: score of the pose, in kcal/mol
     """
 
-    pose: Molecule
-    score: float
+    pose: UUID | None  # for calculation
+    score: Annotated[float, AfterValidator(round_float(3))]
 
 
 class DockingWorkflow(Workflow):
@@ -27,12 +27,15 @@ class DockingWorkflow(Workflow):
     Docking workflow.
 
     Inherited:
-    :param initial_molecule: Molecule of interest (currently unused)
+    :param initial_molecule: Molecule of interest
     :param mode: Mode for workflow (currently unused)
 
     New:
     :param molecules: Molecules to dock (optional)
     :param smiles: SMILES strings of the ligands (optional)
+    :param do_csearch: whether to csearch starting structures
+    :param do_optimization: whether to optimize starting structures
+    :param conformers: UUIDs of optimized conformers
     :param target: PDB of the protein
     :param pocket: center (x, y, z) and size (x, y, z) of the pocket
 
@@ -42,12 +45,14 @@ class DockingWorkflow(Workflow):
 
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    molecules: list[Molecule] = []
-    smiles: list[str] = []
+    do_csearch: bool = True
+    do_optimization: bool = True
+    conformers: list[UUID] = []
 
     target: PDB
     pocket: tuple[Vector3D, Vector3D]
 
+    do_pose_hydrogen_refinement: bool = True
     scores: list[Score] = []
 
     def __str__(self) -> str:
@@ -61,16 +66,6 @@ class DockingWorkflow(Workflow):
 
         return f"<{type(self).__name__} {target} {ligand}>"
 
-    @model_validator(mode="after")
-    def check_molecules(self) -> Self:
-        """Check if molecules are provided."""
-        if self.molecules and self.smiles:
-            raise ValueError("Must provide only one of molecules or smiles, not both")
-        elif not self.molecules and not self.smiles:
-            raise ValueError("Must provide either molecules or smiles")
-
-        return self
-
     @field_validator("pocket", mode="after")
     def validate_pocket(cls, pocket: tuple[Vector3D, Vector3D]) -> tuple[Vector3D, Vector3D]:
         center, size = pocket

{stjames-0.0.50 → stjames-0.0.52/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.50
+Version: 0.0.52
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.50 → stjames-0.0.52}/tests/test_pdb.py

@@ -1,6 +1,6 @@
 from pytest import mark
 
-from stjames.pdb import fetch_pdb, pdb_from_string
+from stjames.pdb import PDB, fetch_pdb, pdb_from_string
 
 
 def test_1ema() -> None:
@@ -15,6 +15,9 @@ def test_read_pdb() -> None:
     pdb = pdb_from_string(data)
     assert pdb.description.code == "1EMA"
 
+    json = pdb.model_dump()
+    PDB.model_validate(json)
+
 
 # fmt: off
 @mark.regression
@@ -41,4 +44,7 @@ def test_read_pdb() -> None:
     ]
 )  # fmt: on
 def test_pdb(code: str) -> None:
-    fetch_pdb(code)
+    pdb = fetch_pdb(code)
+
+    json = pdb.model_dump()
+    PDB.model_validate(json)