stjames 0.0.51__py3-none-any.whl → 0.0.52__py3-none-any.whl

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-0.0.51.dist-info → stjames-0.0.52.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.51
+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-0.0.51.dist-info → stjames-0.0.52.dist-info}/RECORD

@@ -39,7 +39,7 @@ stjames/workflows/bde.py,sha256=cWsZNiNdUy5DGvu8o6bBepLZIB5ohiAD6RKoK3YSq1I,9786
 stjames/workflows/conformer.py,sha256=LnpvH5HmLCn-ddH3r1WhEYONUMX5ohZswdESEPCR6o4,2907
 stjames/workflows/conformer_search.py,sha256=ZQ3VxQoaR_aZ-KSblXooAnGMTFbvOj4IQnM70K0OXhc,13497
 stjames/workflows/descriptors.py,sha256=lRRCsGzad3nIg0wI1090ffaXB0FVh0nRRb2lNxCY0kI,281
-stjames/workflows/docking.py,sha256=MvqfxCEZva91GB_w0qd68v7Dnb-F6AxzhQBsKJXkaeY,2239
+stjames/workflows/docking.py,sha256=K6zy4lo1XfrrMd7ZmKAe_Fd9wvKhtCMoK66gp-TsuJA,2158
 stjames/workflows/electronic_properties.py,sha256=uAIcGKKLhqoHyDgcOZulEXwTU2EjidyvOndZDYyeJEk,4003
 stjames/workflows/fukui.py,sha256=2J23RjkSOZ-40AM3AdnbJkRBGaCevkjkhnV3pVfa6lo,738
 stjames/workflows/hydrogen_bond_basicity.py,sha256=Luvov2DlDvZN06W-mU6YaN7wcIrTLwzdoWww-jNE3x4,517
@@ -52,8 +52,8 @@ stjames/workflows/scan.py,sha256=uNSuUmVMAV4exNvcv1viVe7930i7GZMn7RtEimnwEE8,100
 stjames/workflows/spin_states.py,sha256=b-uCf-pHjF_JHbExeb5GdRToE0pIxP0JTd50U130ckI,4693
 stjames/workflows/tautomer.py,sha256=x3TC8hkMs87ZUodLyhce5EUzYoV276ePfPMi7ISWyNU,651
 stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
-stjames-0.0.51.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.51.dist-info/METADATA,sha256=jzVVfTfwoI1DUMLSneJa8yejvEyOcNZgbBqx1UGVXD8,1689
-stjames-0.0.51.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-stjames-0.0.51.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.51.dist-info/RECORD,,
+stjames-0.0.52.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.52.dist-info/METADATA,sha256=4vbKOo5yexzEQRYM3x6_fYAyAt72lhpU-UKSn_hdOwE,1689
+stjames-0.0.52.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+stjames-0.0.52.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.52.dist-info/RECORD,,