stjames 0.0.59__py3-none-any.whl → 0.0.61__py3-none-any.whl

stjames/workflows/docking.py

@@ -1,8 +1,8 @@
 """Docking workflow."""
 
-from typing import Annotated
+from typing import Annotated, Self
 
-from pydantic import AfterValidator, ConfigDict, field_validator
+from pydantic import AfterValidator, ConfigDict, field_validator, model_validator
 
 from ..base import Base, round_float
 from ..pdb import PDB
@@ -26,6 +26,10 @@ class DockingWorkflow(Workflow):
     """
     Docking workflow.
 
+    Note that the protein can be supplied either by UUID or raw PDB object.
+    We anticipate that the former will dominate deployed usage, but the latter is handy for isolated testing.
+    If, for whatever reason, the workflow is initialized with both a `target_uuid` and a `target`, the UUID will be ignored.
+
     Inherited:
     :param initial_molecule: Molecule of interest
     :param mode: Mode for workflow (currently unused)
@@ -36,7 +40,8 @@ class DockingWorkflow(Workflow):
     :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 target: PDB of the protein.
+    :param target_uuid: UUID of the protein.
     :param pocket: center (x, y, z) and size (x, y, z) of the pocket
 
     Results:
@@ -49,7 +54,8 @@ class DockingWorkflow(Workflow):
     do_optimization: bool = True
     conformers: list[UUID] = []
 
-    target: PDB
+    target: PDB | None = None
+    target_uuid: UUID | None = None
     pocket: tuple[Vector3D, Vector3D]
 
     do_pose_hydrogen_refinement: bool = True
@@ -60,16 +66,25 @@ class DockingWorkflow(Workflow):
 
     def __repr__(self) -> str:
         """Return a string representation of the Docking workflow."""
-        desc = self.target.description
-        target = desc.code or desc.title
-        ligand = "".join(atom.atomic_symbol for atom in self.initial_molecule.atoms)
+        if self.target is not None:
+            desc = self.target.description
+            target = desc.code or desc.title
+        else:
+            target = ""
 
+        ligand = "".join(atom.atomic_symbol for atom in self.initial_molecule.atoms)
         return f"<{type(self).__name__} {target} {ligand}>"
 
+    @model_validator(mode="after")
+    def check_protein(self) -> Self:
+        """Check if protein is provided."""
+        if not self.target and not self.target_uuid:
+            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
         if any(q <= 0 for q in size):
             raise ValueError(f"Pocket size must be positive, got: {size}")
-
         return pocket

{stjames-0.0.59.dist-info → stjames-0.0.61.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.59
+Version: 0.0.61
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.59.dist-info → stjames-0.0.61.dist-info}/RECORD

@@ -44,7 +44,7 @@ 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=K6zy4lo1XfrrMd7ZmKAe_Fd9wvKhtCMoK66gp-TsuJA,2158
+stjames/workflows/docking.py,sha256=boetrhWyF-JAi8DAyiZrH_dFLs4yIe8P6C-ZR73AJgk,2932
 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
@@ -57,8 +57,8 @@ 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-0.0.59.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.59.dist-info/METADATA,sha256=SDY-2LM12v5-wk8e25U1-U6L9ylteTXnMbm1FLkdohc,1713
-stjames-0.0.59.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-stjames-0.0.59.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.59.dist-info/RECORD,,
+stjames-0.0.61.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.61.dist-info/METADATA,sha256=kUkOkCULcbndmuv-hy5nCtBVAIJDNFy6MEI53KNIMDA,1713
+stjames-0.0.61.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+stjames-0.0.61.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.61.dist-info/RECORD,,