stjames 0.0.106__tar.gz → 0.0.109__tar.gz

{stjames-0.0.106/stjames.egg-info → stjames-0.0.109}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.106
+Version: 0.0.109
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.106 → stjames-0.0.109}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.106"
+version = "0.0.109"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.106 → stjames-0.0.109}/stjames/workflows/pka.py

@@ -1,11 +1,12 @@
 """pKa workflow."""
 
-from typing import Annotated, Optional, Self
+from typing import Annotated, Self
 
 from pydantic import AfterValidator, model_validator
 
 from ..base import Base, LowercaseStrEnum, round_float, round_optional_float
 from ..mode import Mode
+from ..molecule import Molecule
 from ..solvent import Solvent
 from .workflow import DBCalculation, MoleculeWorkflow, SMILESWorkflow
 
@@ -33,17 +34,17 @@ class pKaMicrostate(Base):
     :param atom_index: index of the atom
     :param smiles: SMILES of the microstate
     :param structures: DBCalculation for the microstate
-    :param deltaG: relative free energy
-    :param pka: pKa
-    :uncertainty: uncertainty
+    :param deltaG: relative free energy (where applicable)
+    :param pka: pKa value associated with this microstate
+    :uncertainty: uncertainty in the pKa prediction
     """
 
     atom_index: int
-    smiles: Optional[str]
+    smiles: str | None = None
     structures: list[DBCalculation] = []
-    deltaG: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
+    deltaG: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
     pka: Annotated[float, AfterValidator(round_float(3))]
-    uncertainty: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
+    uncertainty: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
 
 
 class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
@@ -73,6 +74,9 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
     :param strongest_base: pKa of the strongest base
     """
 
+    initial_smiles: str = ""
+    initial_molecule: Molecule | None = None  # type: ignore [assignment]
+
     mode: Mode = Mode.CAREFUL
 
     microscopic_pka_method: MicroscopicpKaMethod = MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025

{stjames-0.0.106 → stjames-0.0.109/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.106
+Version: 0.0.109
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames