stjames 0.0.99__tar.gz → 0.0.102__tar.gz

{stjames-0.0.99 → stjames-0.0.102}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright (c) Rowan (https://rowansci.com)
+Copyright (c) Rowan Scientific Corporation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{stjames-0.0.99/stjames.egg-info → stjames-0.0.102}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.99
+Version: 0.0.102
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.99 → stjames-0.0.102}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.99"
+version = "0.0.102"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.99 → stjames-0.0.102}/stjames/molecule.py

@@ -157,12 +157,20 @@ class Molecule(Base):
             return None
         return self.energy + self.thermal_enthalpy_corr
 
+    @property
+    def enthalpy(self) -> Optional[float]:
+        return self.sum_energy_enthalpy
+
     @property
     def sum_energy_free_energy(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_free_energy_corr is None):
             return None
         return self.energy + self.thermal_free_energy_corr
 
+    @property
+    def gibbs_free_energy(self) -> Optional[float]:
+        return self.sum_energy_free_energy
+
     @pydantic.model_validator(mode="after")
     def check_electron_sanity(self) -> Self:
         num_electrons = sum(self.atomic_numbers) - self.charge

{stjames-0.0.99 → stjames-0.0.102}/stjames/workflows/__init__.py

@@ -9,6 +9,7 @@ from .conformer import *
 from .conformer_search import *
 from .descriptors import *
 from .docking import *
+from .double_ended_ts_search import DoubleEndedTSSearchWorkflow
 from .electronic_properties import *
 from .fukui import *
 from .hydrogen_bond_basicity import *
@@ -36,6 +37,7 @@ WORKFLOW_NAME = Literal[
     "conformer_search",
     "descriptors",
     "docking",
+    "double_ended_ts_search",
     "electronic_properties",
     "fukui",
     "hydrogen_bond_basicity",
@@ -63,6 +65,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "conformer_search": ConformerSearchWorkflow,  # type: ignore [dict-item]
     "descriptors": DescriptorsWorkflow,  # type: ignore [dict-item]
     "docking": DockingWorkflow,  # type: ignore [dict-item]
+    "double_ended_ts_search": DoubleEndedTSSearchWorkflow,  # type: ignore [dict-item]
     "electronic_properties": ElectronicPropertiesWorkflow,  # type: ignore [dict-item]
     "fukui": FukuiIndexWorkflow,  # type: ignore [dict-item]
     "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # type: ignore [dict-item]

{stjames-0.0.99 → stjames-0.0.102}/stjames/workflows/basic_calculation.py

@@ -1,5 +1,10 @@
 """Basic calculation workflow."""
 
+from typing import Self
+
+from pydantic import model_validator
+
+from ..engine import Engine
 from ..settings import Settings
 from ..types import UUID
 from .workflow import MoleculeWorkflow
@@ -20,5 +25,12 @@ class BasicCalculationWorkflow(MoleculeWorkflow):
     """
 
     settings: Settings
-    engine: str
+    engine: Engine = None  # type: ignore [assignment]
     calculation_uuid: UUID | None = None
+
+    @model_validator(mode="after")
+    def set_engine(self) -> Self:
+        """Set the calculation engine."""
+        self.engine = self.engine or self.settings.method.default_engine()
+
+        return self

{stjames-0.0.99 → stjames-0.0.102}/stjames/workflows/nmr.py

@@ -29,7 +29,7 @@ class NMRPeak(Base):
 
     nucleus: int
     shift: Annotated[float, AfterValidator(round_float(3))]
-    atom_indices: set[int]
+    atom_indices: list[int]
 
 
 class NMRSpectroscopyWorkflow(MoleculeWorkflow):
@@ -68,6 +68,6 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
     per_conformer_chemical_shifts: list[Annotated[list[float | None], AfterValidator(round_optional_list(3))]] = []
     chemical_shifts: Annotated[list[float | None], AfterValidator(round_optional_list(3))] = []
-    symmetry_equivalent_nuclei: list[set[int]] = []
+    symmetry_equivalent_nuclei: list[list[int]] = []
 
     predicted_peaks: dict[int, list[NMRPeak]] = {}

{stjames-0.0.99 → stjames-0.0.102}/stjames/workflows/solubility.py

@@ -4,10 +4,17 @@ from typing import Annotated, Self
 
 from pydantic import AfterValidator, BaseModel, model_validator
 
-from ..types import round_list
+from ..base import LowercaseStrEnum
+from ..types import round_list, round_optional_list
 from .workflow import SMILESWorkflow
 
 
+class SolubilityMethod(LowercaseStrEnum):
+    FASTSOLV = "fastsolv"
+    KINGFISHER = "kingfisher"
+    ESOL = "esol"
+
+
 class SolubilityResult(BaseModel):
     """
     Solubility result.
@@ -17,7 +24,7 @@ class SolubilityResult(BaseModel):
     """
 
     solubilities: Annotated[list[float], AfterValidator(round_list(6))]
-    uncertainties: Annotated[list[float], AfterValidator(round_list(6))]
+    uncertainties: Annotated[list[float | None], AfterValidator(round_optional_list(6))]
 
     @model_validator(mode="after")
     def check_size(self) -> Self:
@@ -41,9 +48,10 @@ class SolubilityWorkflow(SMILESWorkflow):
     :param solubilities: {solvent: SolubilityResult}
     """
 
+    solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
     initial_smiles: str
-    solvents: list[str]
-    temperatures: list[float] = [273.15, 298.15, 323.15, 348.15, 373.15, 398.15, 423.15]  # 0–150 °C
+    solvents: list[str] = ["O"]
+    temperatures: list[float] = [298.15]
 
     solubilities: dict[str, SolubilityResult] = {}
 
@@ -55,6 +63,22 @@ class SolubilityWorkflow(SMILESWorkflow):
                 raise ValueError(f"Solubilities for {solvent} must have the same length as temperatures.")
 
             if solvent not in self.solvents:
-                raise ValueError(f"Solvent {solvent} not in initial list of solvents")
+                raise ValueError(f"Solvent {solvent} not in initial list of solvents.")
+
+        return self
+
+    @model_validator(mode="after")
+    def check_solvent_temperature(self) -> Self:
+        """Check that models with limited domain of applicability are predicting within correct domain."""
+        match self.solubility_method:
+            case SolubilityMethod.KINGFISHER | SolubilityMethod.ESOL:
+                if (len(self.solvents) > 1) or (self.solvents[0] != "O"):
+                    raise ValueError(f"Method `{self.solubility_method}` can only predict aqueous solubility, so `solvents` must be [`O`] only.")
+                if (len(self.temperatures) > 1) or (abs(self.temperatures[0] - 298.15) > 0.1):
+                    raise ValueError(
+                        f"Method `{self.solubility_method}` can only predict solubility at room temperature, so `temperatures` must be [298.15] only."
+                    )
+            case _:
+                pass
 
         return self

{stjames-0.0.99 → stjames-0.0.102/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.99
+Version: 0.0.102
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames