stjames 0.0.33__tar.gz → 0.0.35__tar.gz

{stjames-0.0.33/stjames.egg-info → stjames-0.0.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.33
+Version: 0.0.35
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -9,6 +9,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydantic>=2.4
+Requires-Dist: numpy
 
 # stjames
 

{stjames-0.0.33 → stjames-0.0.35}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.33"
+version = "0.0.35"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -10,6 +10,7 @@ authors = [
 
 dependencies = [
     "pydantic>=2.4",
+    "numpy",
 ]
 
 [build-system]
@@ -38,3 +39,6 @@ select = [
     "W",  # pycodestyle warnings
 ]
 ignore = ["E741"]
+
+[tool.mypy]
+plugins = ["pydantic.mypy"]

{stjames-0.0.33 → stjames-0.0.35}/stjames/_deprecated_solvent_settings.py

@@ -1,4 +1,4 @@
-import pydantic
+from pydantic import PositiveFloat, PositiveInt
 
 from .base import Base, LowercaseStrEnum
 
@@ -14,6 +14,6 @@ class SolventSettings(Base):
     model: ImplicitSolventModel = ImplicitSolventModel.NONE
     epsilon: float = 78.36
 
-    grid_points_per_atom: pydantic.PositiveInt = 170
-    vdw_scale: pydantic.PositiveFloat = 1.2
-    weight_cutoff: pydantic.PositiveFloat = 1e-8
+    grid_points_per_atom: PositiveInt = 170
+    vdw_scale: PositiveFloat = 1.2
+    weight_cutoff: PositiveFloat = 1e-8

{stjames-0.0.33 → stjames-0.0.35}/stjames/base.py

@@ -1,14 +1,16 @@
 from enum import Enum
-from typing import Annotated, Any, Hashable, TypeVar
+from typing import Annotated, Hashable, TypeVar
 
 import numpy as np
 import pydantic
 
+T = TypeVar("T")
+
 
 class Base(pydantic.BaseModel):
     @pydantic.field_validator("*", mode="before")
     @classmethod
-    def coerce_numpy(cls, val: Any):
+    def coerce_numpy(cls, val: T) -> T | list:
         if isinstance(val, np.ndarray):
             return val.tolist()
         else:
@@ -19,7 +21,8 @@ class LowercaseStrEnum(str, Enum):
     """Enum where hyphens and case are ignored."""
 
     @classmethod
-    def _missing_(cls, value: str):
+    def _missing_(cls, value: str) -> str | None:  # type: ignore
+        # Type note: technically breaking Liskov, value: object in Enum
         for member in cls:
             if member.lower().replace("-", "") == value.lower().replace("-", ""):
                 return member
@@ -27,14 +30,13 @@ class LowercaseStrEnum(str, Enum):
 
 
 # cf. https://github.com/pydantic/pydantic-core/pull/820#issuecomment-1670475909
-# there are python details here I don't really grasp
-T = TypeVar("T", bound=Hashable)
+H = TypeVar("H", bound=Hashable)
 
 
-def _validate_unique_list(v: list[T]) -> list[T]:
+def _validate_unique_list(v: list[H]) -> list[H]:
     if len(v) != len(set(v)):
         raise ValueError("this list must be unique, and isn't!")
     return v
 
 
-UniqueList = Annotated[list[T], pydantic.AfterValidator(_validate_unique_list)]
+UniqueList = Annotated[list[H], pydantic.AfterValidator(_validate_unique_list)]

{stjames-0.0.33 → stjames-0.0.35}/stjames/basis_set.py

@@ -1,4 +1,5 @@
 import pydantic
+from pydantic import PositiveFloat, PositiveInt
 
 try:
     from typing import Optional, Self
@@ -10,8 +11,8 @@ from .base import Base
 
 class BasisSetOverride(Base):
     name: str
-    atomic_numbers: Optional[list[pydantic.PositiveInt]] = None
-    atoms: Optional[list[pydantic.PositiveInt]] = None  # 1-indexed
+    atomic_numbers: Optional[list[PositiveInt]] = None
+    atoms: Optional[list[PositiveInt]] = None  # 1-indexed
 
     @pydantic.model_validator(mode="after")
     def check_override(self) -> Self:
@@ -29,4 +30,4 @@ class BasisSet(Base):
     # value below which a basis function can be ignored
     # (for improving DFT grid calcs, as per Stratmann/Scuseria/Frisch CPL 1996)
     # this shouldn't really need to be modified...
-    cutoff_threshold: pydantic.PositiveFloat = 1e-10
+    cutoff_threshold: PositiveFloat = 1e-10

{stjames-0.0.33 → stjames-0.0.35}/stjames/molecule.py

@@ -1,4 +1,5 @@
 import pydantic
+from pydantic import NonNegativeInt, PositiveInt
 
 try:
     from typing import Optional, Self
@@ -16,17 +17,17 @@ class VibrationalMode(Base):
 
 
 class Atom(Base):
-    atomic_number: pydantic.NonNegativeInt
+    atomic_number: NonNegativeInt
     position: list[float]
 
 
 class Molecule(Base):
     charge: int
-    multiplicity: pydantic.PositiveInt
+    multiplicity: PositiveInt
     atoms: list[Atom]
 
     energy: Optional[float] = None
-    scf_iterations: Optional[pydantic.NonNegativeInt] = None
+    scf_iterations: Optional[NonNegativeInt] = None
     scf_completed: Optional[bool] = None
     elapsed: Optional[float] = None
 
@@ -46,40 +47,36 @@ class Molecule(Base):
     thermal_free_energy_corr: Optional[float] = None
 
     @property
-    def coordinates(self):
+    def coordinates(self) -> list[list[float]]:
         return [a.position for a in self.atoms]
 
     @property
-    def atomic_numbers(self):
+    def atomic_numbers(self) -> list[NonNegativeInt]:
         return [a.atomic_number for a in self.atoms]
 
     @property
     def sum_energy_zpe(self) -> Optional[float]:
         if (self.energy is None) or (self.zero_point_energy is None):
             return None
-        else:
-            return self.energy + self.zero_point_energy
+        return self.energy + self.zero_point_energy
 
     @property
     def sum_energy_thermal_corr(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_energy_corr is None):
             return None
-        else:
-            return self.energy + self.thermal_energy_corr
+        return self.energy + self.thermal_energy_corr
 
     @property
     def sum_energy_enthalpy(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_enthalpy_corr is None):
             return None
-        else:
-            return self.energy + self.thermal_enthalpy_corr
+        return self.energy + self.thermal_enthalpy_corr
 
     @property
     def sum_energy_free_energy(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_free_energy_corr is None):
             return None
-        else:
-            return self.energy + self.thermal_free_energy_corr
+        return self.energy + self.thermal_free_energy_corr
 
     @pydantic.model_validator(mode="after")
     def check_electron_sanity(self) -> Self:

{stjames-0.0.33 → stjames-0.0.35}/stjames/opt_settings.py

@@ -1,4 +1,4 @@
-import pydantic
+from pydantic import Field, PositiveFloat, PositiveInt
 
 from .base import Base, LowercaseStrEnum
 
@@ -19,12 +19,12 @@ class Constraint(Base):
 
 
 class OptimizationSettings(Base):
-    max_steps: pydantic.PositiveInt = 250
+    max_steps: PositiveInt = 250
     transition_state: bool = False
 
     # when are we converged?
-    max_gradient_threshold: pydantic.PositiveFloat = 4.5e-4
-    rms_gradient_threshold: pydantic.PositiveFloat = 3.0e-4
-    energy_threshold: pydantic.PositiveFloat = 1e-6
+    max_gradient_threshold: PositiveFloat = 4.5e-4
+    rms_gradient_threshold: PositiveFloat = 3.0e-4
+    energy_threshold: PositiveFloat = 1e-6
 
-    constraints: list[Constraint] = pydantic.Field(default_factory=list)
+    constraints: list[Constraint] = Field(default_factory=list)

{stjames-0.0.33 → stjames-0.0.35}/stjames/scf_settings.py

@@ -1,6 +1,7 @@
 from typing import Any, Optional
 
 import pydantic
+from pydantic import PositiveFloat, PositiveInt
 
 from .base import Base, LowercaseStrEnum
 from .diis_settings import DIISSettings
@@ -36,36 +37,36 @@ class SCFSettings(Base):
     #### damping
     do_damping: bool = True
     # when should we stop damping?
-    end_damping_error: pydantic.PositiveFloat = 0.1
+    end_damping_error: PositiveFloat = 0.1
     # what damping factor should we use?
     damping_factor: float = pydantic.Field(ge=0, le=1, default=0.7)
 
     #### level shifting
     do_level_shift: bool = True
     # how much? (Eh)
-    level_shift_magnitude: pydantic.PositiveFloat = 0.25
+    level_shift_magnitude: PositiveFloat = 0.25
     # when should we stop?
-    end_level_shift_error: pydantic.PositiveFloat = 0.1
+    end_level_shift_error: PositiveFloat = 0.1
 
     #### incremental
     # do incremental fock build?
     do_incremental: bool = True
     # reset incremental fock build
-    rebuild_frequency: pydantic.PositiveInt = 20
+    rebuild_frequency: PositiveInt = 20
 
     #### when are we converged?
-    energy_threshold: pydantic.PositiveFloat = 1e-6
-    rms_error_threshold: pydantic.PositiveFloat = 1e-8
-    max_error_threshold: pydantic.PositiveFloat = 1e-5
+    energy_threshold: PositiveFloat = 1e-6
+    rms_error_threshold: PositiveFloat = 1e-8
+    max_error_threshold: PositiveFloat = 1e-5
 
     #### DIIS
     do_diis: bool = True
     # error below which we'll start DIIS
     start_diis_max_error: pydantic.PositiveFloat = 0.2
     # first iteration we'll consider starting DIIS
-    start_diis_iter: pydantic.PositiveInt = 3
+    start_diis_iter: PositiveInt = 3
     # iteration past which we'll start DIIS even if error is high
-    start_diis_anyway: pydantic.PositiveInt = 7
+    start_diis_anyway: PositiveInt = 7
 
     # if ``read`` initialization is selected
     initial_density_matrix_guess: Optional[list[list[float]]] = None

{stjames-0.0.33 → stjames-0.0.35}/stjames/settings.py

@@ -1,4 +1,4 @@
-from typing import Any, Optional
+from typing import Any, Optional, TypeVar
 
 import pydantic
 
@@ -13,7 +13,14 @@ from .solvent import SolventSettings
 from .task import Task
 from .thermochem_settings import ThermochemistrySettings
 
-PREPACKAGED_METHODS = [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3, Method.AIMNET2_B973C, Method.GFN2_XTB, Method.GFN1_XTB]
+PREPACKAGED_METHODS = [
+    Method.HF3C,
+    Method.B973C,
+    Method.AIMNET2_WB97MD3,
+    Method.AIMNET2_B973C,
+    Method.GFN2_XTB,
+    Method.GFN1_XTB,
+]
 
 METHODS_WITH_CORRECTION = [
     Method.B97D3,
@@ -23,6 +30,8 @@ METHODS_WITH_CORRECTION = [
     Method.WB97MV,
 ]
 
+T = TypeVar("T")
+
 
 class Settings(Base):
     method: Method = Method.HARTREE_FOCK
@@ -39,8 +48,8 @@ class Settings(Base):
     opt_settings: OptimizationSettings = OptimizationSettings()
     thermochem_settings: ThermochemistrySettings = ThermochemistrySettings()
 
-    @pydantic.computed_field
     @property
+    @pydantic.computed_field
     def level_of_theory(self) -> str:
         if self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
@@ -72,18 +81,17 @@ class Settings(Base):
 
     @pydantic.field_validator("basis_set", mode="before")
     @classmethod
-    def parse_basis_set(cls, v: Any) -> Optional[BasisSet]:
+    def parse_basis_set(cls, v: Any) -> BasisSet | dict | None:
         """Turn a string into a ``BasisSet`` object. (This is a little crude.)"""
         if isinstance(v, BasisSet):
             return None if v.name is None else v
         elif isinstance(v, dict):
-            return None if v["name"] is None else v
+            return None if v.get("name") is None else v
         elif isinstance(v, str):
             if len(v):
                 return BasisSet(name=v)
-            else:
-                # "" is basically None, let's be real here...
-                return None
+            # "" is basically None, let's be real here...
+            return None
         elif v is None:
             return None
         else:
@@ -91,7 +99,7 @@ class Settings(Base):
 
     @pydantic.field_validator("corrections", mode="before")
     @classmethod
-    def remove_empty_string(cls, v: list) -> list:
+    def remove_empty_string(cls, v: list[T]) -> list[T]:
         """Remove empty string values."""
         return [c for c in v if c]
 

{stjames-0.0.33 → stjames-0.0.35}/stjames/workflows/redox_potential.py

@@ -1,4 +1,4 @@
-from typing import Optional, Any
+from typing import Any, Optional
 
 from ..mode import Mode
 from ..solvent import Solvent
@@ -11,7 +11,9 @@ class RedoxPotentialWorkflow(Workflow):
     reduction: bool = True
     oxidation: bool = True
 
+    # legacy values - remove in future release!
     redox_type: Optional[str] = None
+    redox_potential: Optional[float] = None
 
     # uuids
     neutral_molecule: Optional[str] = None
@@ -22,10 +24,14 @@ class RedoxPotentialWorkflow(Workflow):
     oxidation_potential: Optional[float] = None
 
     def model_post_init(self, __context: Any) -> None:
-        """ Keep back-compatible with old schema. """
+        """Keep back-compatible with old schema."""
         if self.redox_type == "oxidation":
             self.oxidation = True
             self.reduction = False
+            if self.oxidation_potential is None:
+                self.oxidation_potential = self.redox_potential
         elif self.redox_type == "reduction":
             self.oxidation = False
             self.reduction = True
+            if self.reduction_potential is None:
+                self.reduction_potential = self.redox_potential

{stjames-0.0.33 → stjames-0.0.35}/stjames/workflows/tautomer.py

@@ -2,7 +2,6 @@ from typing import Optional
 
 from ..base import Base
 from ..mode import Mode
-from .conformer import ConformerSettings
 from .workflow import DBCalculation, Workflow
 
 

{stjames-0.0.33 → stjames-0.0.35/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.33
+Version: 0.0.35
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -9,6 +9,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydantic>=2.4
+Requires-Dist: numpy
 
 # stjames
 

{stjames-0.0.33 → stjames-0.0.35}/stjames.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ stjames/method.py
 stjames/mode.py
 stjames/molecule.py
 stjames/opt_settings.py
+stjames/py.typed
 stjames/scf_settings.py
 stjames/settings.py
 stjames/solvent.py

{stjames-0.0.33 → stjames-0.0.35}/stjames.egg-info/requires.txt

@@ -1 +1,2 @@
 pydantic>=2.4
+numpy

{stjames-0.0.33 → stjames-0.0.35}/stjames/workflows/pka.py

@@ -1,7 +1,7 @@
 from typing import Optional
 
-from ..mode import Mode
 from ..base import Base
+from ..mode import Mode
 from .workflow import DBCalculation, Workflow