stjames 0.0.27__tar.gz → 0.0.29__tar.gz

{stjames-0.0.27/stjames.egg-info → stjames-0.0.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.27
+Version: 0.0.29
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.27 → stjames-0.0.29}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.27"
+version = "0.0.29"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -29,5 +29,12 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [tool.ruff]
 line-length = 160
-select = ["E", "F"]
+
+[tool.ruff.lint]
+select = [
+    "E",  # pycodestyle errors
+    "F",  # pyflakes
+    "I",  # isort
+    "W",  # pycodestyle warnings
+]
 ignore = ["E741"]

{stjames-0.0.27 → stjames-0.0.29}/stjames/__init__.py

@@ -2,6 +2,7 @@
 
 from .calculation import *
 from .molecule import *
+from .workflows import *
 
 from .scf_settings import *
 from .int_settings import *

{stjames-0.0.27 → stjames-0.0.29}/stjames/base.py

@@ -1,7 +1,8 @@
-import pydantic
 from enum import Enum
+from typing import Annotated, Any, Hashable, TypeVar
+
 import numpy as np
-from typing import Any, Annotated, TypeVar, Hashable
+import pydantic
 
 
 class Base(pydantic.BaseModel):

{stjames-0.0.27 → stjames-0.0.29}/stjames/molecule.py

@@ -54,28 +54,28 @@ class Molecule(Base):
         return [a.atomic_number for a in self.atoms]
 
     @property
-    def sum_energy_zpe(self) -> float | None:
+    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
 
     @property
-    def sum_energy_thermal_corr(self) -> float | None:
+    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
 
     @property
-    def sum_energy_enthalpy(self) -> float | None:
+    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
 
     @property
-    def sum_energy_free_energy(self) -> float | None:
+    def sum_energy_free_energy(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_free_energy_corr is None):
             return None
         else:

{stjames-0.0.27 → stjames-0.0.29}/stjames/scf_settings.py

@@ -1,10 +1,11 @@
-from typing import Optional, Any
+from typing import Any, Optional
+
 import pydantic
 
 from .base import Base, LowercaseStrEnum
-from .int_settings import IntSettings
-from .grid_settings import GridSettings
 from .diis_settings import DIISSettings
+from .grid_settings import GridSettings
+from .int_settings import IntSettings
 
 
 class SCFInitMethod(LowercaseStrEnum):

{stjames-0.0.27 → stjames-0.0.29}/stjames/settings.py

@@ -1,17 +1,34 @@
-import pydantic
 from typing import Any, Optional
 
-from .modes import Mode
-from .methods import Method
-from .tasks import Task
+import pydantic
+
 from .base import Base, UniqueList
-from .corrections import Correction
-from .scf_settings import SCFSettings
 from .basis_set import BasisSet
+from .corrections import Correction
+from .methods import Method
+from .modes import Mode
 from .opt_settings import OptimizationSettings
-from .thermochem_settings import ThermochemistrySettings
+from .scf_settings import SCFSettings
 from .solvent_settings import SolventSettings
+from .tasks 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
+]
+
+METHODS_WITH_CORRECTION = [
+    Method.B97D3,
+    Method.WB97XD,
+    Method.WB97XD3,
+    Method.WB97XV,
+    Method.WB97MV,
+]
 
 class Settings(Base):
     method: Method = Method.HARTREE_FOCK
@@ -31,9 +48,10 @@ class Settings(Base):
     @pydantic.computed_field
     @property
     def level_of_theory(self) -> str:
-        # prepackaged methods
-        if self.method in [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3, Method.AIMNET2_B973C, Method.GFN2_XTB, Method.GFN1_XTB] or self.basis_set is None:
+        if self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
+        elif self.method in METHODS_WITH_CORRECTION:
+            method = f"{self.method.value}/{self.basis_set.name.lower()}"
         else:
             corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
             method = f"{self.method.value}-{'-'.join([c.value for c in corrections])}/{self.basis_set.name.lower()}"
@@ -60,7 +78,7 @@ class Settings(Base):
 
     @pydantic.field_validator("basis_set", mode="before")
     @classmethod
-    def parse_basis_set(cls, v: Any) -> BasisSet | None:
+    def parse_basis_set(cls, v: Any) -> Optional[BasisSet]:
         """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

{stjames-0.0.27 → stjames-0.0.29/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.27
+Version: 0.0.29
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.27 → stjames-0.0.29}/stjames/calculation.py

@@ -1,7 +1,7 @@
 from typing import Optional
 
-from .molecule import Molecule
 from .base import Base, LowercaseStrEnum
+from .molecule import Molecule
 from .settings import Settings
 from .status import Status