stjames 0.0.38__tar.gz → 0.0.40__tar.gz

{stjames-0.0.38/stjames.egg-info → stjames-0.0.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.38
+Version: 0.0.40
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.38 → stjames-0.0.40}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.38"
+version = "0.0.40"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

{stjames-0.0.38 → stjames-0.0.40}/stjames/base.py

@@ -18,7 +18,7 @@ class Base(pydantic.BaseModel):
 
 
 class LowercaseStrEnum(str, Enum):
-    """Enum where hyphens and case are ignored."""
+    """Enum where hyphens, underscores, and case are ignored."""
 
     @classmethod
     def _missing_(cls, value: str) -> str | None:  # type: ignore

{stjames-0.0.38 → stjames-0.0.40}/stjames/method.py

@@ -29,7 +29,7 @@ class Method(LowercaseStrEnum):
 
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
 
-    # GFN0_XTB = "gfn1_xtb"
+    GFN0_XTB = "gfn0_xtb"
     GFN1_XTB = "gfn1_xtb"
     GFN2_XTB = "gfn2_xtb"
     GFN_FF = "gfn_ff"

{stjames-0.0.38 → stjames-0.0.40}/stjames/molecule.py

@@ -10,7 +10,7 @@ from .base import Base
 
 
 class VibrationalMode(Base):
-    frequency: float
+    frequency: float  # in cm-1
     reduced_mass: float
     force_constant: float
     displacements: list[list[float]]
@@ -18,7 +18,7 @@ class VibrationalMode(Base):
 
 class Atom(Base):
     atomic_number: NonNegativeInt
-    position: list[float]
+    position: list[float]  # in Å
 
 
 class Molecule(Base):
@@ -26,10 +26,10 @@ class Molecule(Base):
     multiplicity: PositiveInt
     atoms: list[Atom]
 
-    energy: Optional[float] = None
+    energy: Optional[float] = None  # in Hartree
     scf_iterations: Optional[NonNegativeInt] = None
     scf_completed: Optional[bool] = None
-    elapsed: Optional[float] = None
+    elapsed: Optional[float] = None  # in seconds
 
     homo_lumo_gap: Optional[float] = None  # in eV
 
@@ -37,7 +37,7 @@ class Molecule(Base):
 
     mulliken_charges: Optional[list[float]] = None
     mulliken_spin_densities: Optional[list[float]] = None
-    dipole: Optional[list[float]] = None
+    dipole: Optional[list[float]] = None  # in Debye
 
     vibrational_modes: Optional[list[VibrationalMode]] = None
 
@@ -46,6 +46,9 @@ class Molecule(Base):
     thermal_enthalpy_corr: Optional[float] = None
     thermal_free_energy_corr: Optional[float] = None
 
+    def __len__(self) -> int:
+        return len(self.atoms)
+
     @property
     def coordinates(self) -> list[list[float]]:
         return [a.position for a in self.atoms]

{stjames-0.0.38 → stjames-0.0.40}/stjames/settings.py

@@ -20,6 +20,7 @@ PREPACKAGED_METHODS = [
     Method.AIMNET2_WB97MD3,
     Method.GFN2_XTB,
     Method.GFN1_XTB,
+    Method.GFN0_XTB,
     Method.GFN_FF,
 ]
 
@@ -104,7 +105,7 @@ class Settings(Base):
     @classmethod
     def remove_empty_string(cls, v: list[T]) -> list[T]:
         """Remove empty string values."""
-        return [c for c in v if c]
+        return [c for c in v if c] if v is not None else v
 
 
 def _assign_settings_by_mode(settings: Settings) -> None:

{stjames-0.0.38 → stjames-0.0.40}/stjames/solvent.py

@@ -35,6 +35,7 @@ class SolventModel(LowercaseStrEnum):
     CPCM = "cpcm"
     ALPB = "alpb"
     COSMO = "cosmo"
+    CPCMX = "cpcmx"
 
 
 class SolventSettings(Base):

{stjames-0.0.38 → stjames-0.0.40}/stjames/workflows/conformer.py

@@ -13,6 +13,7 @@ class ConformerSettings(Base):
     num_confs_taken: int = 50
     rmsd_cutoff: float = 0.1
 
+    transition_state: bool = False
     final_method: Method = Method.AIMNET2_WB97MD3
     solvent: Optional[Solvent] = Solvent.WATER
     max_energy: float = 5

{stjames-0.0.38 → stjames-0.0.40/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.38
+Version: 0.0.40
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames