stjames 0.0.38__py3-none-any.whl → 0.0.40__py3-none-any.whl

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/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/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/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/solvent.py

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

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.dist-info → stjames-0.0.40.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.40.dist-info}/RECORD

@@ -1,6 +1,6 @@
 stjames/__init__.py,sha256=RJ1b132RSXVbQfptduVM1ZSQrnSTsg0a-VfgBwQn9zo,506
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
-stjames/base.py,sha256=xCdfeDnwNRvZfogbRXSVAW0x0c3l3attxUjW3_2J8-Y,1176
+stjames/base.py,sha256=R49yN4UoiOSjZEkadbMLqLLVNYmysXE4VvCU5JHTCNg,1190
 stjames/basis_set.py,sha256=Fi6vJx-ni2aOozFYH2hrSlc9lL01XzPO4zO6onJliuE,1035
 stjames/calculation.py,sha256=0eCZ59lqmnI_QxEdMp7esrTeutNyO_pIFrZQf_FncSo,848
 stjames/constraint.py,sha256=gkp0y0yQPeii8jdBNllZ9JS8t0o2bkEVTFAkyhShmWk,329
@@ -9,19 +9,19 @@ stjames/diis_settings.py,sha256=QHc7L-hktkbOWBYr29byTdqL8lWJzKJiY9XW8ha4Qzo,552
 stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
 stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
-stjames/method.py,sha256=cxgcWYi8A4o-SiA1rhZqmpCV4hALN7MYe1Y6_w6zUac,789
+stjames/method.py,sha256=iThn9tkkM0x0uX95o3Tcz3QQtad47UYGDL76hW3ySaM,787
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=t0jOmkTMgQE2ayBn9igjpY_4gPyqLPqZLlgtwd4uBOA,2910
+stjames/molecule.py,sha256=G78Bm88r8w-4cx_AOUyxLrn_gIt-TdeoYeBoiociqX8,3032
 stjames/opt_settings.py,sha256=5nTGih8KZ3x_yGfPL7pdGdsuOpCIfuJUrKoSK5YSDJg,458
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=xMMCQ0hVB4nNFSiWesNQZUa_aLsozSZGYWweAPPDGBg,2356
-stjames/settings.py,sha256=KjuuDLP1Dknz1Jmm7wntFyUg6N_XfoewfiXAf1-NWkw,8615
-stjames/solvent.py,sha256=bGh10jZmfHQACZEAid7zYPyf6tx4G1ql3GgINHswy7Y,1120
+stjames/settings.py,sha256=mn9TY2y2Juqou-bfIkXFWM_pbs_90-MgYYzAnWXCwVQ,8660
+stjames/solvent.py,sha256=0Kb2O3kTXMbcTH2br9bg7vtgG-Q7uRzhcMKSdUktVNo,1140
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/task.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
 stjames/workflows/__init__.py,sha256=sy9J04mCJpyVGcG4DecCi6pncwbZVvybI7sJKzavjgo,167
-stjames/workflows/conformer.py,sha256=10mMhXhFoCUsOvSBp06Q16WufD66YiWCBuBcJEZr9vg,2697
+stjames/workflows/conformer.py,sha256=YYwL3l7OaVeea4N9-ihghwa_ieKY6hia9LNbiTraMb0,2732
 stjames/workflows/descriptors.py,sha256=Jqx_4u_ZhdFJrT-ITU6zlFY0n8llh6zhzIhM38e8NCs,255
 stjames/workflows/fukui.py,sha256=FAabgLi_ig6Zp_jiTkuveP0wAObwv68liuumr85rb0g,366
 stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
@@ -29,8 +29,8 @@ stjames/workflows/redox_potential.py,sha256=iPkFt1Dj1sUywS9pLSEBVpCjHZcEwUESluY0
 stjames/workflows/scan.py,sha256=d1ca1uk1nxdzlSwqMLZ0W1_DHyrQMnHJmvPfziCS0SA,773
 stjames/workflows/tautomer.py,sha256=kZSCHo2Q7LzqtQjF_WyyxjECkndG49T9QOM12hsUkx8,421
 stjames/workflows/workflow.py,sha256=6hFe5PZejJu6bZ3yTkoJ9-xQMBn_-8tUsbk4FUZxog0,367
-stjames-0.0.38.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.38.dist-info/METADATA,sha256=g3b6X5V-Co_xbpwRRmj2UMjIArDusYqMyz763DXIEIQ,1626
-stjames-0.0.38.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-stjames-0.0.38.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.38.dist-info/RECORD,,
+stjames-0.0.40.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.40.dist-info/METADATA,sha256=GeuHmCFTQwu5cq521KVGYIdQBKmyOuBwonQ19a3ShO0,1626
+stjames-0.0.40.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+stjames-0.0.40.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.40.dist-info/RECORD,,

{stjames-0.0.38.dist-info → stjames-0.0.40.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any