stjames 0.0.37__py3-none-any.whl → 0.0.38__py3-none-any.whl

stjames/base.py

@@ -24,7 +24,7 @@ class LowercaseStrEnum(str, Enum):
     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("-", ""):
+            if member.lower().replace("-", "").replace("_", "") == value.lower().replace("-", "").replace("_", ""):
                 return member
         return None
 

stjames/method.py

@@ -2,48 +2,37 @@ from .base import LowercaseStrEnum
 
 
 class Method(LowercaseStrEnum):
-    #### Hartree–Fock:
     HARTREE_FOCK = "hf"
-    HF3C = "hf-3c"
+    HF3C = "hf_3c"
 
-    #### DFT:
-    # LDA
-    LSDA = "lsda"
-
-    # local GGA
     PBE = "pbe"
-    BLYP = "blyp"
-    BP86 = "bp86"
-    B97D3 = "b97-d3"
-    B973C = "b97-3c"
-
-    # mGGA
+    B973C = "b97_3c"
     R2SCAN = "r2scan"
+    R2SCAN3C = "r2scan_3c"
     TPSS = "tpss"
     M06L = "m06l"
 
-    # hybrid GGA
     PBE0 = "pbe0"
     B3LYP = "b3lyp"
-    B3PW91 = "b3pw91"
-    B97MV = "b97m_v"
-
-    # hybrid mGGA
-    TPSS0 = "tpss0"
+    TPSSH = "tpssh"
     M06 = "m06"
     M062X = "m062x"
 
-    # range-separated
     CAMB3LYP = "camb3lyp"
-    WB97XD = "wb97x_d"
     WB97XD3 = "wb97x_d3"
     WB97XV = "wb97x_v"
     WB97MV = "wb97m_v"
+    WB97MD3BJ = "wb97m_d3bj"
+    WB97X3C = "wb97x_3c"
+
+    DSDBLYPD3BJ = "dsd_blyp_d3bj"
 
-    # ML methods
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
-    AIMNET2_B973C = "aimnet2_b973c"
 
-    # xTB methods
+    # GFN0_XTB = "gfn1_xtb"
     GFN1_XTB = "gfn1_xtb"
     GFN2_XTB = "gfn2_xtb"
+    GFN_FF = "gfn_ff"
+
+    # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
+    BP86 = "bp86"

stjames/settings.py

@@ -16,18 +16,19 @@ from .thermochem_settings import ThermochemistrySettings
 PREPACKAGED_METHODS = [
     Method.HF3C,
     Method.B973C,
+    Method.R2SCAN3C,
     Method.AIMNET2_WB97MD3,
-    Method.AIMNET2_B973C,
     Method.GFN2_XTB,
     Method.GFN1_XTB,
+    Method.GFN_FF,
 ]
 
 METHODS_WITH_CORRECTION = [
-    Method.B97D3,
-    Method.WB97XD,
     Method.WB97XD3,
     Method.WB97XV,
     Method.WB97MV,
+    Method.WB97MD3BJ,
+    Method.DSDBLYPD3BJ,
 ]
 
 T = TypeVar("T")
@@ -48,15 +49,17 @@ class Settings(Base):
     opt_settings: OptimizationSettings = OptimizationSettings()
     thermochem_settings: ThermochemistrySettings = ThermochemistrySettings()
 
+    # mypy has this dead wrong (https://docs.pydantic.dev/2.0/usage/computed_fields/)
+    @pydantic.computed_field  # type: ignore[misc]
     @property
-    @pydantic.computed_field
     def level_of_theory(self) -> str:
+        corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
+
         if self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
-        elif self.method in METHODS_WITH_CORRECTION:
+        elif self.method in METHODS_WITH_CORRECTION or len(corrections) == 0:
             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()}"
 
         if self.solvent_settings is not None:

stjames/solvent.py

@@ -31,6 +31,7 @@ class Solvent(LowercaseStrEnum):
 
 
 class SolventModel(LowercaseStrEnum):
+    PCM = "pcm"
     CPCM = "cpcm"
     ALPB = "alpb"
     COSMO = "cosmo"

stjames/workflows/conformer.py

@@ -48,7 +48,7 @@ class ConformerWorkflow(Workflow):
         self.settings = csearch_settings_by_mode(self.mode, self.settings)
 
 
-def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings]) -> ConformerSettings:
+def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings] = None) -> ConformerSettings:
     if mode == Mode.MANUAL:
         assert old_settings is not None
         return old_settings

{stjames-0.0.37.dist-info → stjames-0.0.38.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.37
+Version: 0.0.38
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.37.dist-info → stjames-0.0.38.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=GTISjYPBi4KCxAR9DPLf4mp6ZYuh2MwlNI0jZ1N41Io,1142
+stjames/base.py,sha256=xCdfeDnwNRvZfogbRXSVAW0x0c3l3attxUjW3_2J8-Y,1176
 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=e7A3XH808JglgfCzISKyRKAxGDj7BQdcQQtgtTlgfNk,843
+stjames/method.py,sha256=cxgcWYi8A4o-SiA1rhZqmpCV4hALN7MYe1Y6_w6zUac,789
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=t0jOmkTMgQE2ayBn9igjpY_4gPyqLPqZLlgtwd4uBOA,2910
 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=cUiAydIVes9iDEky4coOYQ2kF97AYaLClx5qjJmEpWY,8462
-stjames/solvent.py,sha256=3ssY-vQCCa071srfJbwCYEKDpWos8Mgvmg_dTpAnbJw,1104
+stjames/settings.py,sha256=KjuuDLP1Dknz1Jmm7wntFyUg6N_XfoewfiXAf1-NWkw,8615
+stjames/solvent.py,sha256=bGh10jZmfHQACZEAid7zYPyf6tx4G1ql3GgINHswy7Y,1120
 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=ebzLQ3NRUAmUXWGXzz71c2bjO0XlqsAD8D25rS4ANio,2690
+stjames/workflows/conformer.py,sha256=10mMhXhFoCUsOvSBp06Q16WufD66YiWCBuBcJEZr9vg,2697
 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-0.0.37.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.37.dist-info/METADATA,sha256=fQVcsgREoaKpfr0H9PYUF36dCp30GJwCqNjtttTeJyE,1626
-stjames-0.0.37.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
-stjames-0.0.37.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.37.dist-info/RECORD,,
+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-0.0.37.dist-info → stjames-0.0.38.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any