stjames 0.0.36__tar.gz → 0.0.38__tar.gz

{stjames-0.0.36/stjames.egg-info → stjames-0.0.38}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.36
+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-0.0.36 → stjames-0.0.38}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.36"
+version = "0.0.38"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

{stjames-0.0.36 → stjames-0.0.38}/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-0.0.36 → stjames-0.0.38}/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-0.0.36 → stjames-0.0.38}/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-0.0.36 → stjames-0.0.38}/stjames/solvent.py

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

{stjames-0.0.36 → stjames-0.0.38}/stjames/workflows/conformer.py

@@ -45,12 +45,18 @@ class ConformerWorkflow(Workflow):
     conformers: list[Conformer] = []
 
     def model_post_init(self, __context: Any) -> None:
-        self.settings = csearch_settings_by_mode(self.mode)
+        self.settings = csearch_settings_by_mode(self.mode, self.settings)
 
 
-def csearch_settings_by_mode(mode: Mode) -> 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
+
+    settings: ConformerSettings
+
     if mode == Mode.METICULOUS:
-        return CrestConformerSettings(
+        settings = CrestConformerSettings(
             gfn=2,
             flags="--ewin 15 --noreftopo",
             max_energy=10,
@@ -59,7 +65,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
         )
 
     elif mode == Mode.CAREFUL:
-        return CrestConformerSettings(
+        settings = CrestConformerSettings(
             gfn="ff",
             flags="--quick --ewin 10 --noreftopo",
             num_confs_considered=150,
@@ -67,7 +73,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
         )
 
     elif mode == Mode.RAPID or Mode.AUTO:
-        return RdkitConformerSettings(
+        settings = RdkitConformerSettings(
             num_initial_confs=300,
             max_mmff_energy=15,
             num_confs_considered=100,
@@ -75,7 +81,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
         )
 
     elif mode == Mode.RECKLESS:
-        return RdkitConformerSettings(
+        settings = RdkitConformerSettings(
             num_initial_confs=200,
             max_mmff_energy=10,
             num_confs_considered=50,
@@ -85,3 +91,10 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
 
     else:
         raise ValueError(f"invalid mode ``{mode.value}`` for conformer settings")
+
+    if old_settings is not None:
+        settings.final_method = old_settings.final_method
+        settings.solvent = old_settings.solvent
+        settings.constraints = old_settings.constraints
+
+    return settings

{stjames-0.0.36 → stjames-0.0.38/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.36
+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