stjames 0.0.103__tar.gz → 0.0.105__tar.gz

{stjames-0.0.103/stjames.egg-info → stjames-0.0.105}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.103
+Version: 0.0.105
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.103 → stjames-0.0.105}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.103"
+version = "0.0.105"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

stjames-0.0.105/stjames/workflows/ion_mobility.py

@@ -0,0 +1,85 @@
+"""Ion mobility workflow."""
+
+from typing import Annotated, Self
+
+from pydantic import AfterValidator, computed_field, model_validator
+
+from ..base import Base, round_optional_float
+from ..data import ELEMENT_SYMBOL
+from ..types import UUID, round_list
+from .workflow import MoleculeWorkflow
+
+
+class IonMobilityForcefieldElement(Base):
+    """
+    A single atom specification for the ion-mobility forcefield.
+
+    :param name: the name of the element (e.g. "Hydrogen")
+    :param atomic_number: the element's atomic number
+    :param mass: the mass of the element in Daltons (e.g. 1.00794)
+    :param sigma: the sigma Lennard-Jones parameter, in Å
+    :param epsilon: the epsilon Lennard-Jones parameter, in kcal/mol
+    """
+
+    name: str
+    atomic_number: int
+    mass: float
+    sigma: float
+    epsilon: float
+
+    @computed_field  # type: ignore[misc, prop-decorator, unused-ignore]
+    @property
+    def symbol(self) -> str:
+        return ELEMENT_SYMBOL[self.atomic_number]
+
+
+class IonMobilityWorkflow(MoleculeWorkflow):
+    """
+    Workflow for calculating hydrogen bond basicity.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param protonate: automatically protonate the molecule
+    :param temperature: the temperature, in Kelvin
+    :param do_csearch: whether to perform a conformational search
+    :param do_optimization: whether to perform an optimization
+    :param forcefield: the forcefield used to describe atom–gas interactions.
+        if None, the default forcefield will be used.
+
+    Results:
+    :param conformers: the UUIDs of the conformers
+    :param conformer_ccs: the collision cross section (Å**2) per conformer
+    :param conformer_ccs_stdev: the uncertainty in the same
+    :param conformer_weights: the Boltzmann weights at RT
+    :param average_ccs: the Boltzmann-weighted CCS for the ensemble
+    :param average_ccs_stdev: the uncertainty in the same
+    """
+
+    protonate: bool = False
+    temperature: float = 300
+    do_csearch: bool = True
+    do_optimization: bool = True
+
+    forcefield: list[IonMobilityForcefieldElement] | None = None
+
+    conformers: list[UUID] = []
+
+    conformer_ccs: Annotated[list[float], AfterValidator(round_list(3))] = []
+    conformer_ccs_stdev: Annotated[list[float], AfterValidator(round_list(3))] = []
+    boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
+
+    average_ccs: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
+    average_ccs_stdev: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
+
+    @model_validator(mode="after")
+    def check_supported_atoms(self) -> Self:
+        """Validate that user-supplied forcefields have correct atoms."""
+        if self.forcefield is not None:
+            supported_atoms = set(e.atomic_number for e in self.forcefield)
+            if not all(z in supported_atoms for z in self.initial_molecule.atomic_numbers):
+                raise ValueError("Provided forcefield does not support all elements in input structure!")
+
+        return self

{stjames-0.0.103 → stjames-0.0.105}/stjames/workflows/nmr.py

@@ -9,7 +9,7 @@ from ..mode import Mode
 from ..settings import Settings
 from ..solvent import Solvent
 from ..types import UUID, round_list
-from .conformer_search import ConformerGenSettings, iMTDSettings
+from .conformer_search import ConformerGenSettingsUnion, iMTDSettings
 from .multistage_opt import MultiStageOptSettings
 from .workflow import MoleculeWorkflow
 
@@ -58,7 +58,7 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     nmr_method: NMRMethod = NMRMethod.MAGNETZERO
     solvent: Solvent = Solvent.CHLOROFORM
 
-    conf_gen_settings: ConformerGenSettings | None = iMTDSettings(mode="careful")
+    conf_gen_settings: ConformerGenSettingsUnion | None = iMTDSettings(mode="careful")
     multistage_opt_settings: MultiStageOptSettings | None = MultiStageOptSettings(
         mode=Mode.MANUAL,
         optimization_settings=[Settings(method="aimnet2_wb97md3", tasks=["optimize"])],

{stjames-0.0.103 → stjames-0.0.105}/stjames/workflows/solubility.py

@@ -41,6 +41,7 @@ class SolubilityWorkflow(SMILESWorkflow):
 
     Inputs:
     :param initial_smiles: SMILES string of the molecule
+    :param solubility_method: model used for solubility prediction
     :param solvents: list of solvent SMILES strings
     :param temperatures: temperatures in K
 
@@ -48,8 +49,8 @@ class SolubilityWorkflow(SMILESWorkflow):
     :param solubilities: {solvent: SolubilityResult}
     """
 
-    solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
     initial_smiles: str
+    solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
     solvents: list[str] = ["O"]
     temperatures: list[float] = [298.15]
 

{stjames-0.0.103 → stjames-0.0.105/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.103
+Version: 0.0.105
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

stjames-0.0.103/stjames/workflows/ion_mobility.py

@@ -1,47 +0,0 @@
-"""Ion mobility workflow."""
-
-from typing import Annotated
-
-from pydantic import AfterValidator
-
-from ..base import round_optional_float
-from ..types import UUID, round_list
-from .workflow import MoleculeWorkflow
-
-
-class IonMobilityWorkflow(MoleculeWorkflow):
-    """
-    Workflow for calculating hydrogen bond basicity.
-
-    Inherited:
-    :param initial_molecule: Molecule of interest
-    :param mode: Mode for workflow (currently unused)
-
-    New:
-    :param protonate: automatically protonate the molecule
-    :param temperature: the temperature, in Kelvin
-    :param do_csearch: whether to perform a conformational search
-    :param do_optimization: whether to perform an optimization
-
-    Results:
-    :param conformers: the UUIDs of the conformers
-    :param conformer_ccs: the collision cross section (Å**2) per conformer
-    :param conformer_ccs_stdev: the uncertainty in the same
-    :param conformer_weights: the Boltzmann weights at RT
-    :param average_ccs: the Boltzmann-weighted CCS for the ensemble
-    :param average_ccs_stdev: the uncertainty in the same
-    """
-
-    protonate: bool = False
-    temperature: float = 300
-    do_csearch: bool = True
-    do_optimization: bool = True
-
-    conformers: list[UUID] = []
-
-    conformer_ccs: Annotated[list[float], AfterValidator(round_list(3))] = []
-    conformer_ccs_stdev: Annotated[list[float], AfterValidator(round_list(3))] = []
-    boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
-
-    average_ccs: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
-    average_ccs_stdev: Annotated[float | None, AfterValidator(round_optional_float(3))] = None