stjames 0.0.103__py3-none-any.whl → 0.0.105__py3-none-any.whl

stjames/workflows/ion_mobility.py

@@ -1,14 +1,38 @@
 """Ion mobility workflow."""
 
-from typing import Annotated
+from typing import Annotated, Self
 
-from pydantic import AfterValidator
+from pydantic import AfterValidator, computed_field, model_validator
 
-from ..base import round_optional_float
+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.
@@ -22,6 +46,8 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     :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
@@ -37,6 +63,8 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     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))] = []
@@ -45,3 +73,13 @@ class IonMobilityWorkflow(MoleculeWorkflow):
 
     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/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/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.dist-info → stjames-0.0.105.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.105.dist-info}/RECORD

@@ -49,23 +49,23 @@ stjames/workflows/double_ended_ts_search.py,sha256=ovJgEVFc6c3mijCE3TKAY70YvqNmA
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=095GDGSSEc5PDD1aoKM8J7icgR5tfwS5Bs9XxFQHge4,2387
 stjames/workflows/hydrogen_bond_basicity.py,sha256=q9eXty68ZyCmrB6G_8bfeOT8Ui_IQquRPu6z-3rNreQ,1589
-stjames/workflows/ion_mobility.py,sha256=rvvAt4ZD-Npl0tHL7TEuaS3XKjHiMkSZVzyJoivdyps,1665
+stjames/workflows/ion_mobility.py,sha256=5vUjEYCnF9sN3dTqqEgWAq0jAfdoFvkLubemoXE8DLc,3125
 stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
 stjames/workflows/macropka.py,sha256=Krj0xXuB-u57Kqlf4bbRiHDUWCpliFr6YPiYqPmYaWk,3803
 stjames/workflows/molecular_dynamics.py,sha256=HqWNxxPSAphfI0DdbTERFkq8UeBjEvhnA_ETv0xw_RY,3522
 stjames/workflows/multistage_opt.py,sha256=UN-4WLsT2WEjO5KqDPrcCkb708Co-ZScHx3g2bto768,16597
-stjames/workflows/nmr.py,sha256=2314qzkAFt-Wu6IDC2AI7eedYocqcCxIy9uZWkHMz_Q,2671
+stjames/workflows/nmr.py,sha256=1QEF4SB6dWIr-jzLEZ7V972UnRUOTufOJSHwIGyV3dM,2681
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
 stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
 stjames/workflows/protein_cofolding.py,sha256=ZjHER5DsO2vgCpgqttcNIU8xISN5B4DdqdrTxLKFsKY,2998
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
-stjames/workflows/solubility.py,sha256=DhsOxThAslWihpvOKJINNeMiBWSEzRsdqBlfgo2PwX4,2961
+stjames/workflows/solubility.py,sha256=lfCVvJjqEaddLUpK6WBxjB7u12Sci-K95A5_qIMkIRM,3028
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
 stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.103.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-stjames-0.0.103.dist-info/METADATA,sha256=ncWtuaR7uYzpmbJ89kySb8O5pJwKJDFX9jBQ5OXl9GY,1725
-stjames-0.0.103.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.103.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.103.dist-info/RECORD,,
+stjames-0.0.105.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+stjames-0.0.105.dist-info/METADATA,sha256=H8v2QtQVxJf93AM44xzVNicBeQUgxtKRtIT9T2Llb38,1725
+stjames-0.0.105.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.105.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.105.dist-info/RECORD,,