stjames 0.0.43__py3-none-any.whl → 0.0.45__py3-none-any.whl

stjames/workflows/redox_potential.py

@@ -1,19 +1,56 @@
-from typing import Any
+from typing import Any, TypeVar
+
+from pydantic import ValidationInfo, field_validator, model_validator
 
 from ..mode import Mode
 from ..solvent import Solvent
 from ..types import UUID
+from .multistage_opt import MultiStageOptMixin
 from .workflow import Workflow
 
+_T = TypeVar("_T")
+
+
+class RedoxPotentialWorkflow(Workflow, MultiStageOptMixin):
+    """
+    Workflow for computing spin states of molecules.
+
+    Uses the modes from MultiStageOptSettings.
+
+    Inherited
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow
+    :param multistage_opt_settings: set by mode unless mode=MANUAL (ignores additional settings if set)
+    :param xtb_preopt: pre-optimize with xtb (sets based on mode when None)
+    :param constraints: constraints to add
+    :param transition_state: whether this is a transition state
+    :param frequencies: whether to calculate frequencies
+
+    Overridden:
+    :param mso_mode: Mode for MultiStageOptSettings
+    :param solvent: solvent to use for optimization
+
+    New:
+    :param reduction: whether or not to calculate the reduction half-reaction
+    :param oxidation: whether or not to calculate the oxidation half-reaction
+    :param neutral_molecule: UUID of the calculation for the neutral molecule
+    :param anion_molecule: UUID of the calculation for the anion molecule
+    :param cation_molecule: UUID of the calculation for the cation molecule
+    :param reduction_potential: the final potential, in V
+    :param oxidation_potential: the final potential, in V
+
+    Legacy:
+    :param redox_type: one of "reduction" or "oxidation"
+    :param redox_potential: the corresponding potential, in V
+    """
 
-class RedoxPotentialWorkflow(Workflow):
-    mode: Mode = Mode.RAPID
     solvent: Solvent = Solvent.ACETONITRILE
+
     reduction: bool = True
     oxidation: bool = True
 
     # legacy values - remove in future release!
-    redox_type: UUID | None = None
+    redox_type: str | None = None
     redox_potential: float | None = None
 
     # uuids
@@ -24,6 +61,33 @@ class RedoxPotentialWorkflow(Workflow):
     reduction_potential: float | None = None
     oxidation_potential: float | None = None
 
+    @field_validator("solvent", mode="before")
+    @classmethod
+    def only_mecn_please(cls, val: Solvent | None) -> Solvent:
+        """Only MeCN please!"""
+        if val != Solvent.ACETONITRILE:
+            raise ValueError("Only acetonitrile permitted!")
+
+        return val
+
+    @field_validator("constraints", "transition_state")
+    @classmethod
+    def turned_off(cls, value: _T, info: ValidationInfo) -> _T:
+        if value:
+            raise ValueError(f"{info.field_name} not supported in redox potential workflows.")
+
+        return value
+
+    @model_validator(mode="before")
+    @classmethod
+    def set_mode_and_mso_mode(cls, values: dict[str, Any]) -> dict[str, Any]:
+        """Set the MultiStageOptSettings mode to match current redox potential mode, and select mode if `Auto`."""
+        if ("mode" not in values) or (values["mode"] == Mode.AUTO):
+            values["mode"] = Mode.RAPID
+
+        values["mso_mode"] = values["mode"]
+        return values
+
     def model_post_init(self, __context: Any) -> None:
         """Keep back-compatible with old schema."""
         if self.redox_type == "oxidation":

stjames/workflows/spin_states.py

@@ -49,8 +49,9 @@ class SpinStatesWorkflow(Workflow, MultiStageOptMixin):
 
     Inherited
     :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow
     :param multistage_opt_settings: set by mode unless mode=MANUAL (ignores additional settings if set)
-    :param solvent: solvent to use
+    :param solvent: solvent to use for optimization
     :param xtb_preopt: pre-optimize with xtb (sets based on mode when None)
     :param constraints: constraints to add
     :param transition_state: whether this is a transition state
@@ -60,7 +61,6 @@ class SpinStatesWorkflow(Workflow, MultiStageOptMixin):
     :param mso_mode: Mode for MultiStageOptSettings
 
     New:
-    :param mode: Mode for workflow
     :param states: multiplicities of the spin state targetted
     :param spin_states: resulting spin states data
 
@@ -72,16 +72,12 @@ class SpinStatesWorkflow(Workflow, MultiStageOptMixin):
     '<SpinStatesWorkflow [1, 3, 5] RAPID>'
     """
 
-    mode: Mode
     mso_mode: Mode = _sentinel_mso_mode  # type: ignore [assignment]
     states: list[PositiveInt]
 
     # Results
     spin_states: list[SpinState] = Field(default_factory=list)
 
-    def __str__(self) -> str:
-        return repr(self)
-
     def __repr__(self) -> str:
         if self.mode != Mode.MANUAL:
             return f"<{type(self).__name__} {self.states} {self.mode.name}>"
@@ -121,14 +117,6 @@ class SpinStatesWorkflow(Workflow, MultiStageOptMixin):
         values["mso_mode"] = values["mode"]
         return values
 
-    @field_validator("mode")
-    @classmethod
-    def set_mode_auto(cls, mode: Mode) -> Mode:
-        if mode == Mode.AUTO:
-            return Mode.RAPID
-
-        return mode
-
     @field_validator("spin_states")
     @classmethod
     def validate_spin_states(cls, spin_states: list[SpinState]) -> list[SpinState]:

stjames/workflows/workflow.py

@@ -1,4 +1,4 @@
-from pydantic import BaseModel, ConfigDict
+from pydantic import field_validator
 
 from ..base import Base
 from ..message import Message
@@ -8,30 +8,17 @@ from ..types import UUID
 
 
 class Workflow(Base):
-    """All workflows should have these properties."""
-
-    initial_molecule: Molecule
-    messages: list[Message] = []
-
-
-class DBCalculation(Base):
-    """Encodes a calculation that's in the database. This isn't terribly useful by itself."""
-
-    uuid: UUID
-
-
-class WorkflowInput(BaseModel):
     """
-    Input for a workflow.
+    Base class for Workflows.
 
     :param initial_molecule: Molecule of interest
-    :param mode: Mode for workflow
+    :param mode: Mode to use
+    :param messages: messages to display
     """
 
-    model_config = ConfigDict(extra="forbid")
-
     initial_molecule: Molecule
-    mode: Mode
+    mode: Mode = Mode.AUTO
+    messages: list[Message] = []
 
     def __str__(self) -> str:
         return repr(self)
@@ -39,8 +26,17 @@ class WorkflowInput(BaseModel):
     def __repr__(self) -> str:
         return f"<{type(self).__name__} {self.mode.name}>"
 
+    @field_validator("mode")
+    @classmethod
+    def set_mode_auto(cls, mode: Mode) -> Mode:
+        """Set the mode to RAPID if AUTO is selected."""
+        if mode == Mode.AUTO:
+            return Mode.RAPID
+
+        return mode
 
-class WorkflowResults(BaseModel):
-    """Results of a workflow."""
 
-    model_config = ConfigDict(extra="forbid", frozen=True)
+class DBCalculation(Base):
+    """Encodes a calculation that's in the database. This isn't terribly useful by itself."""
+
+    uuid: UUID

{stjames-0.0.43.dist-info → stjames-0.0.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.43
+Version: 0.0.45
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.43.dist-info → stjames-0.0.45.dist-info}/RECORD

@@ -4,25 +4,25 @@ stjames/atom.py,sha256=w7q-x9xpBw4sJ1WGrWt65WAaStxhz-m7dugXCYEOpq4,2064
 stjames/base.py,sha256=9PvUjBeVSkmA3TaruaB0uvjFMbWYTGKXECISNGAj_AU,1201
 stjames/basis_set.py,sha256=wI3M2q9uPf9jhKpAi4E2DrsyKzloDGLRjAlk7krdYgc,949
 stjames/calculation.py,sha256=O2LwwQ_cOLmDOGXTHA9J71YbUZXigUSbvbLA-fSVm3w,915
-stjames/constraint.py,sha256=IQsQPGbjaoWXZkAOPPBH0_-EGtWwGkkHBhuPg53v5-M,890
-stjames/correction.py,sha256=_pNG3qSylfx0iyUxqwx9HPU0m032YwP6wSPCjbJrD94,358
+stjames/constraint.py,sha256=aD4JkNIyya5uh016R68WLYLd0AK6msgki7Q1kAKGzRs,2203
+stjames/correction.py,sha256=ZVErCcj4TPyZeKrdvXVjHa0tFynsCaoy96QZUVxWFM8,413
 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=xnfphxyiWZotxQcmgvpFMJDmGEM2B-_5cbPkgYZBIws,1245
+stjames/method.py,sha256=a6QQff-0YsutkOTuOcGrdDW76x9ZexiNLdKzzoE1Vcw,1698
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=ZyqerT0p0CIykdn0vWfvy2UbU4LsVPCUQ7mSUeILkUI,10524
+stjames/molecule.py,sha256=v8NikFHfwOahXSo4VKGSqeHKI2HIoRdNjGE0GkZgNS4,10554
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
 stjames/periodic_cell.py,sha256=JDCyynpamggTNi_HnTnnotRbeSMBfYc-srhD-IwUnrg,996
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=xMMCQ0hVB4nNFSiWesNQZUa_aLsozSZGYWweAPPDGBg,2356
-stjames/settings.py,sha256=-MSVrfRcBz6O7aRZA-xTtEfJHRJ8BRxc6Bg9wad2DSY,8786
+stjames/settings.py,sha256=tfgEYns6WdsheQ6wpR6uyI8O4s2iTqyH7YWtNQ36k74,8666
 stjames/solvent.py,sha256=u037tmu-9oa21s-WEDZ7VC7nuNVjkqR2ML4JWjWSME4,1158
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/task.py,sha256=OLINRqe66o7t8arffilwmggrF_7TH0L79u6DhGruxV8,329
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
-stjames/types.py,sha256=2FBtEwpaqBIgN7fmVRORJfkv-am0Lssr8e7ho7Fui8w,206
+stjames/types.py,sha256=CPKR0g_kdFejMjGdKBjtuJRQqfmAZ-uIaSuGR1vBzCQ,245
 stjames/data/__init__.py,sha256=O59Ksp7AIqwOELCWymfCx7YeBzwNOGCMlGQi7tNLqiE,24
 stjames/data/bragg_radii.json,sha256=hhbn-xyZNSdmnULIjN2Cvq-_BGIZIqG243Ls_mey61w,1350
 stjames/data/elements.py,sha256=9BW01LZlyJ0H5s7Q26vUmjZIST41fwOYYrGvmPd7q0w,858
@@ -30,23 +30,25 @@ stjames/data/isotopes.json,sha256=5ba8QnLrHD_Ypv2xekv2cIRwYrX3MQ19-1FOFtt0RuU,83
 stjames/data/nist_isotopes.json,sha256=d5DNk1dX0iB1waEYIRR6JMHuA7AuYwSBEgBvb4EKyhM,14300
 stjames/data/read_nist_isotopes.py,sha256=y10FNjW43QpC45qib7VHsIghEwT7GG5rsNwHdc9osRI,3309
 stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWRQrg,1186
-stjames/workflows/__init__.py,sha256=TQwTrX8hzUKBcCV4C05IvePjnEotsAWTbXv4-b8zDRk,331
+stjames/workflows/__init__.py,sha256=JwcKWrXtrYKJfe6tPbVy6JKSwYxeEaiJWFDL3cVDXf8,363
 stjames/workflows/admet.py,sha256=V8noO0Eb7h2bDFSnj6Pxv4ILm0lGxyVRCi13hE0zmEQ,149
 stjames/workflows/basic_calculation.py,sha256=q48bpab7ZqmRTR4PsGC6bWkuxqkVdJRM8gysevTYXP0,212
-stjames/workflows/bde.py,sha256=rboqtrV1DNwq7MKPht9g5d7ahHxaqGN-PvXlTjGor4M,9831
+stjames/workflows/bde.py,sha256=QAcG-ifw_BSyPspOH4EsLNqc3M3b2Xeu4-I2cj-SqoE,9697
 stjames/workflows/conformer.py,sha256=YYwL3l7OaVeea4N9-ihghwa_ieKY6hia9LNbiTraMb0,2732
+stjames/workflows/conformer_search.py,sha256=PjFvotJ3BEMQqsirRxwH7wOIsnV12VuyXQCIyC2NSKE,12485
 stjames/workflows/descriptors.py,sha256=jQ3RuMi7xk799JZ_AL1ARL3yQfWLG03L_VVsK4KIMeY,281
+stjames/workflows/electronic_properties.py,sha256=y4tQl1r6K-Wt_sTjrVyQkq0zukeFQ4KlBrSZgIBZp6Y,3100
 stjames/workflows/fukui.py,sha256=F5tw5jTqBimo_GiXuThhRpoxauZE5YadZjObLFDCba8,348
-stjames/workflows/molecular_dynamics.py,sha256=ImZN9G1xolkUSXyv0d_KKPtCIPG9uXdkVyJuFdtOToU,1917
-stjames/workflows/multistage_opt.py,sha256=YL-lbpJs8AB5vOERonb7-Q69SIM4feuB9mUtbepYIHA,10040
+stjames/workflows/molecular_dynamics.py,sha256=Y3xUJaCO0A4VHvhEHlqJWu2IrEfruCRTqfnC6SdJu18,2194
+stjames/workflows/multistage_opt.py,sha256=gUHtsl3DRvtaZ13_L8CCzAKwridVRnY-0QBNAN0Fq4g,12964
 stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
-stjames/workflows/redox_potential.py,sha256=u6QThnqheJp6EDuWiJApJEh-fp0TKGfSyKfa8ykf85g,1211
+stjames/workflows/redox_potential.py,sha256=Jteftsi9SLu2Z4Cq5XpKn9kwn0z3Hkbyfx4Y1p8rCsw,3651
 stjames/workflows/scan.py,sha256=hL4Hco3Ns0dntjh2G2HhhWmED1mbt0gA_hsglPQ5Vjg,814
-stjames/workflows/spin_states.py,sha256=hzGbYfG4KGYYQPV4cF0ufCndDMoIVnZt2ZZt7LqvJgc,4854
+stjames/workflows/spin_states.py,sha256=VcCRr7dV-zpazHTkVWb9qds7_4QpTe-Hz_ECdUG9S_Y,4623
 stjames/workflows/tautomer.py,sha256=kZSCHo2Q7LzqtQjF_WyyxjECkndG49T9QOM12hsUkx8,421
-stjames/workflows/workflow.py,sha256=t5Yz-d5WgSQEiHbiZfc4NQ653mEnydiGZ-lEkkPYAKw,994
-stjames-0.0.43.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.43.dist-info/METADATA,sha256=9gZNt8YmerGV47ExAhb0Cie2toEDtPt2SkhgeWf7Yjc,1628
-stjames-0.0.43.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-stjames-0.0.43.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.43.dist-info/RECORD,,
+stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
+stjames-0.0.45.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.45.dist-info/METADATA,sha256=cXN2IrU7jfMFtL93PeemKYzPCGNGZgV7MlQQSOnJL2A,1628
+stjames-0.0.45.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+stjames-0.0.45.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.45.dist-info/RECORD,,

{stjames-0.0.43.dist-info → stjames-0.0.45.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.1.2)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any