stjames 0.0.119__tar.gz → 0.0.121__tar.gz

{stjames-0.0.119/stjames.egg-info → stjames-0.0.121}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.119
+Version: 0.0.121
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.119 → stjames-0.0.121}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.119"
+version = "0.0.121"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.119 → stjames-0.0.121}/stjames/__init__.py

@@ -22,3 +22,4 @@ from .status import *
 from .constraint import *
 from .message import *
 from .types import *
+from .engine import *

{stjames-0.0.119 → stjames-0.0.121}/stjames/calculation.py

@@ -1,10 +1,13 @@
-from typing import Optional
+from typing import Optional, Self
 
-from .base import Base, LowercaseStrEnum
+from pydantic import model_validator
+
+from .base import Base, LowercaseStrEnum, UniqueList
 from .message import Message
 from .molecule import Molecule
 from .settings import Settings
 from .status import Status
+from .task import Task
 from .types import UUID
 
 
@@ -20,6 +23,7 @@ class StJamesVersion(LowercaseStrEnum):
 class Calculation(Base):
     molecules: list[Molecule]
 
+    tasks: UniqueList[Task] = []
     settings: Settings = Settings()
 
     status: Status = Status.QUEUED
@@ -29,8 +33,17 @@ class Calculation(Base):
     logfile: Optional[str] = None
     messages: list[Message] = []
 
+    # DEPRECATED - moving into settings
     engine: Optional[str] = "peregrine"
+
     uuids: list[UUID | None] | None = None
 
     # not to be changed by end users, diff. versions will have diff. defaults
     json_format: str = StJamesVersion.V0
+
+    @model_validator(mode="after")
+    def populate_tasks(self) -> Self:
+        """Set the tasks from the settings, so that we don't have to migrate old entries."""
+        if len(self.tasks) == 0:
+            self.tasks = self.settings.tasks
+        return self

{stjames-0.0.119 → stjames-0.0.121}/stjames/settings.py

@@ -6,6 +6,7 @@ from .base import Base, UniqueList
 from .basis_set import BasisSet
 from .compute_settings import ComputeSettings
 from .correction import Correction
+from .engine import Engine
 from .method import CORRECTABLE_NNP_METHODS, METHODS_WITH_CORRECTION, PREPACKAGED_METHODS, Method
 from .mode import Mode
 from .opt_settings import OptimizationSettings
@@ -20,11 +21,13 @@ _T = TypeVar("_T")
 class Settings(Base):
     mode: Mode = Mode.AUTO
 
+    # DEPRECATED - specify tasks only in BasicCalculationWorkflow or Calculation now
+    tasks: UniqueList[Task] = [Task.ENERGY, Task.CHARGE, Task.DIPOLE]
+
     method: Method = Method.HARTREE_FOCK
     basis_set: Optional[BasisSet] = None
-    tasks: UniqueList[Task] = [Task.ENERGY, Task.CHARGE, Task.DIPOLE]
+    engine: Engine = None  # type: ignore [assignment]
     corrections: UniqueList[Correction] = []
-
     solvent_settings: Optional[SolventSettings] = None
 
     # scf/opt settings will be set automatically based on mode, but can be overridden manually
@@ -33,6 +36,12 @@ class Settings(Base):
     thermochem_settings: ThermochemistrySettings = ThermochemistrySettings()
     compute_settings: ComputeSettings = ComputeSettings()
 
+    @model_validator(mode="after")
+    def set_engine(self) -> Self:
+        """Set the calculation engine."""
+        self.engine = self.engine or self.method.default_engine()
+        return self
+
     # mypy has this dead wrong (https://docs.pydantic.dev/2.0/usage/computed_fields/)
     # Python 3.12 narrows the reason for the ignore to prop-decorator
     @computed_field  # type: ignore[misc, prop-decorator, unused-ignore]

{stjames-0.0.119 → stjames-0.0.121}/stjames/workflows/__init__.py

@@ -4,6 +4,7 @@ from typing import Literal
 
 from .admet import *
 from .basic_calculation import *
+from .batch_docking import *
 from .bde import *
 from .conformer import *
 from .conformer_search import *
@@ -34,6 +35,7 @@ from .workflow import *
 WORKFLOW_NAME = Literal[
     "admet",
     "basic_calculation",
+    "batch_docking",
     "bde",
     "conformers",
     "conformer_search",
@@ -64,6 +66,7 @@ WORKFLOW_NAME = Literal[
 WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "admet": ADMETWorkflow,  # type: ignore [dict-item]
     "basic_calculation": BasicCalculationWorkflow,  # type: ignore [dict-item]
+    "batch_docking": BatchDockingWorkflow,  # type: ignore [dict-item]
     "bde": BDEWorkflow,  # type: ignore [dict-item]
     "conformers": ConformerWorkflow,  # type: ignore [dict-item]
     "conformer_search": ConformerSearchWorkflow,  # type: ignore [dict-item]

{stjames-0.0.119 → stjames-0.0.121}/stjames/workflows/basic_calculation.py

@@ -4,8 +4,10 @@ from typing import Self
 
 from pydantic import model_validator
 
+from ..base import UniqueList
 from ..engine import Engine
 from ..settings import Settings
+from ..task import Task
 from ..types import UUID
 from .workflow import MoleculeWorkflow
 
@@ -25,9 +27,12 @@ class BasicCalculationWorkflow(MoleculeWorkflow):
     """
 
     settings: Settings
-    engine: Engine = None  # type: ignore [assignment]
+    tasks: UniqueList[Task] = [Task.ENERGY, Task.CHARGE, Task.DIPOLE]
     calculation_uuid: UUID | None = None
 
+    # DEPRECATED - specify in settings now
+    engine: Engine = None  # type: ignore [assignment]
+
     @model_validator(mode="after")
     def set_engine(self) -> Self:
         """Set the calculation engine."""

{stjames-0.0.119 → stjames-0.0.121}/stjames/workflows/fukui.py

@@ -36,9 +36,13 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     """
 
     opt_settings: Settings | None = None
+
+    # DEPRECATED - will be removed
     opt_engine: Engine | None = None
 
     fukui_settings: Settings = Settings(method=Method.GFN1_XTB)
+
+    # DEPRECATED - will be removed
     fukui_engine: Engine = None  # type: ignore [assignment]
 
     optimization: UUID | None = None
@@ -52,7 +56,6 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     def set_engines(self) -> Self:
         """Set the engines for optimization and Fukui index calculations."""
         if self.opt_settings is not None and self.opt_engine is None:
-            self.opt_engine = self.opt_settings.method.default_engine()
-        self.fukui_engine = self.fukui_engine or self.fukui_settings.method.default_engine()
-
+            self.opt_engine = self.opt_settings.engine
+        self.fukui_engine = self.fukui_engine or self.fukui_settings.engine
         return self

{stjames-0.0.119 → stjames-0.0.121}/stjames/workflows/molecular_dynamics.py

@@ -96,6 +96,8 @@ class MolecularDynamicsWorkflow(MoleculeWorkflow):
 
     settings: MolecularDynamicsSettings
     calc_settings: Settings
+
+    # DEPRECATED - will remove later
     calc_engine: Engine = None  # type: ignore[assignment]
 
     frames: list[Frame] = []
@@ -103,6 +105,6 @@ class MolecularDynamicsWorkflow(MoleculeWorkflow):
     @model_validator(mode="after")
     def validate_calc_engine(self) -> Self:
         """Ensure that the calc_engine is set."""
-        self.calc_engine = self.calc_engine or self.calc_settings.method.default_engine()
+        self.calc_engine = self.calc_engine or self.calc_settings.engine
 
         return self

{stjames-0.0.119 → stjames-0.0.121}/stjames/workflows/scan.py

@@ -1,12 +1,11 @@
-"""Scan workflow."""
-
-from typing import Annotated
+from typing import Annotated, Self
 
 import numpy as np
 from numpy.typing import NDArray
-from pydantic import AfterValidator, field_validator
+from pydantic import AfterValidator, field_validator, model_validator
 
 from ..base import Base, round_optional_float
+from ..engine import Engine
 from ..molecule import Molecule
 from ..settings import Settings
 from ..types import UUID
@@ -75,7 +74,9 @@ class ScanWorkflow(MoleculeWorkflow):
     scan_settings: ScanSettings | list[ScanSettings]
     scan_settings_2d: ScanSettings | list[ScanSettings] = []
     calc_settings: Settings
-    calc_engine: str
+
+    # DEPRECATED - will be removed in future
+    calc_engine: Engine = None  # type: ignore [assignment]
 
     wavefront_propagation: bool = True
 
@@ -94,3 +95,9 @@ class ScanWorkflow(MoleculeWorkflow):
                 raise ValueError("Concerted scan settings must have same number of steps!")
 
         return val
+
+    @model_validator(mode="after")
+    def set_calc_engine(self) -> Self:
+        """Set the calculation engine."""
+        self.calc_engine = self.calc_engine or self.calc_settings.engine
+        return self

{stjames-0.0.119 → stjames-0.0.121/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.119
+Version: 0.0.121
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames