stjames 0.0.101__tar.gz → 0.0.103__tar.gz

{stjames-0.0.101/stjames.egg-info → stjames-0.0.103}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.101
+Version: 0.0.103
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.101 → stjames-0.0.103}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.101"
+version = "0.0.103"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.101 → stjames-0.0.103}/stjames/engine.py

@@ -4,12 +4,11 @@ from .base import LowercaseStrEnum
 class Engine(LowercaseStrEnum):
     AIMNET2 = "aimnet2"
     MACE = "mace"
-    OCP24 = "ocp24"
     OMOL25 = "omol25"
     ORB = "orb"
     TBLITE = "tblite"
     XTB = "xtb"
-    TERRACHEM = "terrachem"
+    TERACHEM = "terachem"
     PYSCF = "pyscf"
     PSI4 = "psi4"
     OPENFF = "openff"

{stjames-0.0.101 → stjames-0.0.103}/stjames/method.py

@@ -34,12 +34,11 @@ class Method(LowercaseStrEnum):
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
     MACE_MP_0 = "mace_mp_0"
     MACE_MP_0B2_L = "mace_mp_0b2_l"
-    OCP24_S = "ocp24_s"
-    OCP24_L = "ocp24_l"
     OMOL25_CONSERVING_S = "omol25_conserving_s"
     UMA_M_OMOL = "uma_m_omol"
     UMA_S_OMOL = "uma_s_omol"
     ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
+    ORB_V3_CONSERVATIVE_OMOL = "orb_v3_conservative_omol"
 
     GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
@@ -77,11 +76,9 @@ class Method(LowercaseStrEnum):
                 return Engine.AIMNET2
             case Method.MACE_MP_0B2_L:
                 return Engine.MACE
-            case Method.OCP24_S | Method.OCP24_L:
-                return Engine.OCP24
             case Method.OMOL25_CONSERVING_S | Method.UMA_M_OMOL | Method.UMA_S_OMOL:
                 return Engine.OMOL25
-            case Method.ORB_V3_CONSERVATIVE_INF_OMAT:
+            case Method.ORB_V3_CONSERVATIVE_INF_OMAT | Method.ORB_V3_CONSERVATIVE_OMOL:
                 return Engine.ORB
             case method if method in XTB_METHODS:
                 return Engine.TBLITE if is_periodic else Engine.XTB
@@ -96,12 +93,11 @@ class Method(LowercaseStrEnum):
 
 PrepackagedNNPMethod = Literal[
     Method.AIMNET2_WB97MD3,
-    Method.OCP24_S,
-    Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
     Method.UMA_M_OMOL,
     Method.UMA_S_OMOL,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
+    Method.ORB_V3_CONSERVATIVE_OMOL,
     Method.EGRET_1,
     Method.EGRET_1E,
     Method.EGRET_1T,
@@ -109,12 +105,11 @@ PrepackagedNNPMethod = Literal[
 
 PREPACKAGED_NNP_METHODS = [
     Method.AIMNET2_WB97MD3,
-    Method.OCP24_S,
-    Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
     Method.UMA_M_OMOL,
     Method.UMA_S_OMOL,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
+    Method.ORB_V3_CONSERVATIVE_OMOL,
     Method.EGRET_1,
     Method.EGRET_1E,
     Method.EGRET_1T,

{stjames-0.0.101 → stjames-0.0.103}/stjames/types.py

@@ -1,4 +1,4 @@
-from typing import Callable, Iterable, TypeAlias
+from typing import Callable, Iterable, Protocol, TypeAlias, overload
 
 UUID: TypeAlias = str
 
@@ -10,22 +10,32 @@ FloatPerAtom: TypeAlias = list[float]
 Matrix3x3: TypeAlias = tuple[Vector3D, Vector3D, Vector3D]
 
 
-def round_list(round_to: int = 6) -> Callable[[Iterable[float]], list[float]]:
-    """Create a validator that rounds each float in a list to a given number of decimal places."""
+class _Iterable_Rounder(Protocol):
+    """Callable with return types conditioned on the input type(s)."""
 
-    def rounder(values: Iterable[float]) -> list[float]:
-        return [round(value, round_to) for value in values]
+    @overload
+    def __call__(self, values: None, /) -> None: ...
+    @overload
+    def __call__(self, values: Iterable[float], /) -> list[float]: ...
+    @overload
+    def __call__(self, values: Iterable[float | None], /) -> list[float | None]: ...
 
-    return rounder
 
+def round_list(round_to: int = 6) -> _Iterable_Rounder:
+    """Round values (even if Nones), preserving types."""
 
-def round_optional_list(round_to: int = 6) -> Callable[[Iterable[float] | None], list[float] | None]:
-    """Create a validator that rounds each float in a list to a given number of decimal places."""
+    @overload
+    def rounder(values: None, /) -> None: ...
+    @overload
+    def rounder(values: Iterable[float], /) -> list[float]: ...
+    @overload
+    def rounder(values: Iterable[float | None], /) -> list[float | None]: ...
 
-    def rounder(values: Iterable[float] | None) -> list[float] | None:
+    def rounder(values: Iterable[float] | Iterable[float | None] | None, /) -> list[float] | list[float | None] | None:
         if values is None:
             return None
-        return [round(value, round_to) for value in values]
+
+        return [round(v, round_to) if v is not None else None for v in values]
 
     return rounder
 

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/conformer_search.py

@@ -1,7 +1,7 @@
 """Conformer search workflow."""
 
 from abc import ABC
-from typing import Annotated, Self, Sequence, TypeVar
+from typing import Annotated, Literal, Self, Sequence, TypeVar
 
 from pydantic import AfterValidator, BaseModel, Field, field_validator, model_validator
 
@@ -94,6 +94,7 @@ class ETKDGSettings(ConformerGenSettings):
     num_confs_considered: int = 100
     max_mmff_iterations: int = 500
     max_mmff_energy: float | None = 30
+    settings_type: Literal["etkdg"] = "etkdg"
 
     @field_validator("constraints")
     def check_constraints(cls, constraints: Sequence[Constraint]) -> Sequence[Constraint]:
@@ -209,6 +210,7 @@ class iMTDSettings(ConformerGenSettings, ABC):
     speed: iMTDSpeeds = iMTDSpeeds.QUICK
     reopt: bool = _sentinel  # type: ignore [assignment]
     free_energy_weights: bool = False
+    settings_type: Literal["imtd"] = "imtd"
 
     @model_validator(mode="after")
     def validate_and_build_imtdgc_settings(self) -> Self:
@@ -253,6 +255,9 @@ class iMTDsMTDSettings(iMTDSettings):
     run_type: str = "imtd-smtd"
 
 
+ConformerGenSettingsUnion = Annotated[ETKDGSettings | iMTDSettings, Field(discriminator="settings_type")]
+
+
 class ConformerGenMixin(BaseModel):
     """
     Mixin for workflows that need conformer generation.
@@ -265,7 +270,7 @@ class ConformerGenMixin(BaseModel):
     """
 
     conf_gen_mode: Mode = Mode.RAPID
-    conf_gen_settings: ConformerGenSettings = _sentinel  # type: ignore [assignment]
+    conf_gen_settings: ConformerGenSettingsUnion = _sentinel  # type: ignore [assignment]
     constraints: Sequence[Constraint] = tuple()
     nci: bool = False
     max_confs: int | None = None
@@ -273,8 +278,8 @@ class ConformerGenMixin(BaseModel):
     @model_validator(mode="after")
     def validate_and_build_conf_gen_settings(self) -> Self:
         """Validate and build the ConformerGenSettings."""
-        if self.conf_gen_settings is not _sentinel and self.conf_gen_mode != Mode.MANUAL:
-            raise ValueError("Cannot specify conf_gen_settings with non-MANUAL mode")
+        if self.conf_gen_settings is not _sentinel:
+            return self
 
         match self.conf_gen_mode:
             case Mode.MANUAL:

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/docking.py

@@ -7,7 +7,7 @@ from pydantic import AfterValidator, ConfigDict, field_validator, model_validato
 from ..base import Base, round_float
 from ..pdb import PDB
 from ..types import UUID, Vector3D
-from .conformer_search import ConformerGenSettings, ETKDGSettings
+from .conformer_search import ConformerGenSettingsUnion, ETKDGSettings
 from .workflow import MoleculeWorkflow
 
 
@@ -79,12 +79,12 @@ class DockingWorkflow(MoleculeWorkflow):
     pocket: tuple[Vector3D, Vector3D]
 
     do_csearch: bool = True
-    conformer_gen_settings: ConformerGenSettings = ETKDGSettings(mode="reckless")
+    conformer_gen_settings: ConformerGenSettingsUnion = ETKDGSettings(mode="reckless")
 
     do_optimization: bool = True
     # optimization_settings - here in future once we have a cleaner mode sol'n, ccw 7.9.25
 
-    docking_settings: DockingSettings = VinaSettings()
+    docking_settings: VinaSettings = VinaSettings()
 
     do_pose_refinement: bool = True
 

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/macropka.py

@@ -4,7 +4,7 @@ from typing import Annotated, Optional, Self
 
 from pydantic import AfterValidator, model_validator
 
-from ..base import Base, round_float
+from ..base import Base, round_float, round_optional_float
 from ..types import round_list
 from .workflow import SMILESWorkflow
 
@@ -72,9 +72,9 @@ class MacropKaWorkflow(SMILESWorkflow):
 
     microstates: list[MacropKaMicrostate] = []
     pKa_values: list[MacropKaValue] = []
-    isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
-    solvation_energy: Annotated[Optional[float], AfterValidator(round_float(3))] = None
-    kpuu_probability: Annotated[Optional[float], AfterValidator(round_float(3))] = None
+    isoelectric_point: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
+    solvation_energy: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
+    kpuu_probability: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
 
     microstate_weights_by_pH: list[
         tuple[

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/multistage_opt.py

@@ -1,5 +1,6 @@
 """Multi-stage optimization workflow."""
 
+import logging
 import re
 from typing import Self, Sequence
 
@@ -18,6 +19,8 @@ from ..task import Task
 from ..types import UUID
 from .workflow import MoleculeWorkflow
 
+logger = logging.getLogger(__name__)
+
 
 class MultiStageOptSettings(BaseModel):
     """
@@ -109,7 +112,8 @@ class MultiStageOptSettings(BaseModel):
                 pass
 
             case (mode, True):
-                raise ValueError(f"Cannot specify optimization_settings or singlepoint_settings with {mode=}")
+                logger.debug(f"Mode {mode=} specified with optimization_settings or singlepoint_settings, ignoring")
+                pass
 
             case (mode, False):
                 self._assign_settings_by_mode(mode)
@@ -253,7 +257,8 @@ class MultiStageOptMixin(BaseModel):
                 pass
 
             case (mso_mode, msos) if msos is not _sentinel_msos:
-                raise ValueError(f"Cannot specify multistage_opt_settings with {mso_mode=}, {msos=}")
+                logger.debug(f"Mode {mso_mode=} specified with multistage_opt_settings, ignoring")
+                pass
 
             case (mso_mode, _):
                 self.multistage_opt_settings = MultiStageOptSettings(

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/nmr.py

@@ -8,7 +8,7 @@ from ..base import Base, LowercaseStrEnum, round_float
 from ..mode import Mode
 from ..settings import Settings
 from ..solvent import Solvent
-from ..types import UUID, round_list, round_optional_list
+from ..types import UUID, round_list
 from .conformer_search import ConformerGenSettings, iMTDSettings
 from .multistage_opt import MultiStageOptSettings
 from .workflow import MoleculeWorkflow
@@ -66,8 +66,8 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
 
     conformers: list[UUID] = []
     boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
-    per_conformer_chemical_shifts: list[Annotated[list[float | None], AfterValidator(round_optional_list(3))]] = []
-    chemical_shifts: Annotated[list[float | None], AfterValidator(round_optional_list(3))] = []
+    per_conformer_chemical_shifts: list[Annotated[list[float | None], AfterValidator(round_list(3))]] = []
+    chemical_shifts: Annotated[list[float | None], AfterValidator(round_list(3))] = []
     symmetry_equivalent_nuclei: list[list[int]] = []
 
     predicted_peaks: dict[int, list[NMRPeak]] = {}

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/protein_cofolding.py

@@ -5,7 +5,7 @@ from typing import Annotated, Literal
 from pydantic import AfterValidator, BaseModel, ConfigDict
 
 from ..base import LowercaseStrEnum, round_float
-from ..types import UUID, round_optional_list
+from ..types import UUID, round_list
 from .workflow import FASTAWorkflow
 
 
@@ -86,4 +86,4 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
     scores: CofoldingScores | None = None
     model: CofoldingModel = CofoldingModel.BOLTZ_2
     affinity_score: AffinityScore | None = None
-    lddt: Annotated[list[float] | None, AfterValidator(round_optional_list(3))] = None
+    lddt: Annotated[list[float] | None, AfterValidator(round_list(3))] = None

{stjames-0.0.101 → stjames-0.0.103}/stjames/workflows/solubility.py

@@ -4,10 +4,17 @@ from typing import Annotated, Self
 
 from pydantic import AfterValidator, BaseModel, model_validator
 
+from ..base import LowercaseStrEnum
 from ..types import round_list
 from .workflow import SMILESWorkflow
 
 
+class SolubilityMethod(LowercaseStrEnum):
+    FASTSOLV = "fastsolv"
+    KINGFISHER = "kingfisher"
+    ESOL = "esol"
+
+
 class SolubilityResult(BaseModel):
     """
     Solubility result.
@@ -17,7 +24,7 @@ class SolubilityResult(BaseModel):
     """
 
     solubilities: Annotated[list[float], AfterValidator(round_list(6))]
-    uncertainties: Annotated[list[float], AfterValidator(round_list(6))]
+    uncertainties: Annotated[list[float | None], AfterValidator(round_list(6))]
 
     @model_validator(mode="after")
     def check_size(self) -> Self:
@@ -41,9 +48,10 @@ class SolubilityWorkflow(SMILESWorkflow):
     :param solubilities: {solvent: SolubilityResult}
     """
 
+    solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
     initial_smiles: str
-    solvents: list[str]
-    temperatures: list[float] = [273.15, 298.15, 323.15, 348.15, 373.15, 398.15, 423.15]  # 0–150 °C
+    solvents: list[str] = ["O"]
+    temperatures: list[float] = [298.15]
 
     solubilities: dict[str, SolubilityResult] = {}
 
@@ -55,6 +63,22 @@ class SolubilityWorkflow(SMILESWorkflow):
                 raise ValueError(f"Solubilities for {solvent} must have the same length as temperatures.")
 
             if solvent not in self.solvents:
-                raise ValueError(f"Solvent {solvent} not in initial list of solvents")
+                raise ValueError(f"Solvent {solvent} not in initial list of solvents.")
+
+        return self
+
+    @model_validator(mode="after")
+    def check_solvent_temperature(self) -> Self:
+        """Check that models with limited domain of applicability are predicting within correct domain."""
+        match self.solubility_method:
+            case SolubilityMethod.KINGFISHER | SolubilityMethod.ESOL:
+                if (len(self.solvents) > 1) or (self.solvents[0] != "O"):
+                    raise ValueError(f"Method `{self.solubility_method}` can only predict aqueous solubility, so `solvents` must be [`O`] only.")
+                if (len(self.temperatures) > 1) or (abs(self.temperatures[0] - 298.15) > 0.1):
+                    raise ValueError(
+                        f"Method `{self.solubility_method}` can only predict solubility at room temperature, so `temperatures` must be [298.15] only."
+                    )
+            case _:
+                pass
 
         return self

{stjames-0.0.101 → stjames-0.0.103/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.101
+Version: 0.0.103
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames