stjames 0.0.61__py3-none-any.whl → 0.0.62__py3-none-any.whl

stjames/workflows/molecular_dynamics.py

@@ -1,3 +1,5 @@
+"""Molecular dynamics workflow."""
+
 from typing import Self
 
 from pydantic import PositiveFloat, PositiveInt, computed_field, model_validator
@@ -6,22 +8,28 @@ from ..base import Base, LowercaseStrEnum
 from ..constraint import PairwiseHarmonicConstraint, SphericalHarmonicConstraint
 from ..settings import Settings
 from ..types import UUID
-from .workflow import Workflow
+from .workflow import MoleculeWorkflow
 
 
 class MolecularDynamicsInitialization(LowercaseStrEnum):
+    """Initialization method for molecular dynamics."""
+
     RANDOM = "random"
     QUASICLASSICAL = "quasiclassical"
     READ = "read"
 
 
 class ThermodynamicEnsemble(LowercaseStrEnum):
+    """Thermodynamic ensemble for molecular dynamics."""
+
     NPT = "npt"
     NVT = "nvt"
     NVE = "nve"
 
 
 class Frame(Base):
+    """A frame in a molecular dynamics simulation."""
+
     index: int  # what number frame this is within the MD simulation
 
     calculation_uuid: UUID | None = None  # UUID of calculation
@@ -39,6 +47,8 @@ class Frame(Base):
 
 
 class MolecularDynamicsSettings(Base):
+    """Settings for a molecular dynamics simulation."""
+
     ensemble: ThermodynamicEnsemble = ThermodynamicEnsemble.NVT
     initialization: MolecularDynamicsInitialization = MolecularDynamicsInitialization.RANDOM
 
@@ -66,10 +76,25 @@ class MolecularDynamicsSettings(Base):
         return self
 
 
-class MolecularDynamicsWorkflow(Workflow):
+class MolecularDynamicsWorkflow(MoleculeWorkflow):
+    """
+    Workflow for running a molecular dynamics simulation.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param settings: settings for the molecular dynamics simulation
+    :param calc_settings: settings for the gradient calculation
+    :param calc_engine: engine to use for the gradient calculation
+
+    Results:
+    :param frames: Frames from the MD
+    """
+
     settings: MolecularDynamicsSettings
     calc_settings: Settings
     calc_engine: str | None = None
 
-    # UUIDs of scan points
     frames: list[Frame] = []

stjames/workflows/multistage_opt.py

@@ -1,3 +1,5 @@
+"""Multi-stage optimization workflow."""
+
 from typing import Self, Sequence
 
 from pydantic import BaseModel, Field, model_validator
@@ -10,7 +12,7 @@ from ..settings import Settings
 from ..solvent import Solvent, SolventSettings
 from ..task import Task
 from ..types import UUID
-from .workflow import Workflow
+from .workflow import MoleculeWorkflow
 
 
 class MultiStageOptSettings(BaseModel):
@@ -177,9 +179,9 @@ class MultiStageOptSettings(BaseModel):
                 raise NotImplementedError(f"Cannot assign settings for {mode=}")
 
 
-class MultiStageOptWorkflow(Workflow, MultiStageOptSettings):
+class MultiStageOptWorkflow(MoleculeWorkflow, MultiStageOptSettings):
     """
-    Workflow for multi-stage optimizations.
+    MoleculeWorkflow for multi-stage optimizations.
 
     Inherited
     :param initial_molecule: Molecule of interest

stjames/workflows/pka.py

@@ -1,20 +1,54 @@
+"""pKa workflow."""
+
 from typing import Annotated
 
 from pydantic import AfterValidator
 
 from ..base import Base, round_float, round_optional_float
 from ..mode import Mode
-from .workflow import DBCalculation, Workflow
+from .workflow import DBCalculation, MoleculeWorkflow
 
 
 class pKaMicrostate(Base):
+    """
+    A microstate for pKa calculations.
+
+    :param atom_index: index of the atom
+    :param structures: DBCalculation for the microstate
+    :param deltaG: relative free energy
+    :param pka: pKa
+    """
+
     atom_index: int
     structures: list[DBCalculation] = []
     deltaG: Annotated[float, AfterValidator(round_float(3))]
     pka: Annotated[float, AfterValidator(round_float(3))]
 
 
-class pKaWorkflow(Workflow):
+class pKaWorkflow(MoleculeWorkflow):
+    """
+    Workflow for calculating pKa.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow
+
+    New:
+    :param pka_range: range of pKa values to consider
+    :param deprotonate_elements: elements to deprotonate
+    :param deprotonate_atoms: atoms to deprotonate
+    :param protonate_elements: elements to protonate
+    :param protonate_atoms: atom indices to protonate
+    :param reasonableness_buffer: buffer for pKa reasonableness
+
+    Results:
+    :param structures: DBCalculations for the microstates
+    :param conjugate_acids: conjugate acid microstates
+    :param conjugate_bases: conjugate base microstates
+    :param strongest_acid: pKa of the strongest acid
+    :param strongest_base: pKa of the strongest base
+    """
+
     mode: Mode = Mode.CAREFUL
 
     pka_range: tuple[float, float] = (2, 12)

stjames/workflows/redox_potential.py

@@ -1,3 +1,5 @@
+"""Redox potential workflow."""
+
 from typing import Annotated, Any, TypeVar
 
 from pydantic import AfterValidator, ValidationInfo, field_validator, model_validator
@@ -7,12 +9,12 @@ from ..mode import Mode
 from ..solvent import Solvent
 from ..types import UUID
 from .multistage_opt import MultiStageOptMixin
-from .workflow import Workflow
+from .workflow import MoleculeWorkflow
 
 _T = TypeVar("_T")
 
 
-class RedoxPotentialWorkflow(Workflow, MultiStageOptMixin):
+class RedoxPotentialWorkflow(MoleculeWorkflow, MultiStageOptMixin):
     """
     Workflow for computing spin states of molecules.
 

stjames/workflows/scan.py

@@ -1,3 +1,5 @@
+"""Scan workflow."""
+
 from typing import Annotated
 
 import numpy as np
@@ -8,10 +10,19 @@ from ..base import Base, round_optional_float
 from ..molecule import Molecule
 from ..settings import Settings
 from ..types import UUID
-from .workflow import Workflow
+from .workflow import MoleculeWorkflow
 
 
 class ScanPoint(Base):
+    """
+    A point in a scan.
+
+    :param index: index of the point
+    :param molecule: Molecule at the point
+    :param energy: energy of the point
+    :param uuid: UUID of the calculation
+    """
+
     index: int
     molecule: Molecule
     energy: Annotated[float | None, AfterValidator(round_optional_float(6))] = None
@@ -19,6 +30,16 @@ class ScanPoint(Base):
 
 
 class ScanSettings(Base):
+    """
+    Settings for a scan.
+
+    :param type: type of scan (bond, angle, dihedral)
+    :param atoms: indices of atoms to scan
+    :param start: start of scan
+    :param stop: end of scan
+    :param num: number of points in the scan
+    """
+
     type: str  # "bond", "angle", "dihedral" - make Enum later
     atoms: list[int]
     start: float
@@ -32,7 +53,21 @@ class ScanSettings(Base):
         from_attributes = True
 
 
-class ScanWorkflow(Workflow):
+class ScanWorkflow(MoleculeWorkflow):
+    """
+    Workflow for scanning a bond, angle, or dihedral.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param scan_settings: information about what coordinate to scan
+    :param calc_settings: settings for the calculation
+    :param calc_engine: engine to use for the calculation
+    :param scan_points: points along the scan
+    """
+
     scan_settings: ScanSettings
     calc_settings: Settings
     calc_engine: str

stjames/workflows/solubility.py

@@ -0,0 +1,60 @@
+"""Solubility prediction workflow."""
+
+from typing import Annotated, Self
+
+from pydantic import AfterValidator, BaseModel, model_validator
+
+from ..types import round_list
+from .workflow import SMILESWorkflow
+
+
+class SolubilityResult(BaseModel):
+    """
+    Solubility result.
+
+    :param solubilities: solubilities in log(S)/L
+    :param uncertainties: uncertainties in the solubility in log(S)/L
+    """
+
+    solubilities: Annotated[list[float], AfterValidator(round_list(6))]
+    uncertainties: Annotated[list[float], AfterValidator(round_list(6))]
+
+    @model_validator(mode="after")
+    def check_size(self) -> Self:
+        """Confirm that the shapes are the same"""
+        if len(self.solubilities) != len(self.uncertainties):
+            raise ValueError("Solubilities and uncertainties must have the same length.")
+
+        return self
+
+
+class SolubilityWorkflow(SMILESWorkflow):
+    """
+    Solubility prediction workflow.
+
+    Inputs:
+    :param initial_smiles: SMILES string of the molecule
+    :param solvents: list of solvent SMILES strings
+    :param temperatures: temperatures in K
+
+    Results:
+    :param solubilities: {solvent: SolubilityResult}
+    """
+
+    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
+
+    solubilities: dict[str, SolubilityResult] = {}
+
+    @model_validator(mode="after")
+    def check_size(self) -> Self:
+        """Check that the sizes of the lists are consistent."""
+        for solvent, result in self.solubilities.items():
+            if len(result.solubilities) != len(self.temperatures):
+                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")
+
+        return self

stjames/workflows/spin_states.py

@@ -1,3 +1,5 @@
+"""Spin-state prediction workflow."""
+
 from typing import Annotated, Any
 
 from pydantic import AfterValidator, BaseModel, Field, PositiveInt, field_validator, model_validator
@@ -6,7 +8,7 @@ from ..base import round_float
 from ..mode import Mode
 from ..types import UUID
 from .multistage_opt import MultiStageOptMixin
-from .workflow import Workflow
+from .workflow import MoleculeWorkflow
 
 
 class SpinState(BaseModel):
@@ -37,7 +39,7 @@ class SpinState(BaseModel):
 _sentinel_mso_mode = object()
 
 
-class SpinStatesWorkflow(Workflow, MultiStageOptMixin):
+class SpinStatesWorkflow(MoleculeWorkflow, MultiStageOptMixin):
     """
     Workflow for computing spin states of molecules.
 

stjames/workflows/tautomer.py

@@ -1,13 +1,24 @@
+"""Tautomer prediction workflow."""
+
 from typing import Annotated, Optional
 
 from pydantic import AfterValidator
 
 from ..base import Base, round_float, round_optional_float
 from ..mode import Mode
-from .workflow import DBCalculation, Workflow
+from .workflow import DBCalculation, MoleculeWorkflow
 
 
 class Tautomer(Base):
+    """
+    A tautomer.
+
+    :param energy: energy of the tautomer
+    :param weight: statistical weight of the tautomer
+    :param predicted_relative_energy: relative energy of the tautomer
+    :param structures: UUIDs of the structures
+    """
+
     energy: Annotated[float, AfterValidator(round_float(6))]
     weight: Annotated[Optional[float], AfterValidator(round_optional_float(6))] = None
     predicted_relative_energy: Annotated[Optional[float], AfterValidator(round_optional_float(6))] = None
@@ -16,6 +27,17 @@ class Tautomer(Base):
     structures: list[DBCalculation] = []
 
 
-class TautomerWorkflow(Workflow):
+class TautomerWorkflow(MoleculeWorkflow):
+    """
+    A workflow to calculate tautomers.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow
+
+    Results:
+    :param tautomers: resulting Tautomers
+    """
+
     mode: Mode = Mode.CAREFUL
     tautomers: list[Tautomer] = []

stjames/workflows/workflow.py

@@ -1,3 +1,5 @@
+"""Base classes for workflows."""
+
 from pydantic import field_validator
 
 from ..base import Base
@@ -11,18 +13,39 @@ class Workflow(Base):
     """
     Base class for Workflows.
 
-    :param initial_molecule: Molecule of interest
-    :param mode: Mode to use
     :param messages: messages to display
     """
 
-    initial_molecule: Molecule
-    mode: Mode = Mode.AUTO
     messages: list[Message] = []
 
     def __str__(self) -> str:
         return repr(self)
 
+
+class SMILESWorkflow(Workflow):
+    """
+    Base class for Workflows that operate on a single SMILES string.
+
+    :param initial_smiles: SMILES string of interest
+    """
+
+    initial_smiles: str
+
+    def __repr__(self) -> str:
+        return f"<{type(self).__name__} {self.initial_smiles}>"
+
+
+class MoleculeWorkflow(Workflow):
+    """
+    Base class for Workflows that operate on a single molecule.
+
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode to use
+    """
+
+    initial_molecule: Molecule
+    mode: Mode = Mode.AUTO
+
     def __repr__(self) -> str:
         return f"<{type(self).__name__} {self.mode.name}>"
 

{stjames-0.0.61.dist-info → stjames-0.0.62.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.61
+Version: 0.0.62
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -8,11 +8,10 @@ Project-URL: Bug Tracker, https://github.com/rowansci/stjames/issues
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: atomium<2,>=1
 Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
-Requires-Dist: atomium<2.0,>=1.0
 Requires-Dist: requests
+Requires-Dist: rdkit
 
 # stjames
 

{stjames-0.0.61.dist-info → stjames-0.0.62.dist-info}/RECORD

@@ -13,7 +13,7 @@ stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=5hBHk2xQLpxZ52LwJ9FHWaqQMdFKnsbQEOxaVe6O4Go,2321
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=DeNYmFdvbuKeXvLqlu-UxHMyZVK6y4j-Lw3HITGMnHw,12406
+stjames/molecule.py,sha256=GLOWgXPiIsy3cjqRUNAMR0YLQVlzYilGESsGdNIhxww,14075
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
 stjames/pdb.py,sha256=UxbgtIbc28L9O74AESYQiLBeiWZhdEbrBUT3mlyqRt8,25411
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
@@ -24,12 +24,12 @@ 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=hw-3UBikESvN3DzfK5doZB030kIEfx9gC3yBkIbebsI,3764
+stjames/types.py,sha256=rs2CdpkruIfU-PS98rjr9HAJNFGdZDB_zl-u3wa5rAs,4092
 stjames/atomium_stjames/__init__.py,sha256=gZkzC7i9D_fmWUTN55gtygITo3-qvJUda5CXLR0jyCQ,306
 stjames/atomium_stjames/data.py,sha256=-hzwBpTHq5JetsOVyopUJswKnKAkMtJ_XkONxjXVupU,5675
-stjames/atomium_stjames/mmcif.py,sha256=SjyWd1Zg_Pd0zM9OhaZ3rWGg3TDUuRJS88Zsvdbi-5M,27420
+stjames/atomium_stjames/mmcif.py,sha256=llbJ65p2B-aZN31-E_ODVDmrVeBoSw9y_Mg5XjyQvTA,26755
 stjames/atomium_stjames/pdb.py,sha256=C2mEcBDDrnoXD9ZCMIH2uJpjiWPJy6ktXq8IFZsrQKM,22482
-stjames/atomium_stjames/utilities.py,sha256=PSrOGn6MED4sXvbTLb65Jv20Ylptz4slZtjWEDzeRrI,4776
+stjames/atomium_stjames/utilities.py,sha256=-YtM7sRMvMk0wWrC3svWUWH4CGI0NtY77nXsg9tjHfc,4964
 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
@@ -37,28 +37,29 @@ 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=cndGGw9ZGhvbbrT_1mJ1w7gNAjgwmkYGq2Fqt8ml6Hg,2180
-stjames/workflows/admet.py,sha256=V8noO0Eb7h2bDFSnj6Pxv4ILm0lGxyVRCi13hE0zmEQ,149
-stjames/workflows/basic_calculation.py,sha256=q48bpab7ZqmRTR4PsGC6bWkuxqkVdJRM8gysevTYXP0,212
-stjames/workflows/bde.py,sha256=cWsZNiNdUy5DGvu8o6bBepLZIB5ohiAD6RKoK3YSq1I,9786
-stjames/workflows/conformer.py,sha256=LnpvH5HmLCn-ddH3r1WhEYONUMX5ohZswdESEPCR6o4,2907
-stjames/workflows/conformer_search.py,sha256=ZQ3VxQoaR_aZ-KSblXooAnGMTFbvOj4IQnM70K0OXhc,13497
-stjames/workflows/descriptors.py,sha256=lRRCsGzad3nIg0wI1090ffaXB0FVh0nRRb2lNxCY0kI,281
-stjames/workflows/docking.py,sha256=boetrhWyF-JAi8DAyiZrH_dFLs4yIe8P6C-ZR73AJgk,2932
-stjames/workflows/electronic_properties.py,sha256=uAIcGKKLhqoHyDgcOZulEXwTU2EjidyvOndZDYyeJEk,4003
-stjames/workflows/fukui.py,sha256=2J23RjkSOZ-40AM3AdnbJkRBGaCevkjkhnV3pVfa6lo,738
-stjames/workflows/hydrogen_bond_basicity.py,sha256=Luvov2DlDvZN06W-mU6YaN7wcIrTLwzdoWww-jNE3x4,517
-stjames/workflows/irc.py,sha256=3lA3EOXju6d0vETs-PEnRBnGCkshTXDtjw4dVDj0N5A,3333
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-stjames/workflows/pka.py,sha256=vSbMc7wuUKATNLq2kQyfCyX6aUthCj-XGSoXnuk4GMo,1031
-stjames/workflows/redox_potential.py,sha256=oLx3IyezOkJSXTVhtXkveC5GlsD6crR0kNDcNuSoIsg,3822
-stjames/workflows/scan.py,sha256=uNSuUmVMAV4exNvcv1viVe7930i7GZMn7RtEimnwEE8,1000
-stjames/workflows/spin_states.py,sha256=b-uCf-pHjF_JHbExeb5GdRToE0pIxP0JTd50U130ckI,4693
-stjames/workflows/tautomer.py,sha256=x3TC8hkMs87ZUodLyhce5EUzYoV276ePfPMi7ISWyNU,651
-stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
-stjames-0.0.61.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.61.dist-info/METADATA,sha256=kUkOkCULcbndmuv-hy5nCtBVAIJDNFy6MEI53KNIMDA,1713
-stjames-0.0.61.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-stjames-0.0.61.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.61.dist-info/RECORD,,
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+stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
+stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
+stjames/workflows/conformer.py,sha256=18aO6ngMBeGAmQkBdLGCCHr398RIYr1v2hD2IT1u4cc,3005
+stjames/workflows/conformer_search.py,sha256=4yPEKIIedeaVvaAwgjwC1FxiHqM6n2zOF6c9Yk_q1oA,13513
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+stjames/workflows/docking.py,sha256=p-L1s3NxLcliwDs8uLaohcz1Lap01Nuogq9Xe1eOT2k,2949
+stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
+stjames/workflows/fukui.py,sha256=e7CF7Mp2Dt1JTipQx-Sz_37W1urL-iRpjXY-9ItSvhM,1268
+stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
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