stjames 0.0.108__tar.gz → 0.0.110__tar.gz
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- {stjames-0.0.108/stjames.egg-info → stjames-0.0.110}/PKG-INFO +1 -1
- {stjames-0.0.108 → stjames-0.0.110}/pyproject.toml +1 -1
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/pka.py +4 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/protein_cofolding.py +3 -0
- {stjames-0.0.108 → stjames-0.0.110/stjames.egg-info}/PKG-INFO +1 -1
- {stjames-0.0.108 → stjames-0.0.110}/LICENSE +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/README.md +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/setup.cfg +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/__init__.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/_deprecated_solvent_settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atom.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atomium_stjames/__init__.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atomium_stjames/data.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atomium_stjames/mmcif.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atomium_stjames/pdb.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/atomium_stjames/utilities.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/base.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/basis_set.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/calculation.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/compute_settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/constraint.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/correction.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/__init__.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/bragg_radii.json +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/elements.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/isotopes.json +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/nist_isotopes.json +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/read_nist_isotopes.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/data/symbol_element.json +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/engine.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/message.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/method.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/mode.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/molecule.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/opt_settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/optimization/__init__.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/optimization/freezing_string_method.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/pdb.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/periodic_cell.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/py.typed +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/scf_settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/solvent.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/status.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/task.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/thermochem_settings.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/types.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/__init__.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/admet.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/basic_calculation.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/bde.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/conformer.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/conformer_search.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/descriptors.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/docking.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/double_ended_ts_search.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/electronic_properties.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/fukui.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/ion_mobility.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/irc.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/macropka.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/molecular_dynamics.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/multistage_opt.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/nmr.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/pose_analysis_md.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/redox_potential.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/scan.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/solubility.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/spin_states.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/strain.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/tautomer.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames/workflows/workflow.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames.egg-info/SOURCES.txt +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames.egg-info/dependency_links.txt +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames.egg-info/requires.txt +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/stjames.egg-info/top_level.txt +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_constraints.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_from_extxyz.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_molecule.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_pdb.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_rounding.py +0 -0
- {stjames-0.0.108 → stjames-0.0.110}/tests/test_settings.py +0 -0
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@@ -6,6 +6,7 @@ from pydantic import AfterValidator, model_validator
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from ..base import Base, LowercaseStrEnum, round_float, round_optional_float
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from ..mode import Mode
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from ..molecule import Molecule
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from ..solvent import Solvent
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from .workflow import DBCalculation, MoleculeWorkflow, SMILESWorkflow
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@@ -73,6 +74,9 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
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:param strongest_base: pKa of the strongest base
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"""
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initial_smiles: str = ""
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initial_molecule: Molecule | None = None # type: ignore [assignment]
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mode: Mode = Mode.CAREFUL
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microscopic_pka_method: MicroscopicpKaMethod = MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025
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:param predicted_structure_uuid: UUID of the predicted structure
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:param scores: the output cofolding scores
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:param pose: the UUID of the calculation pose
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:param strain: the strain of the ligand, in kcal/mol
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:param predicted_refined_structure_uuid: if the structure has been refined, the UUID of the predicted structure after refinement
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"""
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model_config = ConfigDict(validate_assignment=True)
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pose: CalculationUUID | None = None
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posebusters_valid: bool | None = None
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strain: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
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predicted_refined_structure_uuid: ProteinUUID | None = None
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