stjames 0.0.106__py3-none-any.whl → 0.0.109__py3-none-any.whl

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Files changed (6) hide show
  1. stjames/workflows/pka.py +11 -7
  2. {stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/METADATA +1 -1
  3. {stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/RECORD +6 -6
  4. {stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/WHEEL +0 -0
  5. {stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/licenses/LICENSE +0 -0
  6. {stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/top_level.txt +0 -0
stjames/workflows/pka.py CHANGED
@@ -1,11 +1,12 @@
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  """pKa workflow."""
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- from typing import Annotated, Optional, Self
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+ from typing import Annotated, Self
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  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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@@ -33,17 +34,17 @@ class pKaMicrostate(Base):
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  :param atom_index: index of the atom
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  :param smiles: SMILES of the microstate
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  :param structures: DBCalculation for the microstate
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- :param deltaG: relative free energy
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- :param pka: pKa
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- :uncertainty: uncertainty
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+ :param deltaG: relative free energy (where applicable)
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+ :param pka: pKa value associated with this microstate
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+ :uncertainty: uncertainty in the pKa prediction
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  """
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  atom_index: int
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- smiles: Optional[str]
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+ smiles: str | None = None
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  structures: list[DBCalculation] = []
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- deltaG: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
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+ deltaG: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
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  pka: Annotated[float, AfterValidator(round_float(3))]
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- uncertainty: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None
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+ uncertainty: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
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  class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
@@ -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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+
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  mode: Mode = Mode.CAREFUL
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  microscopic_pka_method: MicroscopicpKaMethod = MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025
{stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: stjames
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- Version: 0.0.106
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+ Version: 0.0.109
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  Summary: standardized JSON atom/molecule encoding scheme
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  Author-email: Corin Wagen <corin@rowansci.com>
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  Project-URL: Homepage, https://github.com/rowansci/stjames
{stjames-0.0.106.dist-info → stjames-0.0.109.dist-info}/RECORD RENAMED
@@ -55,7 +55,7 @@ stjames/workflows/macropka.py,sha256=Krj0xXuB-u57Kqlf4bbRiHDUWCpliFr6YPiYqPmYaWk
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  stjames/workflows/molecular_dynamics.py,sha256=HqWNxxPSAphfI0DdbTERFkq8UeBjEvhnA_ETv0xw_RY,3522
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  stjames/workflows/multistage_opt.py,sha256=UN-4WLsT2WEjO5KqDPrcCkb708Co-ZScHx3g2bto768,16597
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  stjames/workflows/nmr.py,sha256=1QEF4SB6dWIr-jzLEZ7V972UnRUOTufOJSHwIGyV3dM,2681
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- stjames/workflows/pka.py,sha256=t2a2eozMpGgtslk_tVo38-9ZT4Lf-7-q6XUOgeKpvQA,4390
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+ stjames/workflows/pka.py,sha256=24mpGNPMc-hOaVqQFFlUdGadB65fb3DyOt4XXQvB2YY,4593
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  stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
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  stjames/workflows/protein_cofolding.py,sha256=mRdQoBWGYBqT8eEGfQ8yFLAcLJToYT_kIfvOQD68QVc,4039
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  stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
@@ -65,8 +65,8 @@ stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQ
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  stjames/workflows/strain.py,sha256=paYxDDQTB1eYP_c2kLVz1-QX7Vpw0LLb3ujnFin_SOM,1834
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  stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
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  stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
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- stjames-0.0.106.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
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- stjames-0.0.106.dist-info/METADATA,sha256=7Qyi3dJCiwrW2dN_xEK8X7uozRtTPU4s27jkLNs3DSs,1725
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- stjames-0.0.106.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- stjames-0.0.106.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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- stjames-0.0.106.dist-info/RECORD,,
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+ stjames-0.0.109.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
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+ stjames-0.0.109.dist-info/METADATA,sha256=udwI8N7fM3H9Ca_jpyIDVxF1sVMLK1z68-FIaTbvEGY,1725
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+ stjames-0.0.109.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ stjames-0.0.109.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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+ stjames-0.0.109.dist-info/RECORD,,