stjames 0.0.79__tar.gz → 0.0.81__tar.gz

{stjames-0.0.79/stjames.egg-info → stjames-0.0.81}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.79
+Version: 0.0.81
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.79 → stjames-0.0.81}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.79"
+version = "0.0.81"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.79 → stjames-0.0.81}/stjames/types.py

@@ -19,6 +19,17 @@ def round_list(round_to: int = 6) -> Callable[[Iterable[float]], list[float]]:
     return rounder
 
 
+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."""
+
+    def rounder(values: Iterable[float] | None) -> list[float] | None:
+        if values is None:
+            return None
+        return [round(value, round_to) for value in values]
+
+    return rounder
+
+
 def round_vector3d(round_to: int = 6) -> Callable[[Vector3D], Vector3D]:
     """Create a validator that rounds each component of a Vector3D to a given number of decimal places."""
 

stjames-0.0.81/stjames/workflows/protein_cofolding.py

@@ -0,0 +1,61 @@
+"""Protein Cofolding Workflow."""
+
+from typing import Annotated
+
+from pydantic import AfterValidator, BaseModel
+
+from ..base import LowercaseStrEnum, round_float
+from ..types import UUID, round_optional_list
+from .workflow import FASTAWorkflow
+
+
+class CofoldingModel(LowercaseStrEnum):
+    """Cofolding model to be used for prediction."""
+
+    CHAI_1R = "chai_1r"
+    BOLTZ_1 = "boltz_1"
+    BOLTZ_2 = "boltz_2"
+
+
+class CofoldingScores(BaseModel):
+    confidence_score: Annotated[float, AfterValidator(round_float(3))]
+    ptm: Annotated[float, AfterValidator(round_float(3))]  # predicted template modeling score
+    iptm: Annotated[float, AfterValidator(round_float(3))]  # interface predicted template modeling score
+    avg_lddt: Annotated[float, AfterValidator(round_float(3))]
+
+
+class AffinityScore(BaseModel):
+    pred_value: Annotated[float, AfterValidator(round_float(3))]
+    probability_binary: Annotated[float, AfterValidator(round_float(3))]
+    pred_value1: Annotated[float, AfterValidator(round_float(3))]
+    probability_binary1: Annotated[float, AfterValidator(round_float(3))]
+    pred_value2: Annotated[float, AfterValidator(round_float(3))]
+    probability_binary2: Annotated[float, AfterValidator(round_float(3))]
+
+
+class ProteinCofoldingWorkflow(FASTAWorkflow):
+    """
+    A workflow for predicting structures. Especially protein structures.
+
+    Inherited:
+    :param initial_protein_sequences: protein sequences of interest
+    :param initial_smiles_list: SMILES strings of interest
+
+    New:
+    :param use_msa_server: whether to use the MSA server
+    :param use_templates_server: whether to use the templates server
+    :param predicted_structure_uuid: UUID of the predicted structure
+    """
+
+    use_msa_server: bool = False
+    use_templates_server: bool = False
+    use_potentials: bool = False
+    predicted_structure_uuid: UUID | None = None
+    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
+
+
+reduced_mass: Annotated[float, AfterValidator(round_float(3))]  # amu
+solubilities: Annotated[list[float] | None, AfterValidator(round_optional_list(3))]

{stjames-0.0.79 → stjames-0.0.81/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.79
+Version: 0.0.81
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

stjames-0.0.79/stjames/workflows/protein_cofolding.py

@@ -1,53 +0,0 @@
-"""Protein Cofolding Workflow."""
-
-from pydantic import BaseModel
-
-from ..base import LowercaseStrEnum
-from ..types import UUID
-from .workflow import FASTAWorkflow
-
-
-class CofoldingModel(LowercaseStrEnum):
-    """Cofolding model to be used for prediction."""
-
-    CHAI_1R = "chai_1r"
-    BOLTZ_1 = "boltz_1"
-    BOLTZ_2 = "boltz_2"
-
-
-class CofoldingScores(BaseModel):
-    confidence_score: float
-    ptm: float  # predicted template modeling score
-    iptm: float  # interface predicted template modeling score
-
-
-class AffinityScore(BaseModel):
-    pred_value: float
-    probability_binary: float
-    pred_value1: float
-    probability_binary1: float
-    pred_value2: float
-    probability_binary2: float
-
-
-class ProteinCofoldingWorkflow(FASTAWorkflow):
-    """
-    A workflow for predicting structures. Especially protein structures.
-
-    Inherited:
-    :param initial_protein_sequences: protein sequences of interest
-    :param initial_smiles_list: SMILES strings of interest
-
-    New:
-    :param use_msa_server: whether to use the MSA server
-    :param use_templates_server: whether to use the templates server
-    :param predicted_structure_uuid: UUID of the predicted structure
-    """
-
-    use_msa_server: bool = False
-    use_templates_server: bool = False
-    use_potentials: bool = False
-    predicted_structure_uuid: UUID | None = None
-    scores: CofoldingScores | None = None
-    model: CofoldingModel = CofoldingModel.BOLTZ_2
-    affinity_score: AffinityScore | None = None