stjames 0.0.71__tar.gz → 0.0.73__tar.gz

{stjames-0.0.71/stjames.egg-info → stjames-0.0.73}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.71
+Version: 0.0.73
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.71 → stjames-0.0.73}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.71"
+version = "0.0.73"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.71 → stjames-0.0.73}/stjames/method.py

@@ -50,9 +50,25 @@ class Method(LowercaseStrEnum):
 
     RM1 = "rm1"
 
-
-PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
-PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
+    EGRET_1 = "egret_1"
+    EGRET_1E = "egret_1e"
+    EGRET_1H = "egret_1h"
+
+
+PrepackagedNNPMethod = Literal[
+    Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT, Method.EGRET_1, Method.EGRET_1E, Method.EGRET_1H
+]
+
+PREPACKAGED_NNP_METHODS = [
+    Method.AIMNET2_WB97MD3,
+    Method.OCP24_S,
+    Method.OCP24_L,
+    Method.RM1,
+    Method.ORB_V3_CONSERVATIVE_INF_OMAT,
+    Method.EGRET_1,
+    Method.EGRET_1E,
+    Method.EGRET_1H,
+]
 
 CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
 CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]

{stjames-0.0.71 → stjames-0.0.73}/stjames/workflows/macropka.py

@@ -60,6 +60,7 @@ class MacropKaWorkflow(SMILESWorkflow):
     :param microstate_weights_by_pH: the % of different microstates by pH
     :param logD_by_pH: the distribution constant (water/octanol) by pH
     :param aqueous_solubility_by_pH: the log(S)/L of the compound in water, by pH
+    :param kpuu_probability: the probability that Kpuu >= 0.3, the Schrodinger-determined threshold
     """
 
     min_pH: Annotated[float, AfterValidator(round_float(3))] = 0.0
@@ -73,6 +74,7 @@ class MacropKaWorkflow(SMILESWorkflow):
     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
 
     microstate_weights_by_pH: list[
         tuple[

{stjames-0.0.71 → stjames-0.0.73}/stjames/workflows/protein_cofolding.py

@@ -2,14 +2,22 @@
 
 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 = "boltz"
+
+
 class CofoldingScores(BaseModel):
     confidence_score: float
-    ptm: float  # predicted template modelling score
-    iptm: float  # interface predicted template modelling score
+    ptm: float  # predicted template modeling score
+    iptm: float  # interface predicted template modeling score
 
 
 class ProteinCofoldingWorkflow(FASTAWorkflow):
@@ -17,7 +25,8 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
     A workflow for predicting structures. Especially protein structures.
 
     Inherited:
-    :param initial_fasta: fasta string of interest
+    :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
@@ -29,3 +38,4 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
     use_templates_server: bool = False
     predicted_structure_uuid: UUID | None = None
     scores: CofoldingScores | None = None
+    model: CofoldingModel = CofoldingModel.CHAI_1R

{stjames-0.0.71 → stjames-0.0.73}/stjames/workflows/workflow.py

@@ -24,15 +24,17 @@ class Workflow(Base):
 
 class FASTAWorkflow(Workflow):
     """
-    Base class for Workflows that operate on a fasta string.
+    Base class for Workflows that operate on protein sequences and SMILES.
 
-    :param initial_fasta: fasta string of interest
+    :param initial_protein_sequences: protein sequences of interest
+    :param initial_smiles_list: SMILES strings of interest
     """
 
-    initial_fasta: str
+    initial_protein_sequences: list[str]
+    initial_smiles_list: list[str] | None = None
 
     def __repr__(self) -> str:
-        return f"<{type(self).__name__} {self.initial_fasta}>"
+        return f"<{type(self).__name__} {self.initial_protein_sequences} {self.initial_smiles_list}>"
 
 
 class SMILESWorkflow(Workflow):

{stjames-0.0.71 → stjames-0.0.73/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.71
+Version: 0.0.73
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames