stjames 0.0.71__py3-none-any.whl → 0.0.73__py3-none-any.whl

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/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/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/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.dist-info → stjames-0.0.73.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.73.dist-info}/RECORD

@@ -11,7 +11,7 @@ stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
 stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
 stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
-stjames/method.py,sha256=4X2OdeOQCj0Ihtthl9mx6Q26RrZljYhvRUVz-huf0s8,2461
+stjames/method.py,sha256=PXbBVp6pS4wUDr-qoguJgZy2Wqt8NF49aOH1fspd5DM,2680
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=4dakMkn-_I5bSWsijLLY0tn5NkBEuZhmtYDj-MDSJE0,17987
 stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
@@ -50,19 +50,19 @@ stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,17
 stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
 stjames/workflows/ion_mobility.py,sha256=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
 stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
-stjames/workflows/macropka.py,sha256=jFdo0log2ZDeqXYcLpGHq3L9zEUJLBgVQhzrwtKCM44,3566
+stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
 stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
 stjames/workflows/multistage_opt.py,sha256=pPLAZDztHd37q8cxCUkdq8EzOFyrTzZJHNfDV5auiHs,13638
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
-stjames/workflows/protein_cofolding.py,sha256=woDdmyMYVhrmOyB55mxIP56Rpw6iElDoS5YiX5oyixY,883
+stjames/workflows/protein_cofolding.py,sha256=x6csP7IkQqKVhw4MhmGFdLzCFmYXK8nFtl2t2gMJuX8,1184
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
 stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcMpw,1898
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
-stjames/workflows/workflow.py,sha256=dmJbjI3Ng95zHEZd1Qkhhk5Eb1aF4W36Oy_GwZPJdBk,1704
-stjames-0.0.71.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.71.dist-info/METADATA,sha256=jFy2RQUS3wHe4vRo0w-OZskC6Yk3ctdMAhYhDrNPE-Q,1694
-stjames-0.0.71.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-stjames-0.0.71.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.71.dist-info/RECORD,,
+stjames/workflows/workflow.py,sha256=NA4H9W_47UQWnrsdB5UXFODMaZWrmULYqW1pud5ErO4,1900
+stjames-0.0.73.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.73.dist-info/METADATA,sha256=YlsG4MdAL-yJZIMmW1Wll6LvvLyGpaWJONcjBStdpQM,1694
+stjames-0.0.73.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
+stjames-0.0.73.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.73.dist-info/RECORD,,

{stjames-0.0.71.dist-info → stjames-0.0.73.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (79.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any