stjames 0.0.72__py3-none-any.whl → 0.0.73__py3-none-any.whl

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Files changed (8) hide show
  1. stjames/method.py +19 -3
  2. stjames/workflows/macropka.py +2 -0
  3. stjames/workflows/protein_cofolding.py +9 -0
  4. {stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/METADATA +1 -1
  5. {stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/RECORD +8 -8
  6. {stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/WHEEL +1 -1
  7. {stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/licenses/LICENSE +0 -0
  8. {stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/top_level.txt +0 -0
stjames/method.py CHANGED
@@ -50,9 +50,25 @@ class Method(LowercaseStrEnum):
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  RM1 = "rm1"
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-
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- PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
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- PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
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+ EGRET_1 = "egret_1"
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+ EGRET_1E = "egret_1e"
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+ EGRET_1H = "egret_1h"
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+
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+
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+ PrepackagedNNPMethod = Literal[
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+ 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
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+ ]
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+
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+ PREPACKAGED_NNP_METHODS = [
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+ Method.AIMNET2_WB97MD3,
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+ Method.OCP24_S,
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+ Method.OCP24_L,
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+ Method.RM1,
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+ Method.ORB_V3_CONSERVATIVE_INF_OMAT,
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+ Method.EGRET_1,
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+ Method.EGRET_1E,
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+ Method.EGRET_1H,
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+ ]
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  CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
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  CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]
stjames/workflows/macropka.py CHANGED
@@ -60,6 +60,7 @@ class MacropKaWorkflow(SMILESWorkflow):
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  :param microstate_weights_by_pH: the % of different microstates by pH
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  :param logD_by_pH: the distribution constant (water/octanol) by pH
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  :param aqueous_solubility_by_pH: the log(S)/L of the compound in water, by pH
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+ :param kpuu_probability: the probability that Kpuu >= 0.3, the Schrodinger-determined threshold
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  """
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  min_pH: Annotated[float, AfterValidator(round_float(3))] = 0.0
@@ -73,6 +74,7 @@ class MacropKaWorkflow(SMILESWorkflow):
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  pKa_values: list[MacropKaValue] = []
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  isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
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  solvation_energy: Annotated[Optional[float], AfterValidator(round_float(3))] = None
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+ kpuu_probability: Annotated[Optional[float], AfterValidator(round_float(3))] = None
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  microstate_weights_by_pH: list[
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  tuple[
stjames/workflows/protein_cofolding.py CHANGED
@@ -2,10 +2,18 @@
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  from pydantic import BaseModel
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+ from ..base import LowercaseStrEnum
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  from ..types import UUID
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  from .workflow import FASTAWorkflow
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+ class CofoldingModel(LowercaseStrEnum):
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+ """Cofolding model to be used for prediction."""
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+
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+ CHAI_1R = "chai_1r"
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+ BOLTZ = "boltz"
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+
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+
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  class CofoldingScores(BaseModel):
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  confidence_score: float
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  ptm: float # predicted template modeling score
@@ -30,3 +38,4 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
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  use_templates_server: bool = False
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  predicted_structure_uuid: UUID | None = None
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  scores: CofoldingScores | None = None
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+ model: CofoldingModel = CofoldingModel.CHAI_1R
{stjames-0.0.72.dist-info → stjames-0.0.73.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: 0.0.72
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+ Version: 0.0.73
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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-0.0.72.dist-info → stjames-0.0.73.dist-info}/RECORD RENAMED
@@ -11,7 +11,7 @@ stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
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  stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
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  stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
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  stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
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- stjames/method.py,sha256=4X2OdeOQCj0Ihtthl9mx6Q26RrZljYhvRUVz-huf0s8,2461
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+ stjames/method.py,sha256=PXbBVp6pS4wUDr-qoguJgZy2Wqt8NF49aOH1fspd5DM,2680
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  stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
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  stjames/molecule.py,sha256=4dakMkn-_I5bSWsijLLY0tn5NkBEuZhmtYDj-MDSJE0,17987
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  stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
@@ -50,19 +50,19 @@ stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,17
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  stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
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  stjames/workflows/ion_mobility.py,sha256=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
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  stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
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- stjames/workflows/macropka.py,sha256=jFdo0log2ZDeqXYcLpGHq3L9zEUJLBgVQhzrwtKCM44,3566
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+ stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
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  stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
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  stjames/workflows/multistage_opt.py,sha256=pPLAZDztHd37q8cxCUkdq8EzOFyrTzZJHNfDV5auiHs,13638
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  stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
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- stjames/workflows/protein_cofolding.py,sha256=GPryfSu9C1uqZPnXMg6G_TCaV02YlBvyOta76UQrCPE,957
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+ stjames/workflows/protein_cofolding.py,sha256=x6csP7IkQqKVhw4MhmGFdLzCFmYXK8nFtl2t2gMJuX8,1184
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  stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
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  stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
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  stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcMpw,1898
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  stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
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  stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
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  stjames/workflows/workflow.py,sha256=NA4H9W_47UQWnrsdB5UXFODMaZWrmULYqW1pud5ErO4,1900
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- stjames-0.0.72.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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- stjames-0.0.72.dist-info/METADATA,sha256=1nYg2PIeHN5lZzjw-QGtX6cbaqv5r1YA7Eatd6aPGYU,1694
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- stjames-0.0.72.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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- stjames-0.0.72.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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- stjames-0.0.72.dist-info/RECORD,,
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+ stjames-0.0.73.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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+ stjames-0.0.73.dist-info/METADATA,sha256=YlsG4MdAL-yJZIMmW1Wll6LvvLyGpaWJONcjBStdpQM,1694
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+ stjames-0.0.73.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
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+ stjames-0.0.73.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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+ stjames-0.0.73.dist-info/RECORD,,
{stjames-0.0.72.dist-info → stjames-0.0.73.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (78.1.0)
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+ Generator: setuptools (79.0.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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