stjames 0.0.67__tar.gz → 0.0.69__tar.gz

{stjames-0.0.67/stjames.egg-info → stjames-0.0.69}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.67
+Version: 0.0.69
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.67 → stjames-0.0.69}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.67"
+version = "0.0.69"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.67 → stjames-0.0.69}/stjames/method.py

@@ -36,6 +36,7 @@ class Method(LowercaseStrEnum):
     OCP24_S = "ocp24_s"
     OCP24_L = "ocp24_l"
     ORB_V2 = "orb_v2"
+    ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
 
     GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
@@ -50,8 +51,8 @@ class Method(LowercaseStrEnum):
     RM1 = "rm1"
 
 
-PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1]
-PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.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]
 
 CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
 CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]

{stjames-0.0.67 → stjames-0.0.69}/stjames/status.py

@@ -2,7 +2,7 @@ from enum import Enum
 
 
 class Status(int, Enum):
-    # what a job gets when it's created
+    # what a job gets when it's created if user is below max_concurrency
     QUEUED = 0
 
     # still running...
@@ -16,3 +16,6 @@ class Status(int, Enum):
 
     # job was stopped externally, maybe timed out or something
     STOPPED = 4
+
+    # Status if a user has exceeded their allowed max_concurrency
+    AWAITING_QUEUE = 5

{stjames-0.0.67 → stjames-0.0.69}/stjames/workflows/__init__.py

@@ -14,6 +14,7 @@ from .fukui import *
 from .hydrogen_bond_basicity import *
 from .ion_mobility import *
 from .irc import *
+from .macropka import *
 from .molecular_dynamics import *
 from .multistage_opt import *
 from .pka import *
@@ -37,6 +38,7 @@ WORKFLOW_NAME = Literal[
     "hydrogen_bond_basicity",
     "ion_mobility",
     "irc",
+    "macropka",
     "molecular_dynamics",
     "multistage_opt",
     "pka",
@@ -60,6 +62,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # type: ignore [dict-item]
     "ion_mobility": IonMobilityWorkflow,  # type: ignore [dict-item]
     "irc": IRCWorkflow,  # type: ignore [dict-item]
+    "macropka": MacropKaWorkflow,  # type: ignore [dict-item]
     "molecular_dynamics": MolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "multistage_opt": MultiStageOptWorkflow,  # type: ignore [dict-item]
     "pka": pKaWorkflow,  # type: ignore [dict-item]

{stjames-0.0.67 → stjames-0.0.69}/stjames/workflows/fukui.py

@@ -5,6 +5,7 @@ from typing import Annotated
 from pydantic import AfterValidator
 
 from ..base import round_optional_float
+from ..settings import Settings
 from ..types import UUID, FloatPerAtom, round_optional_float_per_atom
 from .workflow import MoleculeWorkflow
 
@@ -17,6 +18,12 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     :param initial_molecule: Molecule of interest
     :param mode: Mode for workflow (currently unused)
 
+    Settings:
+    :param opt_settings: if given, the settings for optimization. if none, no optimization will be conducted.
+    :param opt_engine: the engine for optimization
+    :param fukui_settings: the settings for Fukui index calculations.
+    :param fukui_engine: the engine for Fukui index calculations
+
     Results:
     :param optimization: UUID of optimization
     :param global_electrophilicity_index: global electrophilicity index
@@ -25,7 +32,12 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     :param fukui_zero: Fukui index for zero charges
     """
 
-    # UUID of optimization
+    opt_settings: Settings | None = None
+    opt_engine: str | None = None
+
+    fukui_settings: Settings = Settings(method="gfn1_xtb")
+    fukui_engine: str | None = None
+
     optimization: UUID | None = None
 
     global_electrophilicity_index: Annotated[float | None, AfterValidator(round_optional_float(6))] = None

{stjames-0.0.67 → stjames-0.0.69}/stjames/workflows/macropka.py

@@ -1,6 +1,6 @@
 """pKa workflow."""
 
-from typing import Annotated, Self
+from typing import Annotated, Optional, Self
 
 from pydantic import AfterValidator, model_validator
 
@@ -55,18 +55,41 @@ class MacropKaWorkflow(SMILESWorkflow):
     :param microstate_weights_by_pH: precompute the % of different microstates
     """
 
-    temperature: Annotated[float, AfterValidator(round_float(3))] = 298.0
     min_pH: Annotated[float, AfterValidator(round_float(3))] = 0.0
     max_pH: Annotated[float, AfterValidator(round_float(3))] = 14.0
 
+    max_charge: int = 2
+    min_charge: int = -2
+
     microstates: list[MacropKaMicrostate] = []
     pKa_values: list[MacropKaValue] = []
-    microstate_weights_by_pH: dict[float, Annotated[list[float], AfterValidator(round_list(6))]] = {}
+    microstate_weights_by_pH: list[
+        tuple[
+            Annotated[float, AfterValidator(round_float(3))],
+            Annotated[list[float], AfterValidator(round_list(6))],
+        ]
+    ] = []
+
+    isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
+
+    logD_by_pH: list[
+        tuple[
+            Annotated[float, AfterValidator(round_float(3))],
+            Annotated[float, AfterValidator(round_float(3))],
+        ]
+    ] = []
 
     @model_validator(mode="after")
     def check_weights(self) -> Self:
-        for weights in self.microstate_weights_by_pH.values():
+        for _, weights in self.microstate_weights_by_pH:
             if len(weights) != len(self.microstates):
                 raise ValueError("Length of microstate weights doesn't match!")
 
         return self
+
+    @model_validator(mode="after")
+    def check_minmax_charges(self) -> Self:
+        if self.min_charge >= self.max_charge:
+            raise ValueError("Incoherent min/max charge specification")
+
+        return self

{stjames-0.0.67 → stjames-0.0.69}/stjames/workflows/scan.py

@@ -18,12 +18,14 @@ class ScanPoint(Base):
     A point in a scan.
 
     :param index: index of the point
+    :param index_2d: index of the point in 2nd dimension, if applicable
     :param molecule: Molecule at the point
     :param energy: energy of the point
     :param uuid: UUID of the calculation
     """
 
     index: int
+    index_2d: int = 0
     molecule: Molecule
     energy: Annotated[float | None, AfterValidator(round_optional_float(6))] = None
     uuid: UUID | None = None

{stjames-0.0.67 → stjames-0.0.69/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.67
+Version: 0.0.69
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames