stjames 0.0.29__py3-none-any.whl → 0.0.31__py3-none-any.whl

stjames/__init__.py

@@ -8,15 +8,14 @@ from .scf_settings import *
 from .int_settings import *
 from .opt_settings import *
 from .diis_settings import *
-from .solvent_settings import *
 from .thermochem_settings import *
 from .grid_settings import *
-from .solvent_settings import *
 from .settings import *
 
-from .methods import *
+from .method import *
 from .basis_set import *
-from .tasks import *
-from .corrections import *
-from .modes import *
+from .task import *
+from .correction import *
+from .solvent import *
+from .mode import *
 from .status import *

stjames/settings.py

@@ -4,23 +4,16 @@ import pydantic
 
 from .base import Base, UniqueList
 from .basis_set import BasisSet
-from .corrections import Correction
-from .methods import Method
-from .modes import Mode
+from .correction import Correction
+from .method import Method
+from .mode import Mode
 from .opt_settings import OptimizationSettings
 from .scf_settings import SCFSettings
-from .solvent_settings import SolventSettings
-from .tasks import Task
+from .solvent import SolventSettings
+from .task import Task
 from .thermochem_settings import ThermochemistrySettings
 
-PREPACKAGED_METHODS = [
-    Method.HF3C,
-    Method.B973C,
-    Method.AIMNET2_WB97MD3,
-    Method.AIMNET2_B973C,
-    Method.GFN2_XTB,
-    Method.GFN1_XTB
-]
+PREPACKAGED_METHODS = [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3, Method.AIMNET2_B973C, Method.GFN2_XTB, Method.GFN1_XTB]
 
 METHODS_WITH_CORRECTION = [
     Method.B97D3,
@@ -30,6 +23,7 @@ METHODS_WITH_CORRECTION = [
     Method.WB97MV,
 ]
 
+
 class Settings(Base):
     method: Method = Method.HARTREE_FOCK
     basis_set: Optional[BasisSet] = None

stjames/workflows/__init__.py

@@ -0,0 +1,8 @@
+# ruff: noqa
+
+from .pka import *
+from .conformer import *
+from .tautomer import *
+from .redox_potential import *
+from .scan import *
+from .fukui import *

stjames/workflows/conformer.py

@@ -0,0 +1,90 @@
+from typing import Any, Optional
+
+from ..base import Base
+from ..method import Method
+from ..mode import Mode
+from ..solvent import Solvent
+from .workflow import Workflow
+
+
+class ConformerSettings(Base):
+    num_confs_considered: int = 100
+    num_confs_taken: int = 50
+    rmsd_cutoff: float = 0.1
+
+    final_method: Method = Method.AIMNET2_WB97MD3
+    solvent: Optional[Solvent] = Solvent.WATER
+    max_energy: float = 5
+
+
+class RdkitConformerSettings(ConformerSettings):
+    csearch_program: str = "rdkit"
+
+    num_initial_confs: int = 100
+    max_mmff_energy: float = 10
+    max_mmff_iterations: int = 500
+    num_confs_considered: float = 10
+    num_confs_taken: float = 3
+    rmsd_cutoff: float = 0.1
+
+
+class CrestConformerSettings(ConformerSettings):
+    csearch_program: str = "crest"
+
+    flags: str = "--quick --ewin 10"
+    gfn: int | str = "ff"
+
+
+class Conformer(Base):
+    energy: float
+    weight: Optional[float] = None
+
+    # uuid, optionally
+    uuid: Optional[str] = None
+
+
+class ConformerWorkflow(Workflow):
+    settings: ConformerSettings = ConformerSettings()
+    conformers: list[Conformer] = []
+
+    def model_post_init(self, __context: Any) -> None:
+        self.settings = csearch_settings_by_mode(self.mode)
+
+
+def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
+    if mode == Mode.METICULOUS:
+        return CrestConformerSettings(
+            gfn=2,
+            flags="--ewin 15",
+            max_energy=10,
+            num_confs_considered=500,
+            num_confs_taken=150,
+        )
+
+    elif mode == Mode.CAREFUL:
+        return CrestConformerSettings(
+            gfn="ff",
+            flags="--quick --ewin 10",
+            num_confs_considered=150,
+            num_confs_taken=50,
+        )
+
+    elif mode == Mode.RAPID:
+        return RdkitConformerSettings(
+            num_initial_confs=300,
+            max_mmff_energy=15,
+            num_confs_considered=100,
+            num_confs_taken=50,
+        )
+
+    elif mode == Mode.RECKLESS:
+        return RdkitConformerSettings(
+            num_initial_confs=200,
+            max_mmff_energy=10,
+            num_confs_considered=50,
+            num_confs_taken=20,
+            rmsd_cutoff=0.25,
+        )
+
+    else:
+        raise ValueError(f"invalid mode ``{mode.value}`` for conformer settings")

stjames/workflows/fukui.py

@@ -0,0 +1,13 @@
+from typing import Optional
+
+from .workflow import Workflow
+
+
+class FukuiIndexWorkflow(Workflow):
+    # uuid of optimization
+    optimization: Optional[str] = None
+
+    global_electrophilicity_index: Optional[float] = None
+    fukui_positive: Optional[list[float]] = None
+    fukui_negative: Optional[list[float]] = None
+    fukui_zero: Optional[list[float]] = None

stjames/workflows/pka.py

@@ -0,0 +1,27 @@
+from typing import Optional
+
+from ..base import Base
+from .workflow import DBCalculation, Workflow
+
+
+class pKaMicrostate(Base):
+    atom_index: int
+    structures: list[DBCalculation] = []
+    delta_G: float
+    pKa: float
+
+
+class pKaWorkflow(Workflow):
+    pka_range: tuple[float, float] = (2, 12)
+    deprotonate_elements: list[int] = [7, 8, 16]
+    deprotonate_atoms: list[int] = []
+    protonate_elements: list[int] = [7]
+    protonate_atoms: list[int] = []
+
+    reasonableness_buffer: float = 5
+
+    structures: list[DBCalculation] = []
+    conjugate_acids: list[pKaMicrostate] = []
+    conjugate_bases: list[pKaMicrostate] = []
+    strongest_acid: Optional[float] = None
+    strongest_base: Optional[float] = None

stjames/workflows/redox_potential.py

@@ -0,0 +1,18 @@
+from typing import Optional
+
+from ..solvent import Solvent
+from .workflow import Workflow
+
+
+class RedoxPotentialWorkflow(Workflow):
+    solvent: Solvent = Solvent.ACETONITRILE
+    reduction: bool = True
+    oxidation: bool = True
+
+    # uuids
+    neutral_molecule: Optional[str] = None
+    anion_molecule: Optional[str] = None
+    cation_molecule: Optional[str] = None
+
+    reduction_potential: Optional[float] = None
+    oxidation_potential: Optional[float] = None

stjames/workflows/scan.py

@@ -0,0 +1,38 @@
+from typing import Optional
+
+import numpy as np
+
+from ..base import Base
+from ..molecule import Molecule
+from ..settings import Settings
+from .workflow import Workflow
+
+
+class ScanPoint(Base):
+    index: int
+    molecule: Molecule
+    energy: Optional[float] = None
+    uuid: Optional[str] = None
+
+
+class ScanSettings(Base):
+    type: str  # "bond", "angle", "dihedral" - make Enum later
+    atoms: list[int]
+    start: float
+    stop: float
+    num: int
+
+    def vals(self) -> np.ndarray:
+        return np.linspace(self.start, self.stop, self.num)
+
+    class Config:
+        from_attributes = True
+
+
+class ScanWorkflow(Workflow):
+    scan_settings: ScanSettings
+    calc_settings: Settings
+    engine: str
+
+    # uuids of scan points
+    scan_points: list[str] = []

stjames/workflows/tautomer.py

@@ -0,0 +1,19 @@
+from typing import Optional
+
+from ..base import Base
+from .conformer import ConformerSettings
+from .workflow import DBCalculation, Workflow
+
+
+class Tautomer(Base):
+    energy: float
+    weight: Optional[float] = None
+    predicted_relative_energy: Optional[float] = None
+
+    # uuids, optionally
+    structures: list[DBCalculation] = []
+
+
+class TautomerWorkflow(Workflow):
+    settings: ConformerSettings
+    tautomers: list[Tautomer] = []

stjames/workflows/workflow.py

@@ -0,0 +1,16 @@
+from ..base import Base
+from ..mode import Mode
+from ..molecule import Molecule
+
+
+class Workflow(Base):
+    """All workflows should have these properties."""
+
+    initial_molecule: Molecule
+    mode: Mode
+
+
+class DBCalculation(Base):
+    """Encodes a calculation that's in the database. This isn't terribly useful by itself."""
+
+    uuid: str

{stjames-0.0.29.dist-info → stjames-0.0.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.29
+Version: 0.0.31
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

stjames-0.0.31.dist-info/RECORD

@@ -0,0 +1,32 @@
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stjames-0.0.29.dist-info/RECORD

@@ -1,24 +0,0 @@
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