stjames 0.0.28__tar.gz → 0.0.30__tar.gz

{stjames-0.0.28/stjames.egg-info → stjames-0.0.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.28
+Version: 0.0.30
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.28 → stjames-0.0.30}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.28"
+version = "0.0.30"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -23,11 +23,18 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
 where = ["."]  # list of folders that contain the packages (["."] by default)
-include = ["stjames"]  # package names should match these glob patterns (["*"] by default)
+include = ["stjames", "stjames.*"]  # package names should match these glob patterns (["*"] by default)
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [tool.ruff]
 line-length = 160
-select = ["E", "F"]
+
+[tool.ruff.lint]
+select = [
+    "E",  # pycodestyle errors
+    "F",  # pyflakes
+    "I",  # isort
+    "W",  # pycodestyle warnings
+]
 ignore = ["E741"]

{stjames-0.0.28 → stjames-0.0.30}/stjames/__init__.py

@@ -2,6 +2,7 @@
 
 from .calculation import *
 from .molecule import *
+from .workflows import *
 
 from .scf_settings import *
 from .int_settings import *
@@ -10,12 +11,12 @@ 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-0.0.28 → stjames-0.0.30}/stjames/base.py

@@ -1,7 +1,8 @@
-import pydantic
 from enum import Enum
+from typing import Annotated, Any, Hashable, TypeVar
+
 import numpy as np
-from typing import Any, Annotated, TypeVar, Hashable
+import pydantic
 
 
 class Base(pydantic.BaseModel):

{stjames-0.0.28 → stjames-0.0.30}/stjames/scf_settings.py

@@ -1,10 +1,11 @@
-from typing import Optional, Any
+from typing import Any, Optional
+
 import pydantic
 
 from .base import Base, LowercaseStrEnum
-from .int_settings import IntSettings
-from .grid_settings import GridSettings
 from .diis_settings import DIISSettings
+from .grid_settings import GridSettings
+from .int_settings import IntSettings
 
 
 class SCFInitMethod(LowercaseStrEnum):

{stjames-0.0.28 → stjames-0.0.30}/stjames/settings.py

@@ -1,16 +1,27 @@
-import pydantic
 from typing import Any, Optional
 
-from .modes import Mode
-from .methods import Method
-from .tasks import Task
+import pydantic
+
 from .base import Base, UniqueList
-from .corrections import Correction
-from .scf_settings import SCFSettings
 from .basis_set import BasisSet
+from .correction import Correction
+from .method import Method
+from .mode import Mode
 from .opt_settings import OptimizationSettings
+from .scf_settings import SCFSettings
+from .solvent import SolventSettings
+from .task import Task
 from .thermochem_settings import ThermochemistrySettings
-from .solvent_settings import SolventSettings
+
+PREPACKAGED_METHODS = [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3, Method.AIMNET2_B973C, Method.GFN2_XTB, Method.GFN1_XTB]
+
+METHODS_WITH_CORRECTION = [
+    Method.B97D3,
+    Method.WB97XD,
+    Method.WB97XD3,
+    Method.WB97XV,
+    Method.WB97MV,
+]
 
 
 class Settings(Base):
@@ -31,9 +42,10 @@ class Settings(Base):
     @pydantic.computed_field
     @property
     def level_of_theory(self) -> str:
-        # prepackaged methods
-        if self.method in [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3, Method.AIMNET2_B973C, Method.GFN2_XTB, Method.GFN1_XTB] or self.basis_set is None:
+        if self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
+        elif self.method in METHODS_WITH_CORRECTION:
+            method = f"{self.method.value}/{self.basis_set.name.lower()}"
         else:
             corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
             method = f"{self.method.value}-{'-'.join([c.value for c in corrections])}/{self.basis_set.name.lower()}"

stjames-0.0.30/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-0.0.30/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-0.0.30/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-0.0.30/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-0.0.30/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-0.0.30/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-0.0.30/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-0.0.30/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-0.0.28 → stjames-0.0.30/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.28
+Version: 0.0.30
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.28 → stjames-0.0.30}/stjames.egg-info/SOURCES.txt

@@ -6,22 +6,30 @@ stjames/_deprecated_solvent_settings.py
 stjames/base.py
 stjames/basis_set.py
 stjames/calculation.py
-stjames/corrections.py
+stjames/correction.py
 stjames/diis_settings.py
 stjames/grid_settings.py
 stjames/int_settings.py
-stjames/methods.py
-stjames/modes.py
+stjames/method.py
+stjames/mode.py
 stjames/molecule.py
 stjames/opt_settings.py
 stjames/scf_settings.py
 stjames/settings.py
-stjames/solvent_settings.py
+stjames/solvent.py
 stjames/status.py
-stjames/tasks.py
+stjames/task.py
 stjames/thermochem_settings.py
 stjames.egg-info/PKG-INFO
 stjames.egg-info/SOURCES.txt
 stjames.egg-info/dependency_links.txt
 stjames.egg-info/requires.txt
-stjames.egg-info/top_level.txt
+stjames.egg-info/top_level.txt
+stjames/workflows/__init__.py
+stjames/workflows/conformer.py
+stjames/workflows/fukui.py
+stjames/workflows/pka.py
+stjames/workflows/redox_potential.py
+stjames/workflows/scan.py
+stjames/workflows/tautomer.py
+stjames/workflows/workflow.py

{stjames-0.0.28 → stjames-0.0.30}/stjames/calculation.py

@@ -1,7 +1,7 @@
 from typing import Optional
 
-from .molecule import Molecule
 from .base import Base, LowercaseStrEnum
+from .molecule import Molecule
 from .settings import Settings
 from .status import Status