stjames 0.0.46__py3-none-any.whl → 0.0.47__py3-none-any.whl

stjames/base.py

@@ -12,7 +12,7 @@ class Base(pydantic.BaseModel):
     @classmethod
     def coerce_numpy(cls, val: _T) -> _T | list[Any]:
         if isinstance(val, np.ndarray):
-            return val.tolist()  # type: ignore [no-any-return, unused-ignore]
+            return val.tolist()  # type: ignore [no-any-return, unused-ignore, return-value]
 
         return val
 

stjames/method.py

@@ -43,6 +43,8 @@ class Method(LowercaseStrEnum):
     # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
     BP86 = "bp86"
 
+    OFF_SAGE_2_2_1 = "off_sage_2_2_1"
+
 
 NNPMethod = Literal[Method.AIMNET2_WB97MD3]
 NNP_METHODS = [Method.AIMNET2_WB97MD3]
@@ -53,8 +55,11 @@ XTB_METHODS = [Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB]
 CompositeMethod = Literal[Method.HF3C, Method.B973C, Method.R2SCAN3C, Method.WB97X3C]
 COMPOSITE_METHODS = [Method.HF3C, Method.B973C, Method.R2SCAN3C, Method.WB97X3C]
 
-PrepackagedMethod = XTBMethod | CompositeMethod | NNPMethod
-PREPACKAGED_METHODS = [*XTB_METHODS, *COMPOSITE_METHODS]
+FFMethod = Literal[Method.OFF_SAGE_2_2_1]
+FF_METHODS = [Method.OFF_SAGE_2_2_1]
+
+PrepackagedMethod = XTBMethod | CompositeMethod | NNPMethod | FFMethod
+PREPACKAGED_METHODS = [*XTB_METHODS, *COMPOSITE_METHODS, *NNP_METHODS, *FF_METHODS]
 
 MethodWithCorrection = Literal[Method.WB97XD3, Method.WB97XV, Method.WB97MV, Method.WB97MD3BJ, Method.DSDBLYPD3BJ]
 METHODS_WITH_CORRECTION = [Method.WB97XD3, Method.WB97XV, Method.WB97MV, Method.WB97MD3BJ, Method.DSDBLYPD3BJ, Method.B97D3BJ]

stjames/workflows/__init__.py

@@ -9,6 +9,7 @@ from .conformer_search import *
 from .descriptors import *
 from .electronic_properties import *
 from .fukui import *
+from .hydrogen_bond_basicity import *
 from .molecular_dynamics import *
 from .multistage_opt import *
 from .pka import *
@@ -27,6 +28,7 @@ WORKFLOW_NAME = Literal[
     "descriptors",
     "electronic_properties",
     "fukui",
+    "hydrogen_bond_basicity",
     "molecular_dynamics",
     "multistage_opt",
     "pka",
@@ -45,6 +47,7 @@ WORKFLOW_MAPPING: dict[str, Workflow] = {
     "descriptors": DescriptorsWorkflow,  # type: ignore [dict-item]
     "electronic_properties": ElectronicPropertiesWorkflow,  # type: ignore [dict-item]
     "fukui": FukuiIndexWorkflow,  # type: ignore [dict-item]
+    "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # 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/workflows/conformer_search.py

@@ -9,6 +9,7 @@ from ..base import LowercaseStrEnum
 from ..constraint import Constraint
 from ..method import Method, XTBMethod
 from ..mode import Mode
+from ..task import Task
 from ..types import UUID
 from .multistage_opt import MultiStageOptMixin
 from .workflow import Workflow
@@ -322,6 +323,45 @@ class ConformerSearchMixin(ConformerGenMixin, MultiStageOptMixin):
         """Return a string representation of the ConformerSearch workflow."""
         return f"<{type(self).__name__} {self.conf_gen_mode.name} {self.mso_mode.name}>"
 
+    @model_validator(mode="after")
+    def deduplicate(self) -> Self:
+        """
+        Deduplicate optimizations between conf_gen and multistage_opt.
+
+        Also affects Manual Mode.
+        """
+        cgs = self.conf_gen_settings
+        msos = self.multistage_opt_settings
+
+        if self.transition_state or not msos.optimization_settings:
+            return self
+
+        first_opt = msos.optimization_settings[0]
+        if cgs.conf_opt_method != first_opt.method or "optimize" not in first_opt.tasks:
+            return self
+
+        first_opt.tasks.remove(Task.OPTIMIZE)
+        if msos.singlepoint_settings or len(msos.optimization_settings) > 1:
+            if (not first_opt.tasks) or first_opt.tasks == ["singlepoint"]:
+                msos.optimization_settings = msos.optimization_settings[1:]
+
+        return self
+
+    @model_validator(mode="after")
+    def remove_ts_constraints(self) -> Self:
+        """
+        Remove constraints from optimization if a TS.
+
+        Also affects Manual Mode.
+        """
+        msos = self.multistage_opt_settings
+        if msos.transition_state and msos.constraints:
+            msos.constraints = []
+            for opt_set in msos.optimization_settings:
+                opt_set.opt_settings.constraints = []
+
+        return self
+
 
 class ConformerSearchWorkflow(ConformerSearchMixin, Workflow):
     """

stjames/workflows/electronic_properties.py

@@ -1,4 +1,6 @@
-from pydantic import NonNegativeFloat, NonNegativeInt
+from typing import Annotated, Callable
+
+from pydantic import AfterValidator, NonNegativeFloat, NonNegativeInt
 
 from ..base import Base
 from ..settings import Settings
@@ -6,11 +8,22 @@ from ..types import UUID, FloatPerAtom, Matrix3x3, Vector3D
 from .workflow import Workflow
 
 
+def round_float(round_to: int) -> Callable[[float], float]:
+    """Return a function that rounds a float to a given number of decimal places."""
+
+    def inner_round(v: float) -> float:
+        return round(v, round_to)
+
+    return inner_round
+
+
 class PropertyCubePoint(Base):
-    x: float
-    y: float
-    z: float
-    val: float
+    """A point in a cube file, all values rounded to 6 decimal places."""
+
+    x: Annotated[float, AfterValidator(round_float(3))]
+    y: Annotated[float, AfterValidator(round_float(3))]
+    z: Annotated[float, AfterValidator(round_float(3))]
+    val: Annotated[float, AfterValidator(round_float(6))]
 
 
 class PropertyCube(Base):

stjames/workflows/hydrogen_bond_basicity.py

@@ -0,0 +1,18 @@
+from ..base import Base
+from ..types import UUID
+from .workflow import Workflow
+
+
+class HydrogenBondAcceptorSite(Base):
+    atom_idx: int  # zero-indexed
+    pkbhx: float
+    position: tuple[float, float, float]
+    name: str | None = None
+
+
+class HydrogenBondBasicityWorkflow(Workflow):
+    # UUID of optimization
+    optimization: UUID | None = None
+
+    # hydrogen-bond-acceptor sites
+    hba_sites: list[HydrogenBondAcceptorSite] = []  # noqa: RUF012

stjames/workflows/molecular_dynamics.py

@@ -1,6 +1,6 @@
 from typing import Self
 
-from pydantic import PositiveFloat, PositiveInt, model_validator
+from pydantic import PositiveFloat, PositiveInt, computed_field, model_validator
 
 from ..base import Base, LowercaseStrEnum
 from ..constraint import PairwiseHarmonicConstraint, SphericalHarmonicConstraint
@@ -29,7 +29,13 @@ class Frame(Base):
     pressure: float
     temperature: float
     volume: float
-    energy: float
+    potential_energy: float  # kcal/mol
+    kinetic_energy: float  # kcal/mol
+
+    @computed_field  # type: ignore[misc, prop-decorator, unused-ignore]
+    @property
+    def energy(self) -> float:
+        return self.potential_energy + self.kinetic_energy
 
 
 class MolecularDynamicsSettings(Base):

stjames/workflows/multistage_opt.py

@@ -331,3 +331,29 @@ def build_mso_settings(
         transition_state=transition_state,
         frequencies=frequencies,
     )
+
+
+def multi_stage_opt_settings_from_workflow(msow: MultiStageOptWorkflow) -> MultiStageOptSettings:
+    """
+    Helper function to convert a MultiStageOptWorkflow to MultiStageOptSettings.
+
+    :param msow: MultiStageOptWorkflow
+    :returns: MultiStageOptSettings
+
+    >>> from stjames.molecule import Atom, Molecule
+    >>> He = Molecule(charge=0, multiplicity=1, atoms=[Atom(atomic_number=2, position=[0, 0, 0])])
+    >>> msos = multi_stage_opt_settings_from_workflow(
+    ...     MultiStageOptWorkflow(initial_molecule=He, mode=Mode.RAPID, solvent="water")
+    ... )
+    >>> print(msos)
+    <MultiStageOptSettings RAPID>
+    >>> msos.level_of_theory
+    'r2scan_3c/cpcm(water)//gfn2_xtb'
+    >>> msos.solvent
+    <Solvent.WATER: 'water'>
+    >>> msos.xtb_preopt
+    False
+    """
+    data = dict(msow)
+    del data["calculations"]
+    return MultiStageOptSettings.construct(**data)

stjames/workflows/scan.py

@@ -23,7 +23,7 @@ class ScanSettings(Base):
     num: int
 
     def vals(self) -> NDArray[np.float64]:
-        return np.linspace(self.start, self.stop, self.num)
+        return np.linspace(self.start, self.stop, self.num)  # type: ignore [return-value, unused-ignore]
 
     class Config:
         from_attributes = True

{stjames-0.0.46.dist-info → stjames-0.0.47.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.46
+Version: 0.0.47
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.46.dist-info → stjames-0.0.47.dist-info}/RECORD

@@ -1,7 +1,7 @@
 stjames/__init__.py,sha256=LkWCylP4VeXyQL0iu5w6yeYK1UHjcUH55hwWXTy4mQQ,576
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
 stjames/atom.py,sha256=w7q-x9xpBw4sJ1WGrWt65WAaStxhz-m7dugXCYEOpq4,2064
-stjames/base.py,sha256=9PvUjBeVSkmA3TaruaB0uvjFMbWYTGKXECISNGAj_AU,1201
+stjames/base.py,sha256=hroQjvC8G88UiK520i1TDqnOlgw_ihmzevQGTO5yeUY,1215
 stjames/basis_set.py,sha256=wI3M2q9uPf9jhKpAi4E2DrsyKzloDGLRjAlk7krdYgc,949
 stjames/calculation.py,sha256=O2LwwQ_cOLmDOGXTHA9J71YbUZXigUSbvbLA-fSVm3w,915
 stjames/constraint.py,sha256=B6oV0rYjmAWr8gpi5f03gRy_uuqjUURVDVwoez5Cfbg,2442
@@ -10,7 +10,7 @@ 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=a6QQff-0YsutkOTuOcGrdDW76x9ZexiNLdKzzoE1Vcw,1698
+stjames/method.py,sha256=teV0nQZTu8gRSZdFpMhjHtvLPf-XeTIMy330rYWDeZ8,1855
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=v8NikFHfwOahXSo4VKGSqeHKI2HIoRdNjGE0GkZgNS4,10554
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
@@ -30,25 +30,26 @@ stjames/data/isotopes.json,sha256=5ba8QnLrHD_Ypv2xekv2cIRwYrX3MQ19-1FOFtt0RuU,83
 stjames/data/nist_isotopes.json,sha256=d5DNk1dX0iB1waEYIRR6JMHuA7AuYwSBEgBvb4EKyhM,14300
 stjames/data/read_nist_isotopes.py,sha256=y10FNjW43QpC45qib7VHsIghEwT7GG5rsNwHdc9osRI,3309
 stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWRQrg,1186
-stjames/workflows/__init__.py,sha256=IRcfBNaFWVMmixQHjPKcBJkcUYWRnXNwrx2MUFNiQKM,1843
+stjames/workflows/__init__.py,sha256=XQ89vfQxqz2cWmwcOMp_GKZFQ-RDm8B1s8PqAeQTK3g,1999
 stjames/workflows/admet.py,sha256=V8noO0Eb7h2bDFSnj6Pxv4ILm0lGxyVRCi13hE0zmEQ,149
 stjames/workflows/basic_calculation.py,sha256=q48bpab7ZqmRTR4PsGC6bWkuxqkVdJRM8gysevTYXP0,212
 stjames/workflows/bde.py,sha256=iNrBiAUJA-VaAB-eFddApUO2xIc5PyPYXNtC2stQ_OU,9667
 stjames/workflows/conformer.py,sha256=YYwL3l7OaVeea4N9-ihghwa_ieKY6hia9LNbiTraMb0,2732
-stjames/workflows/conformer_search.py,sha256=zmGaSuka0VClmX36AkKvJAN565-hyp2ZJQIjhkAMQRM,12924
+stjames/workflows/conformer_search.py,sha256=y64WpdVZcrUit9ub-yWwJ0zNK8ofPlcjOG4K6pV6UEM,14241
 stjames/workflows/descriptors.py,sha256=lRRCsGzad3nIg0wI1090ffaXB0FVh0nRRb2lNxCY0kI,281
-stjames/workflows/electronic_properties.py,sha256=DFrzU49rux13Fy5q7pgvuYNjiyC2KwMtqU6FTAxg9jo,3339
+stjames/workflows/electronic_properties.py,sha256=0PqS04CfLM4pzx67Ph3JJTrzc1LCwDTT5E8x4_wW-g8,3888
 stjames/workflows/fukui.py,sha256=CsJ3_gvzqEqcxwYN7bnNIa37F3KlLm7obsU77TGmDgo,348
-stjames/workflows/molecular_dynamics.py,sha256=wx633IhPjRwEYvfyuRnSb0c84lN2WtZJET2q-SJv5DY,2211
-stjames/workflows/multistage_opt.py,sha256=FXSm-adv9TIiE6ftWPO50Yq9ypoJ7GSPkJKpnC0r4kQ,12686
+stjames/workflows/hydrogen_bond_basicity.py,sha256=xn4AP_PbCUluzrj05ufw3LaN-xBMsAmt2mFsVy1bf-8,455
+stjames/workflows/molecular_dynamics.py,sha256=4HmYETU1VT2BA4-PqAayRZLjnj1WuYxd5bqpIyH9g5k,2465
+stjames/workflows/multistage_opt.py,sha256=0ou-UYMGIrewZIg3QZIgwS_eweYdsh2pRplxgRCqLcE,13572
 stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
 stjames/workflows/redox_potential.py,sha256=e7WOyTIC_1NPfh7amvW7YzqQezcswX9YaXT-qPiePAo,3651
-stjames/workflows/scan.py,sha256=Wqimw1nMErKOYHcC7U1hNC8LZb5XPtS-nE1a-c_6_88,814
+stjames/workflows/scan.py,sha256=cQ29DKlLCH7_6_1TFATnaM3ac9G1asUoRoDDlQYAfG0,860
 stjames/workflows/spin_states.py,sha256=TXHqB7ClTkkCy1Yfcsv99v2woAhT8oG1-uaF20-oMbQ,4592
 stjames/workflows/tautomer.py,sha256=owZOOfGlohxlaOG1pGpx7dVPvas8ZEnl_9Ms5F0Kpms,421
 stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
-stjames-0.0.46.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.46.dist-info/METADATA,sha256=sagkuDdeazTP1wvoGMsletsSSFzY_8Qjv0shhmcj17w,1627
-stjames-0.0.46.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-stjames-0.0.46.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.46.dist-info/RECORD,,
+stjames-0.0.47.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.47.dist-info/METADATA,sha256=jJX69FHFW3VDQtIwM7lR7tIZgM_CDeIvbC8qeERRhMU,1627
+stjames-0.0.47.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
+stjames-0.0.47.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.47.dist-info/RECORD,,

{stjames-0.0.46.dist-info → stjames-0.0.47.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.7.0)
 Root-Is-Purelib: true
 Tag: py3-none-any