snapred.backend.dao.state.CalibrantSample package

Submodules

snapred.backend.dao.state.CalibrantSample.Atom module

class snapred.backend.dao.state.CalibrantSample.Atom.Atom(*args: Annotated[str, Strict(strict=True)], symbol: str, coordinates: Tuple[float, float, float], siteOccupationFactor: float, adp: float = 0.1)

Bases: BaseModel

Class containing atomic paramaters used in Calibrant Samples atomic parameters:

symbol: string of chemical symbol coordinates:

x coordinate: float in range [-1, 1] y coordinate: float in range [-1, 1] z coordinate: float in range [-1, 1]

site occupation factor: float in range [0, 1] adp: positive float, default is 0.01

adp: float
coordinates: Tuple[float, float, float]
property getString: str
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

siteOccupationFactor: float
symbol: str
classmethod validate_adp(v)
classmethod validate_atom_coordinates(v)
classmethod validate_site_occupation_factor(v)

snapred.backend.dao.state.CalibrantSample.CalibrantSample module

class snapred.backend.dao.state.CalibrantSample.CalibrantSample.CalibrantSample(*, name: str, unique_id: str, date: float = <factory>, geometry: ~snapred.backend.dao.state.CalibrantSample.Geometry.Geometry, material: ~snapred.backend.dao.state.CalibrantSample.Material.Material, crystallography: ~snapred.backend.dao.state.CalibrantSample.Crystallography.Crystallography | None = None, peakIntensityFractionThreshold: float | None = <factory>, overrides: ~typing.Dict[str, ~typing.Any] | None = None)

Bases: BaseModel

Class containing all information used for a Calibrant Sample

crystallography: Crystallography | None
date: float
geometry: Geometry
material: Material
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str
overrides: Dict[str, Any] | None
peakIntensityFractionThreshold: float | None
classmethod serialize_date(v: float) → str
unique_id: str
classmethod validate_date(v)
classmethod validate_threshold(v) → float

snapred.backend.dao.state.CalibrantSample.Crystallography module

class snapred.backend.dao.state.CalibrantSample.Crystallography.Crystallography(*args: str | MockCrystalStructure, cifFile: str, spaceGroup: str, latticeParameters: Tuple[float, float, float, float, float, float], atoms: List[Atom])

Bases: BaseModel

Class containing Crystallography paramaters used in Calibrant Samples cif file: string, full path to .cif file containing crystallographic properties space group: string, ITOC symbol for the space group lattice parameters: Tuple of 6 floats: a, b, c, alpha, beta, gamma atoms: list of atomic parameters for each atom

atoms: List[Atom]
classmethod calibrationSampleHome() → Path
cifFile: str
latticeParameters: Tuple[float, float, float, float, float, float]
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

property scattererString: str
spaceGroup: str
property spaceGroupString: str
property unitCellString: str
classmethod validate_cifFile(v)
classmethod validate_spaceGroup(v)

snapred.backend.dao.state.CalibrantSample.Geometry module

class snapred.backend.dao.state.CalibrantSample.Geometry.Geometry(*, shape: str, radius: float, height: float | None = None, center: Tuple[float, float, float] = (0, 0, 0), axis: Tuple[float, float, float] = (0, 1, 0))

Bases: BaseModel

Class to hold Geometry data for Calibrant Samples shape: string must be ‘Cylinder’ or ‘Sphere’ radius: single float (cm) height: single float (cm) (not used for sphere) center: list of three floats (cm)

axis: Tuple[float, float, float]
center: Tuple[float, float, float]
dict(**kwargs) → Dict[str, Any]
height: float | None
json(**kwargs) → str
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

radius: float
shape: str
classmethod validate_form(v: Any)

snapred.backend.dao.state.CalibrantSample.Material module

class snapred.backend.dao.state.CalibrantSample.Material.Material(*, packingFraction: float | None = None, massDensity: float | None = None, chemicalFormula: str)

Bases: BaseModel

Class to hold Material information relevant to Calibrant Samples packingFraction: float, [0.0, 1.0] massDensity: float (g/cm^3) chemicalFormula: string following mantid

chemicalFormula: str
dict(**kwargs) → Dict[str, Any]
json(**kwargs) → str
massDensity: float | None
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

packingFraction: float | None
classmethod validate_correctPropertiesToFindDensity(v: Any)
classmethod validate_massDensity(v)
classmethod validate_packingFraction(v)

Module contents