mat3ra-esse 2024.4.8.post0__py3-none-any.whl → 2024.4.8.post2__py3-none-any.whl

mat3ra/esse/models/models_directory/mgga.py

@@ -0,0 +1,218 @@
+# generated by datamodel-codegen:
+#   filename:  models_directory/mgga.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class SlugifiedEntry(BaseModel):
+    name: str
+    """
+    descriptive human-readable name of entry
+    """
+    slug: str
+    """
+    machine-readable identifier
+    """
+
+
+class SlugifiedEntryOrSlug(Enum):
+    mgga = "mgga"
+
+
+class SlugifiedEntryOrSlug152(Enum):
+    ksdft = "ksdft"
+
+
+class SlugifiedEntryOrSlug153(Enum):
+    dft = "dft"
+
+
+class SlugifiedEntryOrSlug154(Enum):
+    qm = "qm"
+
+
+class SlugifiedEntryOrSlug155(Enum):
+    pb = "pb"
+
+
+class DFTMetaGGAFunctionalCategorySchema(BaseModel):
+    subtype: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    type: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug152]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier3: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug153]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier2: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug154]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier1: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug155]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+
+
+class Functional(Enum):
+    scan = "scan"
+
+
+class SpinOrbitCouplingMixin(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    functional: Optional[Functional] = None
+    spinOrbitCoupling: Optional[bool] = None
+
+
+class DispersionCorrection(Enum):
+    dft_d2 = "dft-d2"
+    dft_d3 = "dft-d3"
+    xdm = "xdm"
+    ts = "ts"
+
+
+class DispersionCorrectionMixin(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    functional: Optional[Functional] = None
+    dispersionCorrection: Optional[DispersionCorrection] = None
+
+
+class SpinPolarization(Enum):
+    collinear = "collinear"
+    non_collinear = "non-collinear"
+
+
+class SpinPolarizationMixin(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    functional: Optional[Functional] = None
+    spinPolarization: Optional[SpinPolarization] = None
+
+
+class HubbardType(Enum):
+    u = "u"
+
+
+class HubbardModelMixin(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    functional: Optional[Functional] = None
+    hubbardType: Optional[HubbardType] = None
+
+
+class Type(Enum):
+    literature = "literature"
+
+
+class PagesSchema(BaseModel):
+    start: str
+    end: Optional[str] = None
+
+
+class ExperimentAuthorSchema(BaseModel):
+    first: str
+    middle: Optional[str] = None
+    last: str
+    affiliation: Optional[str] = None
+
+
+class LiteratureReferenceSchema(BaseModel):
+    type: Optional[Type] = None
+    doi: Optional[str] = None
+    """
+    Digital Object Identifier of the reference.
+    """
+    isbn: Optional[str] = None
+    """
+    International Standard Book Number of the reference.
+    """
+    issn: Optional[str] = None
+    """
+    International Standard Serial Number of the reference.
+    """
+    url: Optional[str] = None
+    """
+    Internet address of the reference.
+    """
+    title: Optional[str] = None
+    """
+    Title of the work.
+    """
+    publisher: Optional[str] = None
+    """
+    Publisher of the work.
+    """
+    journal: Optional[str] = None
+    """
+    Journal in which the work appeared.
+    """
+    volume: Optional[str] = None
+    """
+    Volume of the series in which the work appeared.
+    """
+    year: Optional[str] = None
+    """
+    Year in which the reference was published.
+    """
+    issue: Optional[str] = None
+    """
+    Issue of the collection in which the work appeared.
+    """
+    pages: Optional[PagesSchema] = Field(None, title="pages schema")
+    """
+    Start and end pages of the work.
+    """
+    authors: Optional[List[ExperimentAuthorSchema]] = None
+    """
+    List of authors of the work.
+    """
+    editors: Optional[List[ExperimentAuthorSchema]] = None
+    """
+    List of editors of the work.
+    """
+    reference: Optional[List[Dict[str, Any]]] = None
+    """
+    References cited by the work. Reference objects can nest as deeply as needed. This is useful, for example, when tracking the history of a value referenced in a scholarly article; the top level reference would contain information about where the data was accessed while the nested reference would contain information about where it was originally published.
+    """
+
+
+class ModelMetaGeneralizedGradientApproximation(BaseModel):
+    categories: DFTMetaGGAFunctionalCategorySchema = Field(..., title="DFT meta-GGA functional category schema")
+    """
+    Used to categorize entities such as models and methods
+    """
+    parameters: Union[SpinOrbitCouplingMixin, DispersionCorrectionMixin, SpinPolarizationMixin, HubbardModelMixin] = (
+        Field(..., title="Meta-GGA functional mixin")
+    )
+    """
+    Model parameters defined in-place or via model mixins
+    """
+    reference: Optional[LiteratureReferenceSchema] = Field(None, title="literature reference schema")
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """

mat3ra/esse/models/models_directory/re.py

@@ -0,0 +1,160 @@
+# generated by datamodel-codegen:
+#   filename:  models_directory/re.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, Field
+
+
+class SlugifiedEntry(BaseModel):
+    name: str
+    """
+    descriptive human-readable name of entry
+    """
+    slug: str
+    """
+    machine-readable identifier
+    """
+
+
+class SlugifiedEntryOrSlug(Enum):
+    re = "re"
+
+
+class SlugifiedEntryOrSlug230(Enum):
+    ml = "ml"
+
+
+class SlugifiedEntryOrSlug231(Enum):
+    det = "det"
+
+
+class SlugifiedEntryOrSlug232(Enum):
+    st = "st"
+
+
+class RegressionModelCategorySchema(BaseModel):
+    type: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier3: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug230]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier2: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug231]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier1: Optional[Union[SlugifiedEntry, SlugifiedEntryOrSlug232]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    subtype: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+
+
+class Type(Enum):
+    literature = "literature"
+
+
+class PagesSchema(BaseModel):
+    start: str
+    end: Optional[str] = None
+
+
+class ExperimentAuthorSchema(BaseModel):
+    first: str
+    middle: Optional[str] = None
+    last: str
+    affiliation: Optional[str] = None
+
+
+class LiteratureReferenceSchema(BaseModel):
+    type: Optional[Type] = None
+    doi: Optional[str] = None
+    """
+    Digital Object Identifier of the reference.
+    """
+    isbn: Optional[str] = None
+    """
+    International Standard Book Number of the reference.
+    """
+    issn: Optional[str] = None
+    """
+    International Standard Serial Number of the reference.
+    """
+    url: Optional[str] = None
+    """
+    Internet address of the reference.
+    """
+    title: Optional[str] = None
+    """
+    Title of the work.
+    """
+    publisher: Optional[str] = None
+    """
+    Publisher of the work.
+    """
+    journal: Optional[str] = None
+    """
+    Journal in which the work appeared.
+    """
+    volume: Optional[str] = None
+    """
+    Volume of the series in which the work appeared.
+    """
+    year: Optional[str] = None
+    """
+    Year in which the reference was published.
+    """
+    issue: Optional[str] = None
+    """
+    Issue of the collection in which the work appeared.
+    """
+    pages: Optional[PagesSchema] = Field(None, title="pages schema")
+    """
+    Start and end pages of the work.
+    """
+    authors: Optional[List[ExperimentAuthorSchema]] = None
+    """
+    List of authors of the work.
+    """
+    editors: Optional[List[ExperimentAuthorSchema]] = None
+    """
+    List of editors of the work.
+    """
+    reference: Optional[List[Dict[str, Any]]] = None
+    """
+    References cited by the work. Reference objects can nest as deeply as needed. This is useful, for example, when tracking the history of a value referenced in a scholarly article; the top level reference would contain information about where the data was accessed while the nested reference would contain information about where it was originally published.
+    """
+
+
+class ModelRegression(BaseModel):
+    categories: RegressionModelCategorySchema = Field(..., title="regression model category schema")
+    """
+    Used to categorize entities such as models and methods
+    """
+    parameters: Dict[str, Any]
+    """
+    Model parameters defined in-place or via model mixins
+    """
+    reference: Optional[LiteratureReferenceSchema] = Field(None, title="literature reference schema")
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """

mat3ra/esse/models/project.py

@@ -0,0 +1,82 @@
+# generated by datamodel-codegen:
+#   filename:  project.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional
+
+from pydantic import BaseModel, Field
+
+
+class ClusterBasedChargeRate(BaseModel):
+    rate: Optional[float] = None
+    timestamp: Optional[float] = None
+    hostname: Optional[str] = None
+
+
+class Name(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    name: Name
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class ProjectSchema(BaseModel):
+    gid: Optional[float] = None
+    """
+    project GID
+    """
+    clusterBasedChargeRates: Optional[List[ClusterBasedChargeRate]] = None
+    """
+    charge rates info for project
+    """
+    isExternal: Optional[bool] = False
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """
+    metadata: Optional[Dict[str, Any]] = None

mat3ra/esse/models/properties_directory/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra/esse/models/properties_directory/derived_properties.py

@@ -0,0 +1,140 @@
+# generated by datamodel-codegen:
+#   filename:  properties_directory/derived_properties.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import List, Optional, Union
+
+from pydantic import BaseModel, Field, RootModel, confloat
+from typing_extensions import Literal
+
+
+class Name(Enum):
+    volume = "volume"
+
+
+class Units(Enum):
+    angstrom_3 = "angstrom^3"
+
+
+class VolumeSchema(BaseModel):
+    name: Literal["0#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units] = None
+    value: float
+
+
+class Name29(Enum):
+    density = "density"
+
+
+class Units14(Enum):
+    g_cm_3 = "g/cm^3"
+
+
+class DensitySchema(BaseModel):
+    name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units14] = None
+    value: float
+
+
+class Units15(Enum):
+    angstrom = "angstrom"
+
+
+class ScalarSchema(BaseModel):
+    units: Optional[Units15] = None
+    value: float
+
+
+class Name30(Enum):
+    symmetry = "symmetry"
+
+
+class SymmetrySchema(BaseModel):
+    pointGroupSymbol: Optional[str] = None
+    """
+    point group symbol in Schoenflies notation
+    """
+    spaceGroupSymbol: Optional[str] = None
+    """
+    space group symbol in Hermann–Mauguin notation
+    """
+    tolerance: Optional[ScalarSchema] = Field(None, title="scalar schema")
+    """
+    tolerance used for symmetry calculation
+    """
+    name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
+
+
+class Name31(Enum):
+    elemental_ratio = "elemental_ratio"
+
+
+class ElementalRatio(BaseModel):
+    name: Literal["3#-datamodel-code-generator-#-object-#-special-#"]
+    value: confloat(ge=0.0, le=1.0)
+    element: Optional[str] = None
+    """
+    the element this ratio is for
+    """
+
+
+class Name32(Enum):
+    p_norm = "p-norm"
+
+
+class PNorm(BaseModel):
+    name: Literal["4#-datamodel-code-generator-#-object-#-special-#"]
+    degree: Optional[int] = None
+    """
+    degree of the dimensionality of the norm
+    """
+    value: float
+
+
+class Name33(Enum):
+    inchi = "inchi"
+
+
+class InChIRepresentationSchema(BaseModel):
+    name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class Name34(Enum):
+    inchi_key = "inchi_key"
+
+
+class InChIKeyRepresentationSchema(BaseModel):
+    name: Literal["6#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class DerivedPropertiesSchema1(
+    RootModel[
+        Union[
+            VolumeSchema,
+            DensitySchema,
+            SymmetrySchema,
+            ElementalRatio,
+            PNorm,
+            InChIRepresentationSchema,
+            InChIKeyRepresentationSchema,
+        ]
+    ]
+):
+    root: Union[
+        VolumeSchema,
+        DensitySchema,
+        SymmetrySchema,
+        ElementalRatio,
+        PNorm,
+        InChIRepresentationSchema,
+        InChIKeyRepresentationSchema,
+    ] = Field(..., discriminator="name")
+
+
+class DerivedPropertiesSchema(RootModel[List[DerivedPropertiesSchema1]]):
+    root: List[DerivedPropertiesSchema1] = Field(..., title="derived properties schema")

mat3ra/esse/models/properties_directory/electronic_configuration.py

@@ -0,0 +1,20 @@
+# generated by datamodel-codegen:
+#   filename:  properties_directory/electronic_configuration.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Optional
+
+from pydantic import BaseModel
+
+
+class ElectronicConfigurationSchema(BaseModel):
+    charge: Optional[int] = None
+    """
+    total charge of the molecular system
+    """
+    multiplicity: Optional[int] = None
+    """
+    calculated as 2S+1, with S is the total spin angular momentum
+    """

mat3ra/esse/models/properties_directory/elemental/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra/esse/models/properties_directory/elemental/atomic_radius.py

@@ -0,0 +1,34 @@
+# generated by datamodel-codegen:
+#   filename:  properties_directory/elemental/atomic_radius.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel
+
+
+class Name(Enum):
+    atomic_radius = "atomic_radius"
+
+
+class Units(Enum):
+    km = "km"
+    m = "m"
+    pm = "pm"
+    nm = "nm"
+    angstrom = "angstrom"
+    a_u_ = "a.u."
+    bohr = "bohr"
+    fractional = "fractional"
+    crystal = "crystal"
+    cartesian = "cartesian"
+    alat = "alat"
+
+
+class AtomicRadius(BaseModel):
+    name: Optional[Name] = None
+    units: Optional[Units] = None
+    value: float

mat3ra/esse/models/properties_directory/elemental/electronegativity.py

@@ -0,0 +1,19 @@
+# generated by datamodel-codegen:
+#   filename:  properties_directory/elemental/electronegativity.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel
+
+
+class Name(Enum):
+    electronegativity = "electronegativity"
+
+
+class Electronegativity(BaseModel):
+    name: Optional[Name] = None
+    value: float