@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/helpers.py

@@ -1,151 +0,0 @@
-from collections import Counter
-from typing import List, Dict
-
-from mat3ra.esse.models.materials_category_components.entities.core.zero_dimensional.atom import AtomSchema
-
-from .analyzers import (
-    SurfacePassivationMaterialAnalyzer,
-    CoordinationBasedPassivationMaterialAnalyzer,
-)
-from .builder import PassivationBuilder
-from .configuration import PassivationConfiguration
-from .... import MaterialWithBuildMetadata
-from .....analyze.material import MaterialWithCrystalSites
-from .....build_components.entities.core.zero_dimensional.atom.configuration import AtomAtCoordinateConfiguration
-from mat3ra.made.tools.build.processed_structures.two_dimensional.passivation.enums import SurfaceTypesEnum
-
-
-def passivate_surface(
-    material: MaterialWithBuildMetadata,
-    passivant: str = "H",
-    bond_length: float = 1.0,
-    shadowing_radius: float = 2.5,
-    depth: float = 5.0,
-    surface: SurfaceTypesEnum = SurfaceTypesEnum.TOP,
-) -> MaterialWithBuildMetadata:
-    """
-    Create a passivated material by adding passivant atoms to the surface of the provided material.
-
-    Args:
-        material (Material): The material to be passivated. Should have vacuum space above or below the surface.
-        passivant (str): The chemical symbol of the passivating atom (default is 'H').
-        bond_length (float): The bond length for the passivation (default is 1.0). Å
-        shadowing_radius (float): The radius with which an atom shadows/covers underlying atom from being exposed. Å
-        depth (float): The depth from the most top (or bottom) atom into the slab to search for exposed atoms. Å
-        surface (SurfaceTypesEnum): The surface to passivate (TOP, BOTTOM, or BOTH).
-    Returns:
-        Material: The passivated material.
-    """
-    analyzer = SurfacePassivationMaterialAnalyzer(
-        material=material,
-        passivant=passivant,
-        bond_length=bond_length,
-        shadowing_radius=shadowing_radius,
-        depth=depth,
-        surface=surface,
-    )
-
-    passivant_coordinates = analyzer.passivant_coordinates
-    passivant_configs = [
-        AtomAtCoordinateConfiguration(
-            crystal=material, element=AtomSchema(chemical_element=passivant), coordinate=coord
-        )
-        for coord in passivant_coordinates
-    ]
-    config = PassivationConfiguration(
-        merge_components=[material, *passivant_configs], passivant=passivant, bond_length=bond_length
-    )
-
-    builder = PassivationBuilder()
-    return builder.get_material(config)
-
-
-def passivate_dangling_bonds(
-    material: MaterialWithBuildMetadata,
-    passivant: str = "H",
-    bond_length: float = 1.0,
-    coordination_threshold: int = 3,
-    number_of_bonds_to_passivate: int = 1,
-    symmetry_tolerance: float = 0.1,
-    shadowing_radius: float = 2.5,
-    depth: float = 5.0,
-) -> MaterialWithBuildMetadata:
-    """
-    Create a passivated material by adding passivant atoms to the undercoordinated atoms of the provided material.
-
-    Args:
-        material (MaterialWithBuildMetadata): The material to be passivated.
-        passivant (str): The chemical symbol of the passivating atom (default is 'H').
-        bond_length (float): The bond length for the passivation (default is 1.0). Å
-        coordination_threshold (int): The coordination number threshold for an atom to be considered undercoordinated.
-        number_of_bonds_to_passivate (int): The maximum number of bonds to passivate for each undercoordinated atom.
-        symmetry_tolerance (float): The tolerance for symmetry comparison of vectors for bonds.
-        shadowing_radius (float): The radius with which an atom shadows/covers underlying atom from being exposed. Å
-        depth (float): The depth from the most top (or bottom) atom into the slab to search for exposed atoms. Å
-
-    Returns:
-        MaterialWithBuildMetadata: The passivated material with dangling bonds filled.
-    """
-    analyzer = CoordinationBasedPassivationMaterialAnalyzer(
-        material=material,
-        passivant=passivant,
-        bond_length=bond_length,
-        coordination_threshold=coordination_threshold,
-        number_of_bonds_to_passivate=number_of_bonds_to_passivate,
-        symmetry_tolerance=symmetry_tolerance,
-        shadowing_radius=shadowing_radius,
-        depth=depth,
-    )
-
-    passivant_coordinates = analyzer.passivant_coordinates
-    passivant_configs = [
-        AtomAtCoordinateConfiguration(
-            crystal=material, element=AtomSchema(chemical_element=passivant), coordinate=coord
-        )
-        for coord in passivant_coordinates
-    ]
-    config = PassivationConfiguration(
-        merge_components=[material, *passivant_configs], passivant=passivant, bond_length=bond_length
-    )
-
-    builder = PassivationBuilder()
-    return builder.get_material(config)
-
-
-def get_unique_coordination_numbers(
-    material: MaterialWithBuildMetadata,
-    cutoff: float = 3.0,
-) -> List[int]:
-    """
-    Get the unique coordination numbers for the provided passivation configuration and cutoff radius.
-
-    Args:
-        material (MaterialWithBuildMetadata): The material object.
-        cutoff (float): The cutoff radius for defining neighbors.
-    Returns:
-        set: The unique coordination numbers.
-    """
-    material_with_crystal_sites = MaterialWithCrystalSites.from_material(material)
-    material_with_crystal_sites.analyze()
-    return material_with_crystal_sites.get_unique_coordination_numbers(cutoff=cutoff)
-
-
-def get_coordination_numbers_distribution(
-    material: MaterialWithBuildMetadata,
-    cutoff: float = 3.0,
-) -> Dict[int, int]:
-    """
-    Get the unique coordination numbers for the provided passivation configuration and cutoff radius.
-
-    Args:
-        material (MaterialWithBuildMetadata): The material object.
-        cutoff (float): The cutoff radius for defining neighbors.
-    Returns:
-        set: The unique coordination numbers.
-    """
-    material_with_crystal_sites = MaterialWithCrystalSites.from_material(material)
-    material_with_crystal_sites.analyze()
-    coordinatation_numbers = material_with_crystal_sites.get_coordination_numbers(cutoff=cutoff)
-    sorted_coordinatation_numbers = sorted(coordinatation_numbers.values)
-    distribution = dict(Counter(sorted_coordinatation_numbers))
-    return distribution

package/src/py/mat3ra/made/tools/build_components/__init__.py

@@ -1,10 +0,0 @@
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import (
-    BaseBuilderParameters,
-    BaseConfigurationPydantic,
-    BaseConfigurationPydanticChild,
-    BaseSingleBuilder,
-    TypeBuildParameters,
-    TypeConfiguration,
-)
-
-from .metadata import BuildMetadata, MaterialBuildMetadata, MaterialWithBuildMetadata

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/two_dimensional/miller_indices.py

@@ -1,18 +0,0 @@
-from typing import Tuple
-
-from mat3ra.code.entity import InMemoryEntityPydantic
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.miller_indices import (
-    MillerIndicesSchema,
-)
-
-
-class MillerIndices(MillerIndicesSchema, InMemoryEntityPydantic):
-    def to_tuple(self) -> Tuple[int, int, int]:
-        return (self.root[0], self.root[1], self.root[2])
-
-    @staticmethod
-    def format_index(index: int) -> str:
-        return f"{index}" + chr(0x0302) if index < 0 else f"{index}"
-
-    def __str__(self) -> str:
-        return f"({''.join([self.format_index(i) for i in self.root])})"

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/two_dimensional/termination.py

@@ -1,33 +0,0 @@
-from mat3ra.code.entity import InMemoryEntityPydantic
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.termination import (
-    TerminationSchema,
-)
-
-
-class Termination(TerminationSchema, InMemoryEntityPydantic):
-    def __str__(self):
-        return f"{self.chemical_elements}_{self.space_group_symmetry_label}"
-
-    def __repr__(self):
-        return self.__str__()
-
-    def __init__(self, chemical_elements: str, space_group_symmetry_label: str):
-        super().__init__(chemical_elements=chemical_elements, space_group_symmetry_label=space_group_symmetry_label)
-
-    def __eq__(self, other):
-        if not isinstance(other, Termination):
-            return NotImplemented
-        return (
-            self.chemical_elements == other.chemical_elements
-            and self.space_group_symmetry_label == other.space_group_symmetry_label
-        )
-
-    @property
-    def formula(self):
-        return self.chemical_elements
-
-    @classmethod
-    def from_string(cls, termination: str):
-        chemical_elements = termination.split("_")[0]
-        space_group_symmetry_label = "_".join(termination.split("_")[1:])
-        return cls(chemical_elements=chemical_elements, space_group_symmetry_label=space_group_symmetry_label)

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/__init__.py

@@ -1,2 +0,0 @@
-from .crystal_site import CrystalSite
-from .crystal_site_list import CrystalSiteList

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/crystal_site.py

@@ -1,24 +0,0 @@
-from typing import List, Optional
-
-import numpy as np
-from mat3ra.code.entity import InMemoryEntityPydantic
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.zero_dimensional.crystal_site import (
-    CrystalSiteSchema,
-)
-from mat3ra.made.material import Material
-from pydantic import Field
-
-
-class CrystalSite(CrystalSiteSchema, InMemoryEntityPydantic):
-    crystal: Optional[Material] = Field(None, exclude=True)
-    # element: str
-    coordinate: Optional[List[float]] = None
-    nearest_neighbor_vectors: List[np.ndarray] = Field([], exclude=True)
-    # coordination_number: int = 0
-    # see https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list for an example
-
-    wyckoff_letter: Optional[str] = None
-
-    @property
-    def coordination_number(self):
-        return len(self.nearest_neighbor_vectors)

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/crystal_site_list.py

@@ -1,9 +0,0 @@
-from typing import List
-
-from mat3ra.code.array_with_ids import ArrayWithIds
-
-from .crystal_site import CrystalSite
-
-
-class CrystalSiteList(ArrayWithIds):
-    values: List[CrystalSite]

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/builder.py

@@ -1,32 +0,0 @@
-from mat3ra.code.array_with_ids import ArrayWithIds
-from mat3ra.made.basis import Basis, Coordinates
-
-from ......build_components import MaterialWithBuildMetadata
-from ..... import BaseSingleBuilder
-from .configuration import PointDefectSiteConfiguration
-
-
-class PointDefectSiteBuilder(BaseSingleBuilder):
-    """
-    Builder class for creating a material from a PointDefectSite configuration.
-    """
-
-    _ConfigurationType = PointDefectSiteConfiguration
-
-    def _generate(self, configuration: PointDefectSiteConfiguration) -> MaterialWithBuildMetadata:
-        if configuration.crystal is None:
-            raise ValueError("Crystal configuration is required for PointDefectSiteBuilder")
-
-        crystal = configuration.crystal
-        basis = Basis(
-            elements=ArrayWithIds(values=[], ids=[]),
-            coordinates=Coordinates(values=[], ids=[]),
-            units=crystal.basis.units,
-            cell=crystal.basis.cell,
-        )
-        basis.add_atom(
-            element=configuration.element.chemical_element,
-            coordinate=configuration.coordinate,
-            label=configuration.host_atom_label,
-        )
-        return MaterialWithBuildMetadata(name=crystal.name, lattice=crystal.lattice, basis=basis)

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/configuration.py

@@ -1,14 +0,0 @@
-from typing import Optional, Union
-
-from mat3ra.esse.models.materials_category.defective_structures.two_dimensional.adatom.configuration import (
-    PointDefectSiteSchema,
-)
-from mat3ra.esse.models.materials_category_components.entities.core.zero_dimensional.atom import AtomSchema
-from mat3ra.esse.models.materials_category_components.entities.core.zero_dimensional.vacancy import VacancySchema
-
-from ..crystal_site import CrystalSite
-
-
-class PointDefectSiteConfiguration(CrystalSite, PointDefectSiteSchema):
-    element: Union[VacancySchema, AtomSchema]
-    host_atom_label: Optional[Union[int, str]] = None

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/void_region/builder.py

@@ -1,29 +0,0 @@
-from typing import Type
-
-from ......build_components import MaterialWithBuildMetadata
-from ......modify import filter_by_condition_on_coordinates
-from ..point_defect_site.builder import PointDefectSiteBuilder
-from ..void_region.configuration import VoidRegionConfiguration
-
-
-class VoidRegionBuilder(PointDefectSiteBuilder):
-    """
-    Builder class for creating a material with a void region based on a coordinate condition.
-    Uses "Vac" as the element for all atoms that fall outside the specified coordinate condition
-        and those positions will void elements in target crystal when merging.
-    """
-
-    _ConfigurationType: Type[VoidRegionConfiguration] = VoidRegionConfiguration
-
-    def _generate(self, configuration: VoidRegionConfiguration) -> MaterialWithBuildMetadata:
-        filtered_material = filter_by_condition_on_coordinates(
-            configuration.crystal,
-            configuration.coordinate_condition.condition,
-            use_cartesian_coordinates=configuration.use_cartesian_coordinates,
-            invert_selection=not configuration.invert_selection,
-        )
-
-        # Replace all elements with "Vac"
-        filtered_material.basis.elements.values = ["Vac"] * len(filtered_material.basis.elements.values)
-
-        return filtered_material

package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/void_region/configuration.py

@@ -1,19 +0,0 @@
-from typing import Union
-
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.zero_dimensional.void_region import (
-    VoidRegionSchema,
-)
-
-from ......entities.coordinate import BoxCoordinateCondition, CoordinateCondition, SphereCoordinateCondition
-from ..... import MaterialWithBuildMetadata
-
-
-class VoidRegionConfiguration(VoidRegionSchema):
-    crystal: MaterialWithBuildMetadata
-    coordinate_condition: Union[SphereCoordinateCondition, BoxCoordinateCondition, CoordinateCondition]
-    use_cartesian_coordinates: bool = False
-    invert_selection: bool = False
-
-    @property
-    def condition_name(self):
-        return self.coordinate_condition.__class__.__name__.replace("CoordinateCondition", "")

package/src/py/mat3ra/made/tools/build_components/entities/core/two_dimensional/vacuum/builder.py

@@ -1,48 +0,0 @@
-from typing import Any, Optional, Type
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.made.utils import AXIS_TO_INDEX_MAP
-
-from ..... import MaterialWithBuildMetadata
-from ....reusable.base_builder import BaseSingleBuilder, TypeConfiguration
-from .configuration import VacuumConfiguration
-
-
-class VacuumBuilder(BaseSingleBuilder):
-    _ConfigurationType: Type[VacuumConfiguration] = VacuumConfiguration
-
-    def get_material(
-        self,
-        configuration: TypeConfiguration,
-        post_process_parameters: Optional[Any] = None,
-    ) -> Optional[MaterialWithBuildMetadata]:
-        if configuration.size == 0.0:
-            return None
-        return super().get_material(configuration, post_process_parameters)
-
-    def _generate(self, configuration: TypeConfiguration) -> MaterialWithBuildMetadata:
-        reference = configuration.crystal
-        if reference is None:
-            raise ValueError("VacuumConfiguration.crystal must be provided to build a vacuum material.")
-        size = configuration.size
-        direction: AxisEnum = configuration.direction
-
-        lattice_vectors = reference.lattice.vector_arrays.copy()
-
-        # Replace the target direction with the vacuum vector
-        axis = AXIS_TO_INDEX_MAP[direction.value]
-        vacuum_vector = [0.0, 0.0, 0.0]
-        vacuum_vector[axis] = size
-        lattice_vectors[axis] = vacuum_vector
-
-        vacuum_lattice = reference.lattice.from_vectors_array(
-            lattice_vectors, reference.lattice.units, reference.lattice.type
-        )
-
-        return MaterialWithBuildMetadata.create(
-            {
-                "name": "Vacuum",
-                "lattice": vacuum_lattice.to_dict(),
-                "basis": {"elements": [], "coordinates": []},
-            }
-        )

package/src/py/mat3ra/made/tools/build_components/entities/core/two_dimensional/vacuum/configuration.py

@@ -1,17 +0,0 @@
-from typing import Optional, Union
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.esse.models.materials_category_components.entities.core.two_dimensional.vacuum import (
-    VacuumConfigurationSchema,
-)
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseConfigurationPydantic
-
-from ..... import MaterialWithBuildMetadata
-
-
-class VacuumConfiguration(VacuumConfigurationSchema, BaseConfigurationPydantic):
-    type: str = "VacuumConfiguration"
-    size: float = VacuumConfigurationSchema.model_fields["size"].default
-    crystal: Union[Material, MaterialWithBuildMetadata, None] = None
-    direction: Optional[AxisEnum] = AxisEnum.z

package/src/py/mat3ra/made/tools/build_components/entities/core/zero_dimensional/atom/builder.py

@@ -1,25 +0,0 @@
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-
-from ..... import MaterialWithBuildMetadata
-from ...two_dimensional.vacuum.builder import VacuumBuilder
-from ...two_dimensional.vacuum.configuration import VacuumConfiguration
-from .configuration import AtomAtCoordinateConfiguration
-
-
-class AtomAtCoordinateBuilder(VacuumBuilder):
-    _ConfigurationType = AtomAtCoordinateConfiguration
-
-    def _generate(self, configuration: AtomAtCoordinateConfiguration) -> MaterialWithBuildMetadata:
-        if not configuration.crystal:
-            raise ValueError("Crystal must be provided for AtomAtCoordinateConfiguration")
-        vacuum_configuration = VacuumConfiguration(
-            crystal=configuration.crystal,
-            size=configuration.crystal.lattice.c,
-            direction=AxisEnum.z,
-        )
-        new_material = super()._generate(vacuum_configuration)
-        new_material.basis.add_atom(
-            element=configuration.element.chemical_element.value,
-            coordinate=configuration.coordinate,
-        )
-        return new_material

package/src/py/mat3ra/made/tools/build_components/entities/core/zero_dimensional/atom/configuration.py

@@ -1,8 +0,0 @@
-from mat3ra.esse.models.materials_category_components.entities.core.zero_dimensional.atom import AtomSchema
-
-from ....auxiliary.zero_dimensional.point_defect_site.configuration import PointDefectSiteConfiguration
-from ...two_dimensional.vacuum.configuration import VacuumConfiguration
-
-
-class AtomAtCoordinateConfiguration(VacuumConfiguration, PointDefectSiteConfiguration):
-    element: AtomSchema

package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/__init__.py

@@ -1,16 +0,0 @@
-from typing import TypeVar
-
-from .base_configuration_pydantic import BaseConfigurationPydantic
-from .base_single_builder import BaseSingleBuilder, TypeBuildParameters, TypeConfiguration
-from .build_parameters import BaseBuilderParameters
-
-BaseConfigurationPydanticChild = TypeVar("BaseConfigurationPydanticChild", bound="BaseConfigurationPydantic")
-
-__all__ = [
-    "BaseConfigurationPydantic",
-    "BaseBuilderParameters",
-    "BaseSingleBuilder",
-    "TypeConfiguration",
-    "TypeBuildParameters",
-    "BaseConfigurationPydanticChild",
-]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/base_configuration_pydantic.py

@@ -1,5 +0,0 @@
-from mat3ra.code.entity import InMemoryEntityPydantic
-
-
-class BaseConfigurationPydantic(InMemoryEntityPydantic):
-    pass

package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/base_single_builder.py

@@ -1,87 +0,0 @@
-from typing import Any, Generic, Optional, Type, TypeVar
-
-from mat3ra.made.tools.build_components.metadata import MaterialWithBuildMetadata
-from pydantic import BaseModel
-
-from .base_configuration_pydantic import BaseConfigurationPydantic
-from .build_parameters import BaseBuilderParameters
-
-TypeConfiguration = TypeVar("TypeConfiguration", bound=BaseConfigurationPydantic)
-TypeBuildParameters = TypeVar("TypeBuildParameters", bound=BaseBuilderParameters)
-
-
-class BaseSingleBuilder(BaseModel, Generic[TypeConfiguration, TypeBuildParameters]):
-    """
-    Base class for material builders.
-    This class provides an interface for generating materials and getter functions.
-    The builder is meant as a description of the process, while its functions require a
-    "Configuration" class instance to perform the generation.
-
-    The class is designed to be subclassed and the subclass should implement the following methods:
-
-    - `_generate`: Generate the material items, possibly using third-party tools/implementation for items.
-    - `_sort`: Sort the items.
-    - `_select`: Select a subset of the items.
-    - `_post_process`: Post-process the items to convert them to materials (Material class).
-    - `_finalize`: Finalize the materials.
-
-    The subclass should also define the following attributes:
-
-    - `_BuildParametersType`: The data structure model for the build parameters.
-    - `_DefaultBuildParameters`: The default build parameters.
-    - `_ConfigurationType`: The data structure model for the Configuration used during the build.
-    - `_GeneratedItemType`: The type of the generated item.
-    - `_SelectorParametersType`: The data structure model for the selector parameters.
-    - `_PostProcessParametersType`: The data structure model for the post-process parameters.
-    """
-
-    model_config = {"arbitrary_types_allowed": True}
-
-    build_parameters: Optional[TypeBuildParameters] = None
-    _BuildParametersType: Type[TypeBuildParameters] = BaseBuilderParameters
-    _DefaultBuildParameters: TypeBuildParameters = BaseBuilderParameters()
-
-    _ConfigurationType: Type[TypeConfiguration] = BaseConfigurationPydantic
-    _PostProcessParametersType: Any = None
-
-    def __init__(self, build_parameters: Optional[TypeBuildParameters] = None):
-        super().__init__()
-        self.build_parameters = build_parameters if build_parameters is not None else self._DefaultBuildParameters
-
-    def _generate(self, configuration: TypeConfiguration) -> MaterialWithBuildMetadata:
-        raise NotImplementedError
-
-    def _post_process(
-        self,
-        item: MaterialWithBuildMetadata,
-        post_process_parameters: Optional[Any],
-        configuration: Optional[TypeConfiguration] = None,
-    ) -> MaterialWithBuildMetadata:
-        return item
-
-    def _finalize(
-        self, material: MaterialWithBuildMetadata, configuration: TypeConfiguration
-    ) -> MaterialWithBuildMetadata:
-        material_with_metadata = self._update_material_metadata(material, configuration)
-        return self._update_material_name(material_with_metadata, configuration)
-
-    def get_material(
-        self,
-        configuration: TypeConfiguration,
-        post_process_parameters: Optional[Any] = None,
-    ) -> MaterialWithBuildMetadata:
-        generated_item = self._generate(configuration)
-        material = self._post_process(generated_item, post_process_parameters, configuration)
-        finalized_material = self._finalize(material, configuration)
-        return finalized_material
-
-    def _update_material_name(
-        self, material: MaterialWithBuildMetadata, configuration: TypeConfiguration
-    ) -> MaterialWithBuildMetadata:
-        return material
-
-    def _update_material_metadata(
-        self, material: MaterialWithBuildMetadata, configuration: TypeConfiguration
-    ) -> MaterialWithBuildMetadata:
-        material.metadata.add_build_metadata_step(configuration=configuration, build_parameters=self.build_parameters)
-        return material

package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/build_parameters.py

@@ -1,5 +0,0 @@
-from mat3ra.code.entity import InMemoryEntityPydantic
-
-
-class BaseBuilderParameters(InMemoryEntityPydantic):
-    pass

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/__init__.py

@@ -1,4 +0,0 @@
-from .builder import CrystalLatticeLinesBuilder
-from .configuration import CrystalLatticeLinesConfiguration
-
-__all__ = ["CrystalLatticeLinesBuilder", "CrystalLatticeLinesConfiguration"]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/builder.py

@@ -1,46 +0,0 @@
-from typing import Any, Optional, Union
-
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseSingleBuilder, TypeConfiguration
-
-from ......analyze.lattice_lines import CrystalLatticeLinesMaterialAnalyzer
-from ......build.pristine_structures.two_dimensional.slab.utils import get_orthogonal_c_slab
-from ......modify import translate_to_z_level
-from ......operations.core.unary import supercell
-from ..... import MaterialWithBuildMetadata
-from .configuration import CrystalLatticeLinesConfiguration
-
-
-class CrystalLatticeLinesBuilder(BaseSingleBuilder):
-    """
-    Builder for creating a single crystal lattice line with termination.
-    This is similar to CrystalLatticePlanesBuilder but for 1D lines.
-    """
-
-    _PostProcessParametersType: Any = None
-    use_enforce_convention: bool = True
-
-    def _generate(self, configuration: CrystalLatticeLinesConfiguration) -> Material:
-        crystal_lattice_lines_analyzer = CrystalLatticeLinesMaterialAnalyzer(
-            material=configuration.crystal, miller_indices_2d=configuration.miller_indices_2d
-        )
-        miller_supercell_matrix = crystal_lattice_lines_analyzer.miller_supercell_matrix
-        miller_supercell_material = supercell(configuration.crystal, miller_supercell_matrix)
-        # Lattice returned with vector B being treated as the direction to the surface, needs to be swaped with C
-        rotated_material = supercell(miller_supercell_material, [[1, 0, 0], [0, 0, 1], [0, 1, 0]])
-        orthogonal_material = get_orthogonal_c_slab(rotated_material)
-        return orthogonal_material
-
-    def _enforce_convention(self, material: Union[Material, MaterialWithBuildMetadata]) -> Material:
-        if not self.use_enforce_convention:
-            return material
-        return translate_to_z_level(material, "bottom")
-
-    def _post_process(
-        self,
-        item: Material,
-        post_process_parameters: Optional[Any],
-        configuration: Optional[TypeConfiguration] = None,
-    ) -> Material:
-        item = super()._post_process(item, post_process_parameters, configuration)
-        return self._enforce_convention(item)