diff --git a/docs/apidoc/pymatgen.io.aims.rst b/docs/apidoc/pymatgen.io.aims.rst index 800001df3c5..7949c7d0e56 100644 --- a/docs/apidoc/pymatgen.io.aims.rst +++ b/docs/apidoc/pymatgen.io.aims.rst @@ -6,6 +6,14 @@ pymatgen.io.aims package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + :maxdepth: 7 + + pymatgen.io.aims.sets + Submodules ---------- diff --git a/docs/apidoc/pymatgen.io.aims.sets.rst b/docs/apidoc/pymatgen.io.aims.sets.rst new file mode 100644 index 00000000000..29a1aafbd4f --- /dev/null +++ b/docs/apidoc/pymatgen.io.aims.sets.rst @@ -0,0 +1,34 @@ +pymatgen.io.aims.sets package +============================= + +.. automodule:: pymatgen.io.aims.sets + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +pymatgen.io.aims.sets.base module +--------------------------------- + +.. automodule:: pymatgen.io.aims.sets.base + :members: + :undoc-members: + :show-inheritance: + +pymatgen.io.aims.sets.bs module +------------------------------- + +.. automodule:: pymatgen.io.aims.sets.bs + :members: + :undoc-members: + :show-inheritance: + +pymatgen.io.aims.sets.core module +--------------------------------- + +.. automodule:: pymatgen.io.aims.sets.core + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/apidoc/pymatgen.io.rst b/docs/apidoc/pymatgen.io.rst index ed205163887..3d276f7d2fe 100644 --- a/docs/apidoc/pymatgen.io.rst +++ b/docs/apidoc/pymatgen.io.rst @@ -104,6 +104,14 @@ pymatgen.io.gaussian module :undoc-members: :show-inheritance: +pymatgen.io.icet module +----------------------- + +.. automodule:: pymatgen.io.icet + :members: + :undoc-members: + :show-inheritance: + pymatgen.io.jarvis module ------------------------- diff --git a/docs/apidoc/pymatgen.util.rst b/docs/apidoc/pymatgen.util.rst index 807645b00d9..8a645ccb065 100644 --- a/docs/apidoc/pymatgen.util.rst +++ b/docs/apidoc/pymatgen.util.rst @@ -6,6 +6,14 @@ pymatgen.util package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + :maxdepth: 7 + + pymatgen.util.testing + Submodules ---------- @@ -89,14 +97,6 @@ pymatgen.util.string module :undoc-members: :show-inheritance: -pymatgen.util.testing module ----------------------------- - -.. automodule:: pymatgen.util.testing - :members: - :undoc-members: - :show-inheritance: - pymatgen.util.typing module --------------------------- diff --git a/docs/apidoc/pymatgen.util.testing.rst b/docs/apidoc/pymatgen.util.testing.rst new file mode 100644 index 00000000000..0ee4fd38001 --- /dev/null +++ b/docs/apidoc/pymatgen.util.testing.rst @@ -0,0 +1,18 @@ +pymatgen.util.testing package +============================= + +.. automodule:: pymatgen.util.testing + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +pymatgen.util.testing.aims module +--------------------------------- + +.. automodule:: pymatgen.util.testing.aims + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/modules.html b/docs/modules.html index 97adb20638f..d6d5696b2a3 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -4,7 +4,7 @@ - pymatgen — pymatgen 2024.1.27 documentation + pymatgen — pymatgen 2024.3.1 documentation @@ -17,7 +17,7 @@ - + @@ -37,7 +37,7 @@
- 2024.1.27 + 2024.3.1
@@ -2784,6 +2784,7 @@

pymatgen
  • SiteCollection.n_elems
  • SiteCollection.ntypesp
  • SiteCollection.num_sites
    • +
  • SiteCollection.reduced_formula
  • SiteCollection.remove_oxidation_states()
  • SiteCollection.remove_site_property()
  • SiteCollection.remove_spin()
    • @@ -3411,8 +3412,10 @@

    pymatgen
  • Entry.elements
  • Entry.energy
  • Entry.energy_per_atom
    • +
  • Entry.formula
  • Entry.is_element
  • Entry.normalize()
    • +
  • Entry.reduced_formula
  • Submodules
    • @@ -3722,6 +3725,10 @@

    pymatgen
  • pymatgen.io.aims package
    • +
  • pymatgen.io.icet module +
  • pymatgen.io.jarvis module
    • +
  • find_codopant()
  • pymatgen.transformations.site_transformations module
      @@ -5307,6 +5336,28 @@

      pymatgen

  • pymatgen.util package
  • Submodules
    • -
  • pymatgen.dao module
    • +
  • pymatgen.dao module
    • diff --git a/docs/pymatgen.alchemy.html b/docs/pymatgen.alchemy.html index c3d43ab1e1e..31e8b8c3389 100644 --- a/docs/pymatgen.alchemy.html +++ b/docs/pymatgen.alchemy.html @@ -4,7 +4,7 @@ - pymatgen.alchemy package — pymatgen 2024.1.27 documentation + pymatgen.alchemy package — pymatgen 2024.3.1 documentation @@ -17,7 +17,7 @@ - + @@ -37,7 +37,7 @@
    - 2024.1.27 + 2024.3.1
    @@ -175,14 +175,14 @@

    Submodules
    -class AbstractStructureFilter[source]
    -

    Bases: MSONable

    +class AbstractStructureFilter[source] +

    Bases: MSONable, ABC

    AbstractStructureFilter that defines an API to perform testing of Structures. Structures that return True to a test are retained during transmutation while those that return False are removed.

    -abstract test(structure: Structure)[source]
    +abstract test(structure: Structure)[source]

    Method to execute the test.

    Parameters:
    @@ -205,7 +205,7 @@

    Submodules
    -class ChargeBalanceFilter[source]
    +class ChargeBalanceFilter[source]

    Bases: AbstractStructureFilter

    This filter removes structures that are not charge balanced from the transmuter. This only works if the structure is oxidation state @@ -214,7 +214,7 @@

    Submodules
    -test(structure: Structure)[source]
    +test(structure: Structure)[source]

    Method to execute the test.

    Parameters:
    @@ -233,7 +233,7 @@

    Submodules
    -class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]
    +class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]

    Bases: AbstractStructureFilter

    Filter for structures containing certain elements or species. By default compares by atomic number.

    @@ -251,13 +251,13 @@

    Submodules
    -as_dict()[source]
    +as_dict()[source]

    Returns: MSONable dict.

    -classmethod from_dict(dct)[source]
    +classmethod from_dict(dct: dict) → Self[source]
    Parameters:

    dct (dict) – Dict representation.

    @@ -270,7 +270,7 @@

    Submodules
    -test(structure: Structure)[source]
    +test(structure: Structure)[source]

    Method to execute the test.

    Returns:
    @@ -286,7 +286,7 @@

    Submodules
    -class RemoveDuplicatesFilter(structure_matcher: dict | StructureMatcher | None = None, symprec: float | None = None)[source]
    +class RemoveDuplicatesFilter(structure_matcher: dict | StructureMatcher | None = None, symprec: float | None = None)[source]

    Bases: AbstractStructureFilter

    This filter removes exact duplicate structures from the transmuter.

    Remove duplicate structures based on the structure matcher @@ -304,7 +304,7 @@

    Submodules
    -test(structure: Structure) → bool[source]
    +test(structure: Structure) → bool[source]
    Parameters:

    structure (Structure) – Input structure to test.

    @@ -322,7 +322,7 @@

    Submodules
    -class RemoveExistingFilter(existing_structures, structure_matcher=None, symprec=None)[source]
    +class RemoveExistingFilter(existing_structures, structure_matcher=None, symprec=None)[source]

    Bases: AbstractStructureFilter

    This filter removes structures existing in a given list from the transmuter.

    Remove existing structures based on the structure matcher @@ -341,13 +341,13 @@

    Submodules
    -as_dict()[source]
    +as_dict()[source]

    Returns: MSONable dict.

    -test(structure: Structure)[source]
    +test(structure: Structure)[source]

    Method to execute the test.

    Parameters:
    @@ -366,7 +366,7 @@

    Submodules
    -class SpecieProximityFilter(specie_and_min_dist_dict)[source]
    +class SpecieProximityFilter(specie_and_min_dist_dict)[source]

    Bases: AbstractStructureFilter

    This filter removes structures that have certain species that are too close together.

    @@ -382,13 +382,13 @@

    Submodules
    -as_dict()[source]
    +as_dict()[source]

    Returns: MSONable dict.

    -classmethod from_dict(dct)[source]
    +classmethod from_dict(dct: dict) → Self[source]
    Parameters:

    dct (dict) – Dict representation.

    @@ -401,7 +401,7 @@

    Submodules
    -test(structure: Structure)[source]
    +test(structure: Structure)[source]

    Method to execute the test.

    Parameters:
    @@ -420,7 +420,7 @@

    Submodules
    -class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]
    +class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]

    Bases: AbstractStructureFilter

    This filter removes structures that do have two particular species that are not nearest neighbors by a predefined max_dist. For instance, if you are @@ -440,7 +440,7 @@

    Submodules
    -test(structure: Structure)[source]
    +test(structure: Structure)[source]

    Method to execute the test.

    Parameters:
    @@ -469,7 +469,7 @@

    Submodules
    -class TransformedStructure(structure: Structure, transformations: list[AbstractTransformation] | None = None, history: list[AbstractTransformation | dict[str, Any]] | None = None, other_parameters: dict[str, Any] | None = None)[source]
    +class TransformedStructure(structure: Structure, transformations: AbstractTransformation | Sequence[AbstractTransformation] | None = None, history: list[AbstractTransformation | dict[str, Any]] | None = None, other_parameters: dict[str, Any] | None = None)[source]

    Bases: MSONable

    Container object for new structures that include history of transformations.

    @@ -480,8 +480,7 @@

    SubmodulesParameters:

    • structure (Structure) – Input structure

      • -

    • transformations (list[Transformation]) – List of transformations to -apply.

      • +

    • transformations (list[Transformation]) – List of transformations to apply.

    • history (list[Transformation]) – Previous history.

    • other_parameters (dict) – Additional parameters to be added.

    @@ -489,7 +488,7 @@

    Submodules
    -append_filter(structure_filter: AbstractStructureFilter) → None[source]
    +append_filter(structure_filter: AbstractStructureFilter) → None[source]

    Adds a filter.

    Parameters:
    @@ -501,7 +500,7 @@

    Submodules
    -append_transformation(transformation, return_alternatives: bool = False, clear_redo: bool = True) → list[TransformedStructure] | None[source]
    +append_transformation(transformation, return_alternatives: bool = False, clear_redo: bool = True) → list[TransformedStructure] | None[source]

    Appends a transformation to the TransformedStructure.

    Parameters:
    @@ -523,13 +522,13 @@

    Submodules
    -as_dict() → dict[str, Any][source]
    +as_dict() → dict[str, Any][source]

    Dict representation of the TransformedStructure.

    -extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]
    +extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]

    Extends a sequence of transformations to the TransformedStructure.

    Parameters:
    @@ -546,7 +545,7 @@

    Submodules
    -classmethod from_cif_str(cif_string: str, transformations: list[AbstractTransformation] | None = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → TransformedStructure[source]
    +classmethod from_cif_str(cif_string: str, transformations: list[AbstractTransformation] | None = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → TransformedStructure[source]

    Generates TransformedStructure from a cif string.

    Parameters:
    @@ -574,13 +573,13 @@

    Submodules
    -classmethod from_dict(dct) → TransformedStructure[source]
    +classmethod from_dict(dct: dict) → TransformedStructure[source]

    Creates a TransformedStructure from a dict.

    -classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → TransformedStructure[source]
    +classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → TransformedStructure[source]

    Generates TransformedStructure from a poscar string.

    Parameters:
    @@ -595,7 +594,7 @@

    Submodules
    -classmethod from_snl(snl: StructureNL) → TransformedStructure[source]
    +classmethod from_snl(snl: StructureNL) → TransformedStructure[source]

    Create TransformedStructure from SNL.

    Parameters:
    @@ -609,7 +608,7 @@

    Submodules
    -get_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]
    +get_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]

    Returns VASP input as a dict of VASP objects.

    Parameters:
    @@ -624,7 +623,7 @@

    Submodules
    -redo_next_change() → None[source]
    +redo_next_change() → None[source]

    Redo the last undone change in the TransformedStructure.

    Raises:
    @@ -635,7 +634,7 @@

    Submodules
    -set_parameter(key: str, value: Any) → None[source]
    +set_parameter(key: str, value: Any) → TransformedStructure[source]

    Sets a parameter.

    Parameters:
    @@ -644,37 +643,42 @@

    SubmodulesReturns: +

    TransformedStructure

    +

    -property structures: list[Structure][source]
    +property structures: list[Structure][source]

    Copy of all structures in the TransformedStructure. A structure is stored after every single transformation.

    -to_snl(authors, **kwargs) → StructureNL[source]
    -

    Generate SNL from TransformedStructure.

    +to_snl(authors: list[str], **kwargs) → StructureNL[source] +

    Generate a StructureNL from TransformedStructure.

    Parameters:
      -

    • authors – List of authors

      • -

    • **kwargs –

      All kwargs supported by StructureNL.

      -

      • +

    • authors (List[str]) – List of authors contributing to the generated StructureNL.

      • +

    • **kwargs (Any) – All kwargs supported by StructureNL.

    Returns:
    -

    StructureNL

    +

    The generated StructureNL object.

    +
    +
    Return type:
    +

    StructureNL

    -undo_last_change() → None[source]
    +undo_last_change() → None[source]

    Undo the last change in the TransformedStructure.

    Raises:
    @@ -685,7 +689,7 @@

    Submodules
    -property was_modified: bool[source]
    +property was_modified: bool[source]

    Boolean describing whether the last transformation on the structure made any alterations to it one example of when this would return false is in the case of performing a substitution transformation on the @@ -694,7 +698,7 @@

    Submodules
    -write_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]
    +write_vasp_input(vasp_input_set: type[~pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]

    Writes VASP input to an output_dir.

    Parameters:
    @@ -723,7 +727,7 @@

    Submodules
    -class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]
    +class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]

    Bases: StandardTransmuter

    Generates a Transmuter from a cif string, possibly containing multiple structures.

    @@ -745,7 +749,7 @@

    Submodules
    -classmethod from_filenames(filenames, transformations=None, primitive=True, extend_collection=False)[source]
    +classmethod from_filenames(filenames, transformations=None, primitive=True, extend_collection=False)[source]

    Generates a TransformedStructureCollection from a cif, possibly containing multiple structures.

    @@ -765,7 +769,7 @@

    Submodules
    -class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]
    +class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]

    Bases: StandardTransmuter

    Generates a transmuter from a sequence of POSCARs.

    @@ -781,7 +785,7 @@

    Submodules
    -static from_filenames(poscar_filenames, transformations=None, extend_collection=False)[source]
    +static from_filenames(poscar_filenames, transformations=None, extend_collection=False)[source]

    Convenient constructor to generates a POSCAR transmuter from a list of POSCAR filenames.

    @@ -800,13 +804,13 @@

    Submodules
    -class StandardTransmuter(transformed_structures, transformations=None, extend_collection: int = 0, ncores: int | None = None)[source]
    +class StandardTransmuter(transformed_structures, transformations=None, extend_collection: int = 0, ncores: int | None = None)[source]

    Bases: object

    An example of a Transmuter object, which performs a sequence of transformations on many structures to generate TransformedStructures.

    -transformed_structures[source]
    +transformed_structures[source]

    List of all transformed structures.

    Type:
    @@ -836,7 +840,7 @@

    Submodules
    -add_tags(tags)[source]
    +add_tags(tags)[source]

    Add tags for the structures generated by the transmuter.

    Parameters:
    @@ -848,7 +852,7 @@

    Submodules
    -append_transformation(transformation, extend_collection=False, clear_redo=True)[source]
    +append_transformation(transformation, extend_collection=False, clear_redo=True)[source]

    Appends a transformation to all TransformedStructures.

    Parameters:
    @@ -878,7 +882,7 @@

    Submodules
    -append_transformed_structures(trafo_structs_or_transmuter)[source]
    +append_transformed_structures(trafo_structs_or_transmuter)[source]

    Method is overloaded to accept either a list of transformed structures or transmuter, it which case it appends the second transmuter”s structures.

    @@ -892,7 +896,7 @@

    Submodules
    -apply_filter(structure_filter)[source]
    +apply_filter(structure_filter)[source]

    Applies a structure_filter to the list of TransformedStructures in the transmuter.

    @@ -904,7 +908,7 @@

    Submodules
    -extend_transformations(transformations)[source]
    +extend_transformations(transformations)[source]

    Extends a sequence of transformations to the TransformedStructure.

    Parameters:
    @@ -915,7 +919,7 @@

    Submodules
    -classmethod from_structures(structures, transformations=None, extend_collection=0)[source]
    +classmethod from_structures(structures, transformations=None, extend_collection=0)[source]

    Alternative constructor from structures rather than TransformedStructures.

    @@ -938,7 +942,7 @@

    Submodules
    -redo_next_change()[source]
    +redo_next_change()[source]

    Redo the last undone transformation in the TransformedStructure.

    Raises:
    @@ -949,7 +953,7 @@

    Submodules
    -set_parameter(key, value)[source]
    +set_parameter(key, value)[source]

    Add parameters to the transmuter. Additional parameters are stored in the as_dict() output.

    @@ -964,7 +968,7 @@

    Submodules
    -undo_last_change()[source]
    +undo_last_change()[source]

    Undo the last transformation in the TransformedStructure.

    Raises:
    @@ -975,7 +979,7 @@

    Submodules
    -write_vasp_input(**kwargs)[source]
    +write_vasp_input(**kwargs)[source]

    Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{formula}_{number}.

    @@ -989,7 +993,7 @@

    Submodules
    -batch_write_vasp_input(transformed_structures: Sequence[TransformedStructure], vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, subfolder: Callable[[TransformedStructure], str] | None = None, include_cif: bool = False, **kwargs)[source]
    +batch_write_vasp_input(transformed_structures: Sequence[TransformedStructure], vasp_input_set: type[VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, subfolder: Callable[[TransformedStructure], str] | None = None, include_cif: bool = False, **kwargs)[source]

    Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

    diff --git a/docs/pymatgen.analysis.chemenv.connectivity.html b/docs/pymatgen.analysis.chemenv.connectivity.html index 923a0b85d0a..45d3e8b8ab2 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity package — pymatgen 2024.1.27 documentation + pymatgen.analysis.chemenv.connectivity package — pymatgen 2024.3.1 documentation @@ -17,7 +17,7 @@ - + @@ -37,7 +37,7 @@
    - 2024.1.27 + 2024.3.1
    @@ -175,7 +175,7 @@

    Submodules
    -class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]
    +class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]

    Bases: MSONable

    Class used to describe the connected components in a structure in terms of coordination environments.

    Constructor for the ConnectedComponent object.

    @@ -198,7 +198,7 @@

    Submodules
    -as_dict()[source]
    +as_dict()[source]

    Bson-serializable dict representation of the ConnectedComponent object.

    Returns:
    @@ -212,7 +212,7 @@

    Submodules
    -compute_periodicity(algorithm='all_simple_paths') → None[source]
    +compute_periodicity(algorithm='all_simple_paths') → None[source]
    Parameters:

    () (algorithm) –

    @@ -222,19 +222,19 @@

    Submodules
    -compute_periodicity_all_simple_paths_algorithm()[source]
    +compute_periodicity_all_simple_paths_algorithm()[source]

    Get the periodicity vectors of the connected component.

    -compute_periodicity_cycle_basis() → None[source]
    +compute_periodicity_cycle_basis() → None[source]

    Compute periodicity vectors of the connected component.

    -coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]
    +coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]

    Get the coordination sequence for a given node.

    Parameters:
    @@ -284,7 +284,7 @@

    Submodules
    -description(full=False)[source]
    +description(full=False)[source]
    Parameters:

    full (bool) – Whether to return a short or full description.

    @@ -300,7 +300,7 @@

    Submodules
    -elastic_centered_graph(start_node=None)[source]
    +elastic_centered_graph(start_node=None)[source]
    Parameters:

    () (start_node) –

    @@ -316,12 +316,12 @@

    Submodules
    -classmethod from_dict(d)[source]
    +classmethod from_dict(dct: dict) → Self[source]

    Reconstructs the ConnectedComponent object from a dict representation of the ConnectedComponent object created using the as_dict method.

    Parameters:
    -

    d (dict) – dict representation of the ConnectedComponent object

    +

    dct (dict) – dict representation of the ConnectedComponent object

    Returns:

    The connected component representing the links of a given set of environments.

    @@ -334,7 +334,7 @@

    Submodules
    -classmethod from_graph(g)[source]
    +classmethod from_graph(g)[source]

    Constructor for the ConnectedComponent object from a graph of the connected component.

    Parameters:
    @@ -351,7 +351,7 @@

    Submodules
    -property graph[source]
    +property graph[source]

    Return the graph of this connected component.

    Returns:
    @@ -369,37 +369,37 @@

    Submodules
    -property is_0d: bool[source]
    +property is_0d: bool[source]

    Whether this connected component is 0-dimensional.

    -property is_1d: bool[source]
    +property is_1d: bool[source]

    Whether this connected component is 1-dimensional.

    -property is_2d: bool[source]
    +property is_2d: bool[source]

    Whether this connected component is 2-dimensional.

    -property is_3d: bool[source]
    +property is_3d: bool[source]

    Whether this connected component is 3-dimensional.

    -property is_periodic: bool[source]
    +property is_periodic: bool[source]

    Whether this connected component is periodic.

    -make_supergraph(multiplicity)[source]
    +make_supergraph(multiplicity)[source]
    Parameters:

    () (multiplicity) –

    @@ -415,19 +415,19 @@

    Submodules
    -property periodicity[source]
    +property periodicity[source]

    Get periodicity of this connected component.

    -property periodicity_vectors[source]
    +property periodicity_vectors[source]

    Get periodicity vectors of this connected component.

    -show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]
    +show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]

    Displays the graph using the specified drawing type.

    Parameters:
    @@ -445,7 +445,7 @@

    Submodules
    -draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]
    +draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]

    Draw network of environments in a matplotlib figure axes.

    Parameters:
    @@ -462,7 +462,7 @@

    Submodules
    -make_supergraph(graph, multiplicity, periodicity_vectors)[source]
    +make_supergraph(graph, multiplicity, periodicity_vectors)[source]

    Make super graph from a graph of environments.

    Parameters:
    @@ -487,31 +487,33 @@

    Submodules
    -class ConnectivityFinder(multiple_environments_choice=None)[source]
    +class ConnectivityFinder(multiple_environments_choice=None)[source]

    Bases: object

    Main class used to find the structure connectivity of a structure.

    Constructor for the ConnectivityFinder.

    Parameters:
    -

    multiple_environments_choice – defines the procedure to apply when

    +
      +

    • multiple_environments_choice – defines the procedure to apply when

      • +

    • one (the environment of a given site is described as a "mix" of more than) –

      • +

    • environments. (coordination) –

      • +
    -

    the environment of a given site is described as a “mix” of more than one -coordination environments.

    -get_structure_connectivity(light_structure_environments)[source]
    +get_structure_connectivity(light_structure_environments)[source]

    Get the structure connectivity from the coordination environments provided as an input.

    Parameters:
    -

    light_structure_environments – LightStructureEnvironments with the

    +
      +

    • light_structure_environments – LightStructureEnvironments with the

      • +

    • structure (relevant coordination environments in the) –

      • +
    -
    -

    relevant coordination environments in the structure

    -
    -
    Returns:
    -

    a StructureConnectivity object describing the connectivity of

    +
    Returns:
    +

    a StructureConnectivity object describing the connectivity of

    the environments in the structure

    @@ -519,7 +521,7 @@

    Submodules
    -setup_parameters(multiple_environments_choice)[source]
    +setup_parameters(multiple_environments_choice)[source]

    Setup of the parameters for the connectivity finder.

    @@ -531,7 +533,7 @@

    Submodules
    -class AbstractEnvironmentNode(central_site, i_central_site)[source]
    +class AbstractEnvironmentNode(central_site, i_central_site)[source]

    Bases: MSONable

    Abstract class used to define an environment as a node in a graph.

    Constructor for the AbstractEnvironmentNode object.

    @@ -546,104 +548,104 @@

    Submodules
    -ATOM = 6[source]
    +ATOM = 6[source]

    -CE_NNBCES_NBCES_LIGANDS = -1[source]
    +CE_NNBCES_NBCES_LIGANDS = -1[source]
    -COORDINATION_ENVIRONMENT = 0[source]
    +COORDINATION_ENVIRONMENT = 0[source]
    -DEFAULT_EXTENSIONS = (6, 0)[source]
    +DEFAULT_EXTENSIONS = (6, 0)[source]
    -LIGANDS_ARRANGEMENT = 4[source]
    +LIGANDS_ARRANGEMENT = 4[source]
    -NEIGHBORING_CES = 2[source]
    +NEIGHBORING_CES = 2[source]
    -NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
    +NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
    -NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
    +NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
    -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
    +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
    -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
    +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
    -NUMBER_OF_NEIGHBORING_CES = 1[source]
    +NUMBER_OF_NEIGHBORING_CES = 1[source]
    -NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
    +NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
    -property atom_symbol[source]
    +property atom_symbol[source]

    Symbol of the atom on the central site.

    -property ce[source]
    +property ce[source]

    Coordination environment of this node.

    -property ce_symbol[source]
    +property ce_symbol[source]

    Coordination environment of this node.

    -abstract property coordination_environment[source]
    +abstract property coordination_environment[source]

    Coordination environment of this node.

    -everything_equal(other)[source]
    +everything_equal(other)[source]

    Checks equality with respect to another AbstractEnvironmentNode using the index of the central site as well as the central site itself.

    -property isite[source]
    +property isite[source]

    Index of the central site.

    -property mp_symbol[source]
    +property mp_symbol[source]

    Coordination environment of this node.

    @@ -651,7 +653,7 @@

    Submodules
    -class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]
    +class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]

    Bases: AbstractEnvironmentNode

    Class used to define an environment as a node in a graph.

    Constructor for the EnvironmentNode object.

    @@ -667,13 +669,13 @@

    Submodules
    -property coordination_environment[source]
    +property coordination_environment[source]

    Coordination environment of this node.

    -everything_equal(other)[source]
    +everything_equal(other)[source]

    Compare with another environment node.

    Returns:
    @@ -689,7 +691,7 @@

    Submodules
    -get_environment_node(central_site, i_central_site, ce_symbol)[source]
    +get_environment_node(central_site, i_central_site, ce_symbol)[source]

    Get the EnvironmentNode class or subclass for the given site and symbol.

    Parameters:
    @@ -711,7 +713,7 @@

    Submodules
    -class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]
    +class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]

    Bases: MSONable

    Main class containing the connectivity of a structure.

    Constructor for the StructureConnectivity object.

    @@ -732,7 +734,7 @@

    Submodules
    -add_bonds(isite, site_neighbors_set)[source]
    +add_bonds(isite, site_neighbors_set)[source]

    Add the bonds for a given site index to the structure connectivity graph.

    Parameters:
    @@ -746,19 +748,19 @@

    Submodules
    -add_sites()[source]
    +add_sites()[source]

    Add the sites in the structure connectivity graph.

    -as_dict()[source]
    +as_dict()[source]

    Convert to MSONable dict.

    -environment_subgraph(environments_symbols=None, only_atoms=None)[source]
    +environment_subgraph(environments_symbols=None, only_atoms=None)[source]
    Parameters:

    -

    - - - - - - \ No newline at end of file + + +