def get_structure_components(bonded_structure, inc_orientation=False,
                             inc_site_ids=False, inc_molecule_graph=False):
    """
    Gets information on the components in a bonded structure.

    Correctly determines the dimensionality of all structures, regardless of
    structure type or improper connections due to periodic boundary conditions.

    Requires a StructureGraph object as input. This can be generated using one
    of the NearNeighbor classes. For example, using the CrystalNN class::

        bonded_structure = CrystalNN().get_bonded_structure(structure)

    Based on the modified breadth-first-search algorithm described in:

    P. Larsem, M. Pandey, M. Strange, K. W. Jacobsen, 2018, arXiv:1808.02114

    Args:
        bonded_structure (StructureGraph): A structure with bonds, represented
            as a pymatgen structure graph. For example, generated using the
            CrystalNN.get_bonded_structure() method.
        inc_orientation (bool, optional): Whether to include the orientation
            of the structure component. For surfaces, the miller index is given,
            for one-dimensional structures, the direction of the chain is given.
        inc_site_ids (bool, optional): Whether to include the site indices
            of the sites in the structure component.
        inc_molecule_graph (bool, optional): Whether to include MoleculeGraph
            objects for zero-dimensional components.

    Returns:
        (list of dict): Information on the components in a structure as a list
        of dictionaries with the keys:

        - "structure_graph": A pymatgen StructureGraph object for the
            component.
        - "dimensionality": The dimensionality of the structure component as an
            int.
        - "orientation": If inc_orientation is `True`, the orientation of the
            component as a tuple. E.g. (1, 1, 1)
        - "site_ids": If inc_site_ids is `True`, the site indices of the
            sites in the component as a tuple.
        - "molecule_graph": If inc_molecule_graph is `True`, the site a
            MoleculeGraph object for zero-dimensional components.
    """
    import networkx as nx  # optional dependency therefore not top level import

    comp_graphs = (bonded_structure.graph.subgraph(c) for c in
                   nx.weakly_connected_components(bonded_structure.graph))

    components = []
    for graph in comp_graphs:
        dimensionality, vertices = calculate_dimensionality_of_site(
            bonded_structure, list(graph.nodes())[0], inc_vertices=True)

        component = {'dimensionality': dimensionality}

        if inc_orientation:
            if dimensionality in [1, 2]:
                vertices = np.array(vertices)

                g = vertices.sum(axis=0) / vertices.shape[0]

                # run singular value decomposition
                _, _, vh = np.linalg.svd(vertices - g)

                # get direction (first column is best fit line,
                # 3rd column is unitary norm)
                index = 2 if dimensionality == 2 else 0
                orientation = get_integer_index(vh[index, :])
            else:
                orientation = None

            component['orientation'] = orientation

        if inc_site_ids:
            component['site_ids'] = tuple(graph.nodes())

        if inc_molecule_graph and dimensionality == 0:
            component['molecule_graph'] = zero_d_graph_to_molecule_graph(
                bonded_structure, graph)

        component_structure = Structure.from_sites(
            [bonded_structure.structure[n] for n in sorted(graph.nodes())])

        sorted_graph = nx.convert_node_labels_to_integers(
            graph, ordering="sorted")
        component_graph = StructureGraph(
            component_structure,
            graph_data=json_graph.adjacency_data(sorted_graph))
        component['structure_graph'] = component_graph

        components.append(component)
    return components
def get_structure_components ( bonded_structure , inc_orientation = False , inc_site_ids = False , inc_molecule_graph = False ) : import networkx as nx comp_graphs = ( bonded_structure . graph . subgraph ( c ) for c in nx . weakly_connected_components ( bonded_structure . graph ) ) components = [ ] for graph in comp_graphs : dimensionality , vertices = calculate_dimensionality_of_site ( bonded_structure , list ( graph . nodes ( ) ) [ 0 ] , inc_vertices = True ) component = { 'dimensionality' : dimensionality } if inc_orientation : if dimensionality in [ 1 , 2 ] : vertices = np . array ( vertices ) g = vertices . sum ( axis = 0 ) / vertices . shape [ 0 ] _ , _ , vh = np . linalg . svd ( vertices - g ) index = 2 if dimensionality == 2 else 0 orientation = get_integer_index ( vh [ index , : ] ) else : orientation = None component [ 'orientation' ] = orientation if inc_site_ids : component [ 'site_ids' ] = tuple ( graph . nodes ( ) ) if inc_molecule_graph and dimensionality == 0 : component [ 'molecule_graph' ] = zero_d_graph_to_molecule_graph ( bonded_structure , graph ) component_structure = Structure . from_sites ( [ bonded_structure . structure [ n ] for n in sorted ( graph . nodes ( ) ) ] ) sorted_graph = nx . convert_node_labels_to_integers ( graph , ordering = "sorted" ) component_graph = StructureGraph ( component_structure , graph_data = json_graph . adjacency_data ( sorted_graph ) ) component [ 'structure_graph' ] = component_graph components . append ( component ) return components
Gets information on the components in a bonded structure.

    Correctly determines the dimensionality of all structures, regardless of
    structure type or improper connections due to periodic boundary conditions.

    Requires a StructureGraph object as input. This can be generated using one
    of the NearNeighbor classes. For example, using the CrystalNN class::

        bonded_structure = CrystalNN().get_bonded_structure(structure)

    Based on the modified breadth-first-search algorithm described in:

    P. Larsem, M. Pandey, M. Strange, K. W. Jacobsen, 2018, arXiv:1808.02114

    Args:
        bonded_structure (StructureGraph): A structure with bonds, represented
            as a pymatgen structure graph. For example, generated using the
            CrystalNN.get_bonded_structure() method.
        inc_orientation (bool, optional): Whether to include the orientation
            of the structure component. For surfaces, the miller index is given,
            for one-dimensional structures, the direction of the chain is given.
        inc_site_ids (bool, optional): Whether to include the site indices
            of the sites in the structure component.
        inc_molecule_graph (bool, optional): Whether to include MoleculeGraph
            objects for zero-dimensional components.

    Returns:
        (list of dict): Information on the components in a structure as a list
        of dictionaries with the keys:

        - "structure_graph": A pymatgen StructureGraph object for the
            component.
        - "dimensionality": The dimensionality of the structure component as an
            int.
        - "orientation": If inc_orientation is `True`, the orientation of the
            component as a tuple. E.g. (1, 1, 1)
        - "site_ids": If inc_site_ids is `True`, the site indices of the
            sites in the component as a tuple.
        - "molecule_graph": If inc_molecule_graph is `True`, the site a
            MoleculeGraph object for zero-dimensional components.