pymatgen.analysis.chemenv.connectivity.structure_connectivity module¶
Structure connectivity class.
-
class
StructureConnectivity
(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]¶ Bases:
monty.json.MSONable
Main class containing the connectivity of a structure.
Constructor for the StructureConnectivity object.
- Parameters
light_structure_environment – a LightStructureEnvironments object containing the relevant local environments for the sites in the structure.
connectivity_graph – the networkx MultiGraph if it has already been computed, e.g. stored in a file or dict and StructureConnectivity is reconstructed from that file or dict.
environment_subgraphs – the different subgraphs of environments that have been computed if any (as for connectivity_graph, only if it is reconstructed from a file or dict).
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add_bonds
(isite, site_neighbors_set)[source]¶ Add the bonds for a given site index to the structure connectivity graph.
- Parameters
isite – Index of the site for which the bonds have to be added.
site_neighbors_set – site_neighbors_set: Neighbors set of the site
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environment_subgraph
(environments_symbols=None, only_atoms=None)[source]¶ - Parameters
() (only_atoms) –
() –
Returns:
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get_connected_components
(environments_symbols=None, only_atoms=None)[source]¶ - Parameters
() (only_atoms) –
() –
Returns:
-
setup_atom_environment_subgraph
(atom_environment)[source]¶ - Parameters
() (atom_environment) –
Returns:
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setup_atom_environments_subgraph
(atoms_environments)[source]¶ - Parameters
() (atoms_environments) –
Returns: