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).
- 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
- environment_subgraph(environments_symbols=None, only_atoms=None)[source]
- Parameters
() (only_atoms) –
() –
Returns:
- 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:
- setup_atom_environments_subgraph(atoms_environments)[source]
- Parameters
() (atoms_environments) –
Returns: