pymatgen.analysis.chemenv.utils.graph_utils module

This module contains some graph utils that are used in the chemenv package.

class MultiGraphCycle(nodes, edge_indices, validate=True, ordered=None)

Bases: monty.json.MSONable

Class used to describe a cycle in a multigraph.

nodes are the nodes of the cycle and edge_indices are the indices of the edges in the cycle. The nth index in edge_indices corresponds to the edge index between the nth node in nodes and the (n+1)th node in nodes with the exception of the last one being the edge index between the last node in nodes and the first node in nodes

Example: A cycle

nodes: 1 - 3 - 4 - 0 - 2 - (1) edge_indices: 0 . 1 . 0 . 2 . 0 . (0)

Parameters

• nodes –

• edge_indices –

• validate –

• ordered –

order(raise_on_fail=True)

Orders the SimpleGraphCycle.

The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the first node. If raise_on_fail is set to True a RuntimeError will be raised if the ordering fails.

Parameters

raise_on_fail – If set to True, will raise a RuntimeError if the ordering fails.

Returns

None

validate(check_strict_ordering=False)

Parameters

check_strict_ordering –

Returns

class SimpleGraphCycle(nodes, validate=True, ordered=None)

Bases: monty.json.MSONable

Class used to describe a cycle in a simple graph (graph without multiple edges).

Note that the convention used here is the networkx convention for which simple graphs allow to have self-loops in a simple graph. No simple graph cycle with two nodes is possible in a simple graph. The graph will not be validated if validate is set to False. By default, the “ordered” parameter is None, in which case the SimpleGraphCycle will be ordered. If the user explicitly sets ordered to False, the SimpleGraphCycle will not be ordered.

Parameters

• nodes –

• validate –

• ordered –

as_dict()

Returns

MSONAble dict

classmethod from_dict(d, validate=False)

Serialize from dict. :param d: :param validate: :return:

classmethod from_edges(edges, edges_are_ordered=True)

Constructs SimpleGraphCycle from a list edges.

By default, the edges list is supposed to be ordered as it will be much faster to construct the cycle. If edges_are_ordered is set to False, the code will automatically try to find the corresponding edge order in the list.

order(raise_on_fail=True)

Orders the SimpleGraphCycle.

The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the first node. If raise_on_fail is set to True a RuntimeError will be raised if the ordering fails.

Parameters

raise_on_fail – If set to True, will raise a RuntimeError if the ordering fails.

Returns

None

validate(check_strict_ordering=False)

Parameters

check_strict_ordering –

Returns

get_all_elementary_cycles(graph)

Parameters

graph –

Returns

get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True)

Get all the simple path and edges. :param graph: :param source: :param target: :param cutoff: :param data: :return:

get_delta(node1, node2, edge_data)

Get the delta. :param node1: :param node2: :param edge_data: :return: