import networkx as nx
import numpy as np
[docs]def connectivity_to_edges(connectivity, indices=None):
"""Convert a Numpy connectivity matrix into a list of NetworkX
compatible edges.
"""
if indices is None:
indices = np.arange(connectivity.shape[0], dtype=int)
edges = []
for i, c in enumerate(connectivity):
lower_diagonal = c[:i + 1]
for j, v in enumerate(lower_diagonal):
edges += [(indices[i], indices[j], 1)] * int(v)
return edges
[docs]def isomorphic_molecules(graph0, graph1):
"""Check whether two molecule graphs are isomorphic."""
em = nx.algorithms.isomorphism.numerical_edge_match('bonds', 1)
nm = nx.algorithms.isomorphism.numerical_node_match('number', 1)
isomorphic = nx.is_isomorphic(graph0, graph1, edge_match=em, node_match=nm)
return isomorphic