Compute graph edit distance between two molecules using RDKit and Networkx

graph_edit_distance.py

'''
Written by Jan H. Jensen, 2020
'''

from rdkit import Chem
import networkx as nx

def get_graph(mol):
  Chem.Kekulize(mol)
  atoms = [atom.GetAtomicNum() for atom in mol.GetAtoms()]
  am = Chem.GetAdjacencyMatrix(mol,useBO=True)
  for i,atom in enumerate(atoms):
    am[i,i] = atom
  G = nx.from_numpy_matrix(am)
  return G

mol1 = Chem.MolFromSmiles('c1ccccc1')
#mol2 = Chem.MolFromSmiles('c1cnccc1')
mol2 = Chem.MolFromSmiles('C=CC=CC=C') 

G1 = get_graph(mol1)
G2 = get_graph(mol2)

GDE = nx.graph_edit_distance(G1, G2, edge_match=lambda a,b: a['weight'] == b['weight'])

print(GDE)