Does isomorphism.GraphMatcher consider attributes?

[Herman Bergwerf]

I just want to make sure. I need to build a function that compares two molecules (simple small molecules, in an exercise for secondary school students). I wanted to use networkx, build two graphs and then use  isomorphism.GraphMatcher (this way I can also detect when the student to forgot to add a molecule somewhere or added one too much). Is it sufficient to build two graphs using add_edge (with element indices) and add use set_node_attributes to add an element attribute to each node? Would that correctly compare the two molecular graphs?

Thanks!

Herman

[Edouard KLEIN]

Hi !

You need to specify the node_match function:

import networkx

h2o = networkx.Graph()

h2o.add_edge(1, 2)

h2o.add_edge(0, 1)

networkx.set_node_attributes(h2o, 'name', {0: 'H', 1: 'O', 2: 'H'})

co2 = networkx.Graph()

co2.add_edge(1, 2)

co2.add_edge(0, 1)

networkx.set_node_attributes(co2, 'name', {0: 'O', 1: 'C', 2: 'O'})

networkx.isomorphism.is_isomorphic(h2o, co2)  # Returns True, not what you want

networkx.isomorphism.is_isomorphic(h2o, co2, node_match=lambda n1, n2: n1['name'] == n2['name'])  # Returns False, what you want

The arguments to networkx.isomorphism.is_isomorphic are the same as those to the constructor of GraphMatcher.

Cheers,

Edouard.