Uses of graph isomorphism and pynauty?

[j2kun]

Hello, I'm doing background research for a book and was browsing projects that relate to graph isomorphism. I've interviewed a bunch of computational chemists about this already (e.g., the developers of RDKit), and from that I've come to believe that most uses of graph isomorphism are actually subgraph isomorphism for substructure search and multiple common substructure (MCS).

So I was curious to see the mention of nauty and pynauty in the docs here. However, it's not clear to me what value a chemist might get from counting the automorphisms of a chemical graph. Could someone familiar with this (perhaps who wrote that doc) explain this to me, if it's not too much trouble?

[wojdyr]

Hi, I wrote these docs (BTW, the rendered version is here).

I tested building a graph in nauty with two potential uses in mind:

1. Calculating RMSD, as described in in this post and discussed in [Feature Request] RMSD for comparing small molecules #43.
2. A colleague was interested in using nauty for small molecules, but I don't remember what for.

I don't think that anyone used it so far, and I don't know how practical would it be to use it for 1.

[j2kun]

Thanks!