I believe the RDKit uses the vf2 algorithm:
L. P. Cordella, P. Foggia, C. Sansone, and M. Vento.
An improved algorithm for matching large graphs.
In: 3rd IAPR-TC15 Workshop on Graph-based Representations in Pattern
Recognition, pp. 149-159, Cuen, 2001.
If you google search for vf2 substructure search you will find plenty of
benchmarks
Brian Kelley
> On Jan 9, 2017, at 4:49 AM, Axel Rudling wrote:
>
> Hello,
>
> I've been benchmarking different softwares for substructure searching of
> molecules. From what I can tell, RDKits substructureMatch appears to do the
> job. I have been looking around the documentation and this forum for a
> description of how it actually works. As I understand it, it does the
> calculation from a molecule object that is created from the smile?
>
> How does substructureMatch work? Is it still fingerprint based? How accurate
> is it? Is there a description of some standardised term for what is happening
> there?
>
> Best,
> Axel
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