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 <axru6...@gmail.com> 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 > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
