On Mon, Feb 23, 2015 at 4:24 PM, Patrick Walters <wpwalt...@gmail.com>
wrote:
> I agree that there are plenty of implementations of clustering, machine
> learning, etc. It would be better for the RDKit developers to focus on
> cheminformatics. This being said, there are some opportunities for domain
> specific performance enhancement. One of the slow steps in many clustering
> algorithms is the calculation of a distance matrix and identification of
> neighbors. If you're clustering fingerprints, I'd recommend looking at Andrew
> Dalke's ChemFP <http://chemfp.com/>. Andrew has applied a multitude of
> tricks that can make clustering blazingly fast. The ChemFP examples
> include an implementation of Taylor-Butina clustering. Even better, ChemFP
> works "out of the box" with the RDKit.
>
Actually, coupling chemfp to a hierarchical clustering algorithm like the
"Murtagh" code the RDKit includes would be pretty cool...
-greg
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