I previously mentioned a comparison of various tools to cluster large datasets. I've now updated the Vortex to allow the user to select the centroid of each cluster. I tried it on a 4.3 million structure clustered dataset and the script only took a few seconds to run.

The page on clustering is here and the Vortex script can be downloaded here http://macinchem.org/reviews/vortex_scripts/ChoseCentreFromClusters.vpy.zip.