[BioPython] Spatial clustering

[Shu-Hsien Sheu]

Hi,

I am now working on a mapping protein binding site project which would 
generate thousands of small organic molecules in cartesian coordinates. 
Next step would be to cluster these small molecules. Is there any 
modules available for this kind of task? PyCluster seems to work with 2D 
gene expression data only, thoug through some modifications I can use it 
as well. I am thinking of using RMSD matrix and then a density-based 
algorithym. The following paper gave me some general ideas about the 
approaches I can take:

http://prlab.ee.memphis.edu/frigui/CLUSTER_PAPERS/Ericasurvey.pdf

Any comments here?

thanks!

-shuhsien