Clustering Methods

[ryanmcgreevy]

ModelMaker needs to support clustering methods beyond the default Rosetta one. As of this commit, Keith's python clustering script has been integrated in an initial implementation. This script requires several python packages which I will list in the docs soon. To use this clustering method, the user needs to specify it in the -cluster option of analyze. Initially this will be -cluster 1 (a more user-friendly mode selection will come later). The default is still -cluster 0, the Rosetta method. @trudack , could you please test this when you get a chance?

[trudack]

The following still needs to be done:
add input options:
either give the number of clusters or use the script to evaluate the best number
output option:
Write the representative pdb of the cluster and dcds with all structures of each cluster

@jribeiroUIUC mentioned that the code is still pretty messy and needs to be cleaned up at a later point when the rest is working