Water

Hey guys,
This is a new distance metric 'solventfp' for dealing with indistinguishable particles (solvent / water) as described in
http://www.biomedcentral.com/1471-2105/14/S2/S8

In addition to the new metric, I've modified CreateAtomIndices.py to pick out water molecules and I've included a new script "AssignOuter.py" that takes two clusterings and combines them into one clustering, as required by the algorithm

Also, I'm realizing by looking at the diff that eclipse has "formatted" the files I was working with, which explains the many changes in whitespace