Add chemical clustering code

[apayne97]

Intro

Simple idea, which is to use a version of hierarchical clustering where instead of using a metric of distance computed once, instead use a maximum-common substructure algorithm to find the # of atoms in the common substructure.

In a sense, I'm trying to match a Medicinal Chemists intuition of what the scaffolds are for a set of heterogeneous hits you might get from a screen. I've found that doing this with fingerprint distances, etc doesn't really work in the way I'd like.

I think this similar to how MedChemica's MCPairs algorithm works, so I might end up just recommending that instead, but I think this will be a good exercise and potentially useful to a few different projects I'm working on.

To-Do

• add a way to traverse backward through the clusters to collect all the molecules that belong to each cluster
• add the final while loop
• add a filtering step to avoid calculating MCSS's that will time out "truncate" anyways
• add Bemis-Murcko scaffold clustering
• add tests and a good test case of molecules that isn't a proprietary (?) molecule screen

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