[WIP] "Fix" for failing lprmsd test case

added low qsqr nested if statements from reference code from Doug Theobald's implementation that I thought would help me fix an issue I was having. In this (https://gist.github.com/schwancr/648d2955b2315835234f) example, there are three atoms in a line, but the code cannot correctly return the rotation matrix. 

I have tried several variants of this, and they all fail. However, if you put the atoms in a configuration that is not a line, then it works just fine. So I'm thinking this is just some failure mode of the code.

Anyone have any insight?

In light of this branch not actually fixing my problem, I don't think we have to pull it in, though we could since it's in the original implementation and was left out of the lprmsd code in mdtraj.