Speed up RMSD comparison

[Gabriella439]

This potential performance improvement was brought to my attention by Andrew Gallant. He noted that I could improve the performance of the Kabsch algorithm by replacing it with a more specialized method developed by Liu and Theobald. He provided links to the original implementation and on in Go, too:

http://theobald.brandeis.edu/qcp/

https://github.com/TuftsBCB/structure/blob/master/qc.go

[godotgildor]

Cool. The code looks pretty easy to implement. The nice thing is that it separates the RMSD and the rotation matrix, so we can do the uber fast RMSD calc, and only if it meets the threshold set by the user then do the more in-depth rotation matrix calculation.