rmcgibbo/mdtraj — pull request #470 by leeping (2014-06-05 01:13:43+00:00)
Title: Cone H-bond criterion and periodic angles/torsions

This PR implements the hydrogen bond criterion described in this paper: http://www.sciencemag.org/content/304/5673/995.short

![criterion](https://cloud.githubusercontent.com/assets/1441560/3182287/6078e4ea-ec4e-11e3-9987-b31b37b5cd3b.png)

The distance cutoff falls off with the H-bond angle (i.e. a bent bond has a shorter cutoff).

Since this will be used to investigate H-bond networks in water, I also implemented a periodic version of the `geometry.angles` function which takes advantage of the periodic features in `geometry.distance.displacement`.

I also implemented periodic versions of measuring dihedral angles although these are untested.