rmcgibbo/mdtraj — pull request #522 by leeping (2014-08-02 22:43:43+00:00)
Title: Add ability to get hydrogen bond lists from baker_hubbard.

I tried the baker_hubbard criterion to get a listing of hydrogen bonds, and in some ways it's better than the wernet_nilsson criterion (the latter identifies more H-bonds, such that I end up with a mean that's higher than the normal by about 0.2).

This PR doesn't change the way `baker_hubbard` works but moves most of its code into `baker_hubbard_internal`. The `baker_hubbard_list` function does what I want (i.e. get a list of hydrogen bonds for each frame).

I also fixed a bug where it would crash if there are no NH hydrogen bond donors (the case for water).

Thanks,

- Lee-Ping