rmcgibbo/mdtraj — pull request #218 by rmcgibbo (2013-11-27 07:01:14+00:00)
Title: Identification of hydrogen bonds

I'm not sure exactly how this compares to the procedure that @gkiss and @schwancr have used. This is pretty simple: it looks for donor-H...acceptor angles that are greater than 120 and H...acceptor distances that are less than 2.5 angstroms, which is the procedure that [Baker and Hubbard](http://www.sciencedirect.com/science/article/pii/0079610784900075#) (1984, 1442 citations) propose. They were mostly just looking at backbone hbonds, but instead I had this look at OH and NH donors, (and just O acceptors).

The hbonds that this criterion selects (as existing in at least 10% of the frames) in 2EQQ are annotated in this pymol file. They look pretty reasonable to my eye.

https://www.dropbox.com/s/oi410vimcxjq0s1/2EQQ_hbonds.pse

cc: #212