A recapitulation of Willy Wriggers' and Klaus Schulten's Hingefind algorithm in 
python. This script also makes use of the prody API and Christoph Gohlke's 
transpformations.py . Mostly because I want to be able to run the hinge 
calculation over a trajectory outside of VMD. The script can take domain numbers
as arguments (as in the original hinge tcl function) or if VMD atom selections 
if you don't want to run the domain finding component.

USAGE
- Running with no arguments calculates the hinge-bending angle between domains
  1 and 2 of 1lfg/h (with domain 2 as mobile) as used in the original script.

- To determine the hinge-bending angle between domains 0 and 1 of 1lfg/h:
	(-d2 is mobile)
	> hingefind.py  -d1 0 -d2 1 -e 1 -m 1lfg.pdb -r 1lfh.pdb 

- To determine the hinge-bending angle between domains using atom selections:
	> hingefind.py  -d1 "resid 5 to 85 87 88 90 91 251 to 293 295 to 302 304 to
	 332 685 687 to 689 691 and name CA" -d2 "resid 92 to 100 104 to 140 143 to
	 218 220 to 250 and name CA" -e 1 -m 1lfg.pdb -r 1lfh.pdb

- How to calculate the hinge-bending angle over a trajectory:
	> hingefind.py -s ionized.pdb  -d1 0 -d2 1 -e 1 -m open.pdb -r closed.pdb 
	 -s ionized.pdb -t trajectory.dcd

	- Note: Inputs for -m and -r are used for the domain-finding. The results 
	  are then applied to the inputs for -s and -t

REFERENCES/APIs
- Hingefind original:
	http://biomachina.org/disseminate/hingefind/hingefind.html
	doi: 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J,

- ProDy:
	http://prody.csb.pitt.edu/
	doi: 10.1093/bioinformatics/btr168

- transoformations.py:
	http://www.lfd.uci.edu/~gohlke/code/transformations.py.html
	https://github.com/malcolmreynolds/transformations.git