plot updates and organized some files. protein.cpp needs to be updated to print relevant files (membrane.dats, out files etc) in the appropriate directories
removed emacs junk
updated protein.cpp to reflect new file printing locations. not yet tested.
more fixes to protein.cpp printing
fixed segfault issue
changed shoe_area_rating.py
Merged with Rene and added a totally different file structure. Merge branch 'master' of https://github.com/renezeto/protein

Conflicts:
	protein.cpp
	pyplots/extrema.py
	showatp.py
git pickup added to data directories
more stuff
.
Merge branch 'master' of https://github.com/renezeto/protein