Merge pull request #10 from jeffschulte/master

New
Merge pull request #11 from jeffschulte/master

new stuff
extrema.py debugging
extrema.py
extrema.py working, but vector scaling is strange.
working plot
extrema.py and time_map.py updated to save loaded figure automatically for natp
made shell script which will run extrema.py, time_map.py, show_area_rating.py to save the plot figures in the appropriate locations. this shell script takes the usual command line parameters, so we can edit the make file to run the shell script for each interesting simulation we want to save
And here's the makefile. type make plots
includes catalog.txt change
updating
now protein will only print to catalog.txt if it finishes the simulation (which is better).
catalog.txt bug fix
added area_rating flag. type a 7th command line argument equal to 1 to flag that you only want to compute area rating
began work on a microscopy version of the code.
working so far
working microscopy printouts and updated Makefile
microscopy view files will print starting with m_
moved common file loading to a module
brand new working file loader. easier to change things. vfield.py needs to be update (will do later today) but extrema, time_map, showatp are all working. plots now also look at the other 3 protein types we've been neglecting till now