Added a bunch of stuff

I think we shouldn't use a global class, seems kind of shitty
programming but we'll see.
Also every struct is just a collection of variables, we should just make
those inner classes i think, and there own file if they are used in more
than one file.
Added more class and some basic functionality

Still don't understand metapop class. And SS_Type is coming up
everywhere, it is an integer, and stands for Secondary  Structure type,
but I still don't quite get it.
Merge pull request #2 from germoose/master

Added a bunch of classes and objects and stuff, not much functionality thought