new setup.py
added the sampled longrange stats
Added stats files
Minor setup file change
Speed testing
Speed improvements
Fixed the perloop energy to work with sequences with just one loop and moved the average atom positions script to forgi
Removed a ton of command line options
Removed a bunch of old energies
Removed some comments
Align fragments and replace all but the first base
Moved reconstruct_element to reconstructor.py
Fixed the loading of sampled fiveprime and threeprime regions
Mostly working CCD reconstruction.
Moved some test files
Added a test file and replaced choice with random.choice
Replaced teh stem_defs, angle_defs, etc... with one single elem_defs in forgi.builder.models