P4-P6 stepwise_design benchmark

[rhiju]

@calebgeniesse i can't find a branch where you have the work that you did with meghan to create a benchmark for stepwise_design of all motifs for P4-P6, from summer 2015. I want to kick off some big runs for the j5/5a redesign, and also use these as test cases for the 'interstitial' variable loop length design.

Can you get your/meghan's stuff into a pull request?

Or, if you don't have a branch, can you send me a directory on biox3 where I can figure out the target information? I can do the commit myself.

[calebgeniesse]

@rhiju the design work was done on my calebgeniesse/swa_revival branch, which I have renamed to calebgeniesse/devel. I also renamed the setup file setup_motifs.py to setup_parsed_motifs_info_file_from_pdb.py for clarity.

I can work on getting all of this into a pull request, however it will take some refactoring--my branch has diverged quite a bit from master as I started implementing a more object-oriented setup and unit tests awhile back!

I think getting this into master should be one of the goals of a more generalized, overall re-factor of this code base into a more modular/reusable class-based and unit tested framework early 2016.

In the meantime, I can show you how to use the current design setup code in calebgeniesse/devel!