Merge pull request #924 from RosettaCommons/rhiju/bps_updates
Rhiju/bps updates
+ needed for farna renovation (which will be a separate pull request), and for use of base pair steps in various RNA modeling applications in Das lab.
+ changes to stepwise integration tests appear to be due to a numerical instability induced by different compiler optimization of protocols.d_5 code. Evidence for this being a negligible instability is in .swa_rna_gagu_10_prepend_and_ccd_close (where a number z = 5.89095e-14 changes to z = 5.33868e-14).
+ unit test for -extra_res_fa failed, but is getting fixed in Andy's pull request #943.