Merge pull request #5308 from RosettaCommons/Rosetta/trRosetta_into_Rosetta_incremental_merge_1
Incremental merge 1 for trRosetta integration into Rosetta
This PR attempts to pull the basic trRosetta calculator functionality (the `trRosettaProtocolBase` and `trRosettaProtocol_v1` classes) into their own pull request, along with all the test files for this base functionality, while leaving the mover and constraint generator (and all of their tests) for a later pull request. It is intended to be merged before pull requests #5119 and #5309.
As a guide, the infrastructure in basic in this image is already in master. This PR adds the stuff in protocols.2. Subsequent PRs will add the stuff that's higher up.
