Merge pull request #713 from RosettaCommons/JWLabonte/sugars/loops2
CCD Loop Closure/Carbohydrates: making CCD work with polysaccharides
One of the main reasons I helped @weitzner refactor CCD last year (#51) was to set up a better framework that would allow one to close saccharide loops as well. However, there was still a collection of hard-coded assumptions deep in the code that prevented sugar loops from working with cut-point variants. This merge seeks to remove those assumptions, freeing the new CCD to do its job on carbohydrate loops, such as for the project I briefly described at the end of my talk at RosettaCON.
This merge also fixes some silent bugs regarding ring conformations.
All unit tests pass.
CCD and carbohydrates integration test changes expected.
code_duplication test is from new whitespace.
cppcheck was not functioning properly at the time of this merge.
hotspot_graph, place_siumltaneously, inverse_rotamer_remodel, and rs_loophash are all still broken.