Chainbreak Scoring: Enabled chainbreak scoring for carbohydrates
NEWS:
* Added cutpoint variants for sugars
* Refactored ChainbreakEnergy
- Made work with cutpoint variants that do not require 3 overlapping points
- Removed duplicated code
- Added lots of explannatory comments
* Refactored add_cutpoint_variants() and add_single_cutpoint_variants()
- Removed duplicated code
- Enabled to work with sugars
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Unit test status: Pass
Integration test status: 25
rings:
change in number of ResidueTypes reported
inverse_rotamer_remodel, loop_creation, antibody_graft, SnugDock,
hybridization, mr_protocols, antibody_legacy, antibody_H3_legacy,
remodel_disulfides, remodel:
cosmetic output changes
swa_rna_gaga_23_append_and_kic_close,
swa_rna_gaga_22_prepend_and_kic_close,
swa_rna_gaga_10_append_and_ccd_close,
swa_rna_gaga_18_rebuild_bulge:
strange output of "10 BulgeApplier" in new (huh?)
10 other loop-related tests:
trajectory changes (I don't THINK I broke anything here, as the unit
tests for ChainbreakEnergy and all loop and closure unit tests passed,
and I had another set of eyes double check my work; however, if you
are concerned, please e-mail me. I did slightly change the logic of
ChainbreakEnergy, but only in a way that should make a difference in
results in a specific case I do not believe can ever happen with any
ResidueTypes currently in Rosetta -- or ever likely in Rosetta. I am
of course willing to revert if needed.)