Revert "Carbohydrates: adding most of the PDB 3-letter codes for sugars" This reverts commit b0e4edf8d9e52c739324f240651b3da2ffa41123.

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Merge remote-tracking branch 'origin/master'

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Carbohydrates: adding most of the PDB 3-letter codes for sugars database changes only All unit tests passed. No integration test changes.

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Merge pull request #560 from RosettaCommons/jkleman/fix_int_tests fixing integration tests for mp_quick_relax and mp_mutate_relax and renamed test from mp_quickrelax to mp_quick_relax to be consistent with exe and all else

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Merge pull request #561 from RosettaCommons/vmullig/perturb_torsion Add a "perturb" option to the SetTorsion mover Currently, the mover lets you set a torsion value, or randomize it completely. A "perturb" option will let the mover take an existing torsion value and add a small random value to it. Tasks: Fix uninitialized variables in this mover. Update comments in this mover. Add the perturb functionality, with support for uniform or Gaussian perturbation. Add RosettaScripts hooks. Add an integration test. Update documentation. Debug.

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Merge pull request #558 from RosettaCommons/dougrenfrew/tcre_energy_methods_clean Adding a two-component reference energy (TCRE, a.k.a. split unfolded) term. It is intended to serve as a replacement for the unfolded term and should be applicable for the design of alpha/beta/gamma-peptides, peptoids, OOPs, HBSs, and other NCBBs as it is evaluated based on atom type composition. Riley and Andy have contributed this greatly.

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Merge pull request #559 from RosettaCommons/kimdn/inte [update of SandwichFeatures] better dependency definition (for format_converter) revived integration test for SandwichFeatures better tracer for unit test

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Adding Jason as observer to code_duplication integration test

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Adding Andy as observer to code_duplication integration test

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Merge pull request #543 from RosettaCommons/JWLabonte/sugars/input PDB Input/Output: Allowing for alternative 3-letter codes This will allow Rosetta to handle alternative 3-letter codes, a list of which are provided in simple text files. Usage of this new feature is described on our user-facing documentation wiki here: http://www.rosettacommons.org/docs/wiki/Preparing-PDB-files-for-non-peptide-polymers#Alternate-3-Letter-Codes-Files Thank you to all those who provided feedback during the pull request process! :rat: Testing: All unit tests passed, with the exception of a PyRosetta unit test, which I've seen randomly fail in the past. If it turns out it was something I did after all, I'll revert. carbohydrate integration test change expected: renamed an atom type and added loading of sugar with GLYCAM 3-letter codes as an example/test code_duplication test change expected: deleted commented-out code, thus changing reported line numbers of duplications All other tests were already broken.

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Merge pull request #557 from RosettaCommons/kimdn/sw_unit [update of SandwichFeatures] - added unit test - much better dependency definition (3 features are required) - clearer comment in integration test

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Merge pull request #547 from RosettaCommons/chnorn/seqprofcon Chnorn/seqprofcon

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Merge pull request #556 from RosettaCommons/vmullig/fix_fragment_filter Fixing the FragmentLookupFilter's unstable behaviour The FragmentLookupFilter had a number of uninitialized variables in its default constructor. I was scratching my head as to why it seemed to work some of the time and not other times until I figured this out. No test changes expected (or seen when the branch was tested), except for the currently-unstable integration.mpi test that I still need to fix.

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Merge pull request #551 from RosettaCommons/mpacella88/centroid_carbohydrate_atom_types adding carbohydrate atom types to the centroid atom type set This is a database-only change so I have only performed integration testing. Outside of the broken membrane tests the only changes that occur involve printing of the the newly added atom types from the core.chemical tracer.

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Adding post-processing to Simian output. This should make code_duplication test results more stable.

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Merge pull request #555 from RosettaCommons/BridgeChainsMigration Rename ConnectJumps mover to "BridgeChains" and migrate it from devel

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