Merge pull request #3029 from RosettaCommons/vmullig/tweak_icc_compile_settings Adding compile settings for icc+serialization and icc+cxx11thread extras. This should allow compilation of rosetta_scripts_jd3 with MPI/serialization/threading support with the Intel compiler.

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Merge pull request #3025 from RosettaCommons/vmullig/update_ncaas Adding properties and BACKBONE_AA to some NCAAs. It should now be possible to score all L-alpha-amino acids with ref2015, provided the params files have either BACKBONE_AA lines or mainchain potentials defined. This pull request aims to update some params files with PROPERTIES and BACKBONE_AA lines. It also updates the H and O atoms so that they depend on the lower and upper connections, respectively.

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Merge pull request #3008 from RosettaCommons/JackMaguire/MCHBNetCorrection (MC HBNet) Cleaning up my own development mess While developing MC HBNet, I created a set of graph classes: - HBondGraph: Stores hbond info between rotamers at a residue-residue level - AtomLevelHBondGraph: Stores hbond info between rotamers at an atomic level (nodes are still rotamers but each edge contains info about the atoms that participate in hbonds) - LKAtomLevelHBondGraph: Similar to AtomLevelHBondGraph but contains extra info for bridging waters. - AbstractHBondGraph: base class for all of these graphs. It turns out that this polymorphism is completely unnecessary. AtomLevelHBondGraph is the only one that is used anywhere in Rosetta and there is not enough extra info required for bridging waters to require a new class. LKAtomLevelHBondGraph never made it into master but the other 3 did. The goal of this PR is to wipe out HBondGraph and AbstractHBondGraph leaving only AtomLevelHBondGraph. Most of the changes in this PR are erasing the traces of HBondGraph and AbstractHBondGraph I also am using this PR to do a bit of housekeeping: - commented out a few unused `#include`s in HBNet.cc and sorted the remainders to make it easier to read (mostly my fault because I originally put all of the MC HBNet `#include`s in their own section). - Added a `boost::unordered_object_pool` for AtomLevelHBondNode creation.

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Merge pull request #3014 from RosettaCommons/kkappel1/drrafter_bugfix DRRAFTER updates and integration tests

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Merge pull request #3026 from RosettaCommons/vmullig/serialize_sequence_constraints Add serialization support for sequence constraints I currently can't use sequence constraints with RosettaScripts-JD3 because I forgot to add serialization support. Fixing this. @aleaverfay -- Is it possible to get serialization tests for classes that derive from `Constraint`?

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Merge pull request #3027 from RosettaCommons/sergey/binder updating bindings for `std::list`, adding conditional bindings for `remove` function

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Merge pull request #3024 from RosettaCommons/sergey/binder adding bindings for std::list

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Merge pull request #3021 from RosettaCommons/BYachnin/fix_EnzScore_filter_bug Fix EnzScore filter bug A recent refactoring of the EnzScore filter code caused get_ligand_id to be called whenever res_num or pdb_num were not provided. This normally does not pose a problem, but if the pose is too complex for get_ligand_id to work, execution would fail even if whole_pose=1 or cstid was specified (i.e. there is no need to determine resnum because the whole pose is being examine or it is being specified via cstid). This fix causes the get_ligand_id code to be executed only if whole_pose=0, cstid="", and res_num/pdb_num are not provided, resolving the issue. Failed tests (KIC_with_fragments and rotamer_recovery) are pre-existing and unrelated to this merge.

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Merge pull request #3022 from RosettaCommons/revert-2892-weitzner/pymol-pyrosetta-link Revert "Update PyMOL<–>Rosetta link to be python 2/3 compatible"

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Merge pull request #2995 from RosettaCommons/ckrivacic/FragmentScoreFilter_test Ckrivacic/fragment score filter test

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Merge pull request #3019 from CyrusBiotechnology/forcommons_recentmaster/smlewis/coupledmoves_segfault CoupledMovesProtocol segfaults if you pass no design mutations; fix that: now CoupledMovesProtocol throws an informative exception that you are required to have at least one designing position. Also the tracer name is wrong; I fixed that. Cosmetic itest changes from the tracer name change expected. * beautification issue is in OptionCollection.cc; not part of this PR; currently separately reported as a problem on Slack * integration tests: KICfrags has a timing element present, noise failure. rotamer recovery is crashing both before and after. coupled_moves is cosmetic as expected. * profile tests: it's fine if you look at it, they're just noisy

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Merge pull request #2953 from RosettaCommons/jadolfbr/ab_integration Small Antibody_H3 and SnugDock updates - Add setPoseExtraScores run to `InterfaceAnalyzerMover`(IAM) if calling non-const apply. This enables their output into the proper score file. - Add running of `IAM` for `Antibody_H3` and `SnugDock` protocols if an antigen is present. - Enable option `-run_snugdock` at the end of `Antibody_H3` for final models if needed.

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Merge pull request #3016 from RosettaCommons/sergey/binder updating PyRosetta build system so it better detect cases when CMake needs to be re-run

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Merge pull request #3015 from RosettaCommons/sergey/ui merging latest version of ui workbench app

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Merge pull request #2983 from RosettaCommons/yhsia/register_CloseContactResidueSelector Register CloseContactResidueSelector

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Merge pull request #2533 from RosettaCommons/mlnance/carbohydrates/fixing_SmallMover_for_sugar_use Carbohydrates: Fixing major bug in SmallMover Finally merging a resolution to issue #2506... This merge also introduces a `get_non_NU_TorsionID_from_AtomIDs()` function. All unit tests pass. `KIC_with_fragments` and `rotamer_recovery` appear to be broken. `dock_glycan` changes expected.

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