commit 5ecebcadacdf48ede3c1981444601bf1cd47ce0d
Merge: 47c74e9 c72d370
Date:   Fri Mar 23 13:02:49 2018 -0700

    Merge pull request #3055 from RosettaCommons/everyday847/stepwise_dna
    
    Stepwise on DNA residues

commit 47c74e92184177cd7c693475d00afcbe1df8ab68
Merge: 5714f50 d6cd4a5
Date:   Fri Mar 23 09:27:07 2018 -0700

    Merge pull request #3045 from RosettaCommons/aleaverfay/fix_jd3_out_path_all
    
    output path handling for structures written by JD3
    
    Pose outputters for JD3 now respect the -out::path, -out::path::all, and -out::path::pdb flags.
    
    Addressing issue brought up by @BYachnin: https://github.com/RosettaCommons/main/issues/3034

commit 5714f5086d5dfcddcda0e206e413d073f0dc8435
Date:   Thu Mar 22 18:59:55 2018 -0400

    beautifying

commit f73d86d0e0441daed9de7db9f2e811738e153554
Merge: 5d3c24d 849adaf
Date:   Thu Mar 22 00:10:59 2018 -0700

    Merge pull request #3051 from RosettaCommons/everyday847/disable_vanity_metapatches
    
    Disable vanity metapatches

commit 5d3c24d4dec54542535bd518a214cde1cd777f66
Merge: fd97e8f fe37bd2
Date:   Wed Mar 21 11:41:25 2018 -0700

    Merge pull request #3048 from RosettaCommons/everyday847/new_frags
    
    New fragment libraries

commit fd97e8f80c56a553e41a76cac26ff9e99469817b
Merge: d3889a5 b51792e
Date:   Wed Mar 21 08:40:31 2018 -0700

    Merge pull request #3046 from RosettaCommons/kalekundert/fix_fkic_itest
    
    Fix the kic_with_fragments integration test.

commit d3889a5133f0d37b7e12f09e670b1df8dadd3632
Merge: bccbde1 1293ddb
Date:   Wed Mar 21 01:52:55 2018 -0700

    Merge pull request #2866 from RosettaCommons/everyday847/cps_part_three
    
    Third part of cyclic peptide stepwise merge

commit bccbde17b1aac79d5baa3e19e85ad9d553472401
Merge: 83d537b 835a1e2
Date:   Tue Mar 20 19:36:02 2018 -0700

    Merge pull request #3049 from RosettaCommons/everyday847/python3_integration_tests
    
    Changes to integration test infrastructure needed for python3 compatibility

commit 83d537be1f0a6819688665e275c321b477c06bf6
Merge: be6f71a d4d2385
Date:   Tue Mar 20 11:07:11 2018 -0400

    Merge pull request #3033 from RosettaCommons/roccomoretti/release_unit_test_fix
    
    Fix remaining release-mode unit test issues
    
    Minor: Change real comparison epsilon in GeneralizedEigenSolverTests to be less stringent.
    
    Major: The Tracer set_ios_hook machinery was ostensibly insensitive to command line muting /visibility settings. However, the release-mode `operator<<` override triggers on visibility, and ignores if the ios_hook has been set. This results in a debug/release difference when `-mute all` is on.
    
    The agreed upon fix for the moment is to change the ios_hook machinery such that it obeys the command line mute/visibility settings. That is, output from muted/invisible channels will no longer be present in the attached ios_hook stream. (However, to maintain the behavior of -mpi_tracer_to_file, the (non-command line) supermute setting will still affect only the main tracer output, not the ios_hook output.)
    
    This change will probably not affect you unless you use the tracer redirection machinery in PyRosetta.

commit be6f71aff722fe3ce34d3bc0612b473f7d16df48
Merge: 602baaa f88cf84
Date:   Mon Mar 19 23:35:23 2018 -0700

    Merge pull request #3040 from RosettaCommons/vmullig/fix_bluegene_runtime_issue
    
    Fix a runtime issue on Blue Gene created by the new fconfig system
    
    The new fconfig system is now preventing program execution on the Blue Gene/Q system. (Note: this is not @jadolfbr's fault. The problem couldn't reasonably have been anticipated before the changes went into operation.) It seems that some systems don't allow certain system calls, and this creates an unhandled exception when Rosetta starts asking for home directories and whatnot. Adding a try/catch block to handle this.

commit 602baaa888793eb74ce02d69f751d84a3932f80c
Merge: fe2fae5 c5fd3f1
Date:   Mon Mar 19 16:40:01 2018 -0700

    Merge pull request #3039 from RosettaCommons/vmullig/fix_uninit_in_layerdesign
    
    Fixing an uninitialized variable in LayerDesign.
    
    One of the constructors failed to initialize use_symmetry_.

commit fe2fae5a616ec19a3da5e2998e4ce96a143ee8f8
Merge: ed1c7bb 8450def
Date:   Fri Mar 16 23:35:52 2018 -0700

    Merge pull request #3032 from RosettaCommons/kalekundert/layerdesign_nataa
    
    Make the behavior of <LayerDesign ignore_pikaa_natro="..."/> match the documentation.

commit ed1c7bbdca48fedd8df367b98916dafa2e4f65b8
Merge: 40643b8 7b0b442
Date:   Fri Mar 16 17:27:51 2018 -0700

    Merge pull request #3036 from RosettaCommons/ckrivacic/FragmentScoreFilter_test
    
    Fixed logic in calculating residue adjustment

commit 40643b8d3e22747d2137fa824ee71eb7dae74283
Merge: f135638 c710a96
Date:   Fri Mar 16 08:28:20 2018 -0400

    Merge pull request #3031 from RosettaCommons/JWLabonte/sugars/branching
    
    Carbohydrates: Fix bug when glycosylating with a core glycosylated glycan
    
    All units test pass. `KIC_with_fragments` and `rotamer_recovery` integration tests are broken. `carbohydrates` integration test change expected.

commit f135638771bd025482a82d132ee3545320c196fe
Merge: a844ffd 376bd1e
Date:   Thu Mar 15 14:00:51 2018 -0700

    Merge pull request #2991 from RosettaCommons/everyday847/better_sugar_sampler
    
    Better sugar sampler for stepwise

commit a844ffd8b1f1ddb549eb2810af34b9876595bd49
Merge: 7c7790f d29ac79
Date:   Wed Mar 14 13:20:45 2018 -0700

    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.

commit 7c7790fbb898f8210b54513b9f9c8a927c3e8d7f
Merge: a2a4869 e55fce7
Date:   Wed Mar 14 13:19:04 2018 -0700

    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.

commit a2a48692b0017415a667d18a1a8f61bb5477004a
Merge: 71bb4d1 5de1df8
Date:   Wed Mar 14 14:07:42 2018 -0400

    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.

commit 71bb4d194c07c7c154d6c26b74972d603f72a44f
Merge: 6a674f8 36b9d1a
Date:   Tue Mar 13 23:54:16 2018 -0700

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

commit 6a674f8a653c14e4ad7f396984c3088d1456153c
Merge: 4af647a 67eef61
Date:   Tue Mar 13 18:57:18 2018 -0700

    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`?

commit 4af647ae801c3aaa531691a38e1dbca1492b2881
Merge: 21590cd 6f5f168
Date:   Tue Mar 13 18:33:55 2018 -0600

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

commit 21590cde38fcdaee1a348202a139e5ac6920a8b0
Merge: ad5d013 f424a1d
Date:   Tue Mar 13 10:58:07 2018 -0600

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

commit ad5d013e54dcf6bb9cd108fd50cc6b0eae79bc99
Merge: a8ae485 4715be3
Date:   Tue Mar 13 12:26:37 2018 -0400

    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.

commit a8ae485b5d875235851f78a21fd770ef5eede24f
Merge: 61765b0 28f4d08
Date:   Mon Mar 12 18:02:51 2018 -0600

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

commit 61765b05afc76fd8f729f0fffb2bd03eab97f7f0
Merge: e2dad9e 40a7f33
Date:   Mon Mar 12 11:35:00 2018 -0700

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

commit e2dad9e4cc9271f26a23c04ab805ccd886c45857
Merge: 7cf04e0 f555e98
Date:   Sun Mar 11 16:35:25 2018 -0700

    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

commit 7cf04e02c9b3578bd19bb2d2e10a7ac70d34ce27
Merge: 526159d f76606b
Date:   Sun Mar 11 10:04:59 2018 -0500

    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.

commit 526159d4306343546b65a82162a17deb6bf5626f
Merge: a96e03a bf3d390
Date:   Sat Mar 10 19:23:18 2018 -0700

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

commit a96e03ac38e5d08c557dd48fc9394207a96ac937
Merge: c7e377c 7865c1a
Date:   Sat Mar 10 17:19:29 2018 -0700

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

commit c7e377c894b671f25f62f2204dc7d7ce93e8256a
Merge: e6def2c 1bcbd5b
Date:   Fri Mar 9 10:54:37 2018 -0800

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

commit e6def2c6b9904f76829d472694bc9f49925a2f96
Merge: 871667a a99f96c
Date:   Fri Mar 9 01:11:43 2018 -0500

    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.

commit 871667abbc00aee72c006feb9f5bd026a838bdab
Merge: bdd325a eea1114
Date:   Thu Mar 8 15:28:19 2018 -0600

    Merge pull request #3010 from RosettaCommons/jadolfbr/fix_integration_tests
    
    Fix 2 integration tests that were failing
    
    Fix integration test commands for `homodimer_fnd_ref2015_memb` and `fold_from_loops` that I broke with a missing letter in the `-testing:INTEGRATION_TEST` flag.

commit bdd325a0ef3d5d53deef57c12be5ebc859c47304
Merge: 1868c06 44a0bf1
Date:   Wed Mar 7 15:07:24 2018 -0700

    Merge pull request #3005 from RosettaCommons/benchmark
    
    Adding support for build.clean.* build tests.

commit 1868c062dd30d60e8d6dd41822f7ee81964b7886
Merge: cad6fe2 a45a76a
Date:   Wed Mar 7 08:50:19 2018 -0800

    Merge pull request #3002 from RosettaCommons/xingjiepan/fix_KIC_with_fragments_integration_test
    
    Xingjiepan/fix kic with fragments integration test

commit cad6fe20fc8f70205a00406615280896bf086bd6
Merge: f71adfc bedbd45
Date:   Tue Mar 6 16:15:27 2018 -0700

    Merge pull request #3003 from RosettaCommons/benchmark
    
    adding support for release-mode unit tests

commit f71adfc5e6476f6a19e9f7550c0c218e99b0a9e0
Merge: 529d335 5635df9
Date:   Tue Mar 6 14:01:09 2018 -0800

    Merge pull request #3001 from RosettaCommons/vmullig/fix_ubsan_tests
    
    Fixing ubsan unit tests.
    
    Initialization of a newly-added Boolean private member variable was omitted in two of the SetupForSymmetryMover's constructors.

commit 529d335a5417819986236595a131a4166c5c2149
Merge: 83d96e0 730ff21
Date:   Tue Mar 6 14:46:27 2018 -0600

    Merge pull request #2982 from RosettaCommons/jadolfbr/config
    
    Support for common Flag Config files
    
    This PR adds the ability for rosetta to find and read common flag config (fconfig) files.  This allows us to always run rosetta with a set of custom common options.
    
    If a file named `common` is found in `$HOME/.rosetta/flags` or if it/they are in the current working directory, we use that instead. You can set any number of flag configurations with the `-fconfig` option By default, we have:
    ```
       -fconfig common
    ```
    
     This is useful if you have a set of flags for different purposes - like design, glycans, and antibody, so you could do something like:
    
    ```
      -fconfig common antibody
    ```
    
     That would load both the common and antibody configurations.
    
    
     If you have a common flag file (which is loaded by default if present), you skip loading through an option
    ```
      -no_config
    ```
    
    * Note, `-no_fconfig` is used for both unit and integration tests.

commit 83d96e0611f48ccdf16dcf0f587b9ec6f3e92e59
Merge: 9cedfe5 530ca38
Date:   Tue Mar 6 10:55:41 2018 -0800

    Merge pull request #2988 from RosettaCommons/kalekundert/trajectory_log
    
    Add more sophisticated logging the the loop modeling protocol.

commit 9cedfe5655e1c222346ee120624c3508e841187b
Merge: 8b87010 5e293cd
Date:   Tue Mar 6 10:46:20 2018 -0800

    Merge pull request #2996 from RosettaCommons/kkappel1/quick_drrafter_fixes
    
    DRRAFTER setup and error estimation

commit 8b870108d95f4a80f55e6d37fb0229b19783d6ec
Merge: f6c0e78 8f4cf1c
Date:   Mon Mar 5 14:42:55 2018 -0800

    Merge pull request #2994 from RosettaCommons/vmullig/correct_flag_error
    
    Promoting warning about -correct flag to an actual error.
    
    Users have been using the `-correct` flag with `ref2015` without realizing that this results in invalid behaviour.  The warning message is easily missed.  This promotes it to an error, so that they can't use it accidentally.
    
    A small handful of score12-era integration tests were also still using the `-correct` flag despite having been updated to use `ref2015`.  These now correctly do _not_ use `-correct`.  This will result in some integration test changes.

commit f6c0e7850caa749e775099b04f6ca482304ffb8a
Date:   Sat Mar 3 00:31:41 2018 -0500

    RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

commit 3004378785eb3bb85212a7151e50c72df14e6ee6
Merge: 14b89c6 a2971c8
Date:   Thu Mar 1 22:29:55 2018 -0800

    Merge pull request #2985 from RosettaCommons/everyday847/fix_farnesyl
    
    Fix integration test timeout (farnesyl)

commit 14b89c6db7ee507717a5a4e40e46a80bd18099ca
Merge: 45270ac 06c8a55
Date:   Thu Mar 1 18:44:18 2018 -0800

    Merge pull request #2986 from RosettaCommons/vmullig/fix_rotamertrials_unit_test
    
    Correct RotamerTrials unit test
    
    The RotamerTrials unit test was taking the sin and cos of values that were in degrees rather than in radians. Correcting.

commit 45270ac00bcad4f19b7914b2f54a2dc66b00f437
Merge: dbb9263 9dfc695
Date:   Thu Mar 1 15:23:45 2018 -0500

    Merge pull request #2971 from RosettaCommons/jtseffer/RosettaResidue
    
    jtseffer/RosettaResidue

commit dbb92630d3f7df2ecd291cde4758d814258a90fa
Merge: a9e5692 e544593
Date:   Thu Mar 1 10:47:15 2018 -0800

    Merge pull request #2970 from RosettaCommons/xingjiepan/improve_loop_modeling
    
    Xingjiepan/improve loop modeling

commit a9e56925cc403bd0438fb55b19ae5924c44a49b1
Merge: 290a1e2 d84ac55
Date:   Thu Mar 1 10:12:25 2018 -0500

    Merge pull request #2980 from RosettaCommons/mpacella88/print_atom_pair_energies_pyrosetta
    
    adding print methods to supplement the etable_atom_pair_energy pyrosetta tool

commit 290a1e26f1aafa3975a62f3e4aeca4a09f948552
Merge: 333d996 1bccbdc
Date:   Mon Feb 26 15:00:02 2018 -0800

    Merge pull request #2943 from RosettaCommons/sboyken/fix_rna_intra_issue_in_numhbondcalc
    
    fixing NumberHbondsCalculator for DNA and RNA