commit b1dc16ff17da7a38b52c000abb74f85e4f0333c8
Merge: 9af87c1 57ae7b8
Date:   Wed Oct 25 13:12:29 2017 -0700

    Merge pull request #2648 from RosettaCommons/fordas/calculatorfilter_on_reported
    
    Update CalculatorFilter to bind reported filter values.

commit 9af87c136a6c82aa65ef85c82aa49ae0793505d1
Merge: 25b1abe 2289827
Date:   Wed Oct 25 13:11:48 2017 -0700

    Merge pull request #2646 from RosettaCommons/fordas/cmake_install
    
    Add support for cmake "install" commands with proper rpath handling.

commit 25b1abed01dfb7bae9cdc2caf56566f3cdf3f822
Merge: b72060b 703d3b0
Date:   Wed Oct 25 12:55:19 2017 +0300

    Merge pull request #2525 from RosettaCommons/orlypolo/head-to-tail-cyclization-filter
    
    Orlypolo/head to tail cyclization filter

commit b72060b9f43e09203fc73cab1b731350682bfab5
Date:   Tue Oct 24 15:27:01 2017 -0700

    @bcov77 told me to.

commit a839499eeb68792494157673a05d05f42a4a0409
Date:   Tue Oct 24 16:28:56 2017 -0400

    Fixing Binder submodule

commit 01a1b3a30f9a9fb769505de8b3857b6b97967c59
Merge: e3c3799 0a021f7
Date:   Tue Oct 24 10:32:27 2017 -0700

    Merge pull request #2657 from RosettaCommons/bcov/NeighbohoodUpdateGraph
    
    NeighborhoodResidueSelector clone/update_residue_neighbors() + some util functions

commit e3c3799a02dde3f1f6184cf90d3cd0802945fca4
Merge: ea5610f 3575089
Date:   Tue Oct 24 10:31:17 2017 -0700

    Merge pull request #2500 from RosettaCommons/bcov/JoinEmptyCheck
    
    Added empty() check to templated utility::join() functions

commit ea5610feafd9eaf517c6879d499d57041e0eae33
Merge: f44f45d a45d7a4
Date:   Tue Oct 24 13:14:50 2017 -0400

    Merge pull request #2661 from RosettaCommons/aleaverfay/add_no_sc_to_ia_option
    
    Avoid shape complementarity calculation due to crash in InterfaceAnalyzer
    
    Shape-complementarity score is reliably crashing on my cluster, but works fine
    on my workstation, so I am adding a short circuit in the interface analyzer:
    put "-compute_interface_sc false" on your command line to skip that calculation.
    
    I'm trying to debug the problem, but valgrind is turning up jack squat. In the mean time, I need InterfaceAnalyzer to work.

commit f44f45d89d204553bd7074af9b580e3c9c214c12
Merge: 6ebc318 48da2c4
Date:   Mon Oct 23 12:28:39 2017 -0700

    Merge pull request #2398 from RosettaCommons/vmullig/energy_based_clustering
    
    Make "bettercluster" (now "energy_based_clustering") into a public app in anticipation of publication
    
    Tasks:
    - [x] Move to public apps.
    - [x] Rename to "energy_based_clustering" (internally, too).
    - [x] Add copyright info.
    - [x] Correct tracer names.
    - [x] Move bulk of functionality to protocols.
    - [x] Trim app down to a bare-bones thing that calls functionality in protocols.
    - [x] Move options to `options_rosetta.py`.
         - [x] Add to options_rosetta.py.
         - [x] Remove from app.
         - [x] Update app to take an options object, with option to set from global options system.
    - [x] Disable PCA analysis for now.
    - [x] Check generality -- there may be old hard-coded assumptions about mainchain torsion names, _etc_.
    - [x] Unit tests.
         - [x] Cyclic alpha/oligourea peptide, Cartesian-based clustering.
         - [x] Cyclic alpha/oligourea peptide, dihedral-based clustering.
         - [x] Cyclic alpha/oligourea peptide, with symmetry, Cartesian-based clustering.
         - [x] Cyclic alpha peptide, Cartesian-based clustering with cyclic permutations.
         - [x] Cyclic alpha peptide, dihedral-based clustering.
    - [x] Integration test -- cyclic peptides.
    - [x] Integration test -- torsion-based clustering.
    - [ ] Documentation.
    - [x] Beauty.
    
    Note: the `vmullig/oligourea` branch has been merged into this branch.  As such, pull request #2528 must be merged before this one -- DONE.
    
    For the future:
    - Check that this works for Jacob's test cases (fragments of proteins).
    - Check that this works for Christine's test cases (linker-containing peptides).
    - Check that this works for Parisa's test case (which caused a segfault before).
    - Check that this works for Tim's test cases (N-methyl amino acids).

commit 6ebc31814c624b26b02be7c70aea2110a9ca5a61
Merge: edcb86b 406eb4c
Date:   Sun Oct 22 15:03:20 2017 +0300

    Merge pull request #2658 from RosettaCommons/orlypolo/remove_cst_handling_fpd
    
    Fixing bug in FlexPepDock where low-resolution constraints were overr…

commit edcb86b354698d7a2704a5dc216b1f0f8a0bcfc6
Merge: 6ba1344 0f65cc2
Date:   Sat Oct 21 17:38:53 2017 -0700

    Merge pull request #2655 from RosettaCommons/vmullig/fix_oligourea_design_test
    
    Fix oligourea_design integration test
    
    The SCORE lines in the output silent file currently contain timing information. They ought not to. Andy pointed me to the -run:no_prof_info_in_silentout flag to disable this. (Thanks, Andy!)

commit 6ba134477d6b49324b90a289b70d660ea748c5f3
Merge: dd5c89f b9cd9c2
Date:   Sat Oct 21 16:18:35 2017 -0700

    Merge pull request #2652 from RosettaCommons/xingjiepan/loophash_kic_keep_aa_identity
    
    Add an option loophash_seqposes_no_mutate to the LoopHashKIC

commit dd5c89fddcb3a0d7f3d33ab94051a66c44b61ff3
Merge: a0da70d e783d36
Date:   Sat Oct 21 10:39:31 2017 -0500

    Merge pull request #2640 from RosettaCommons/roccomoretti/JobOutputterFactoryFix
    
    Fix issue with missing mmCIFJobOutputter
    
    For score_jd2, the mmCIFJobOutputter case wasn't being called, due to copy-paste coding.
    Centralize the JobOutputter logic, to coordinate these two cases.

commit a0da70d9774be13889b606d2f62541d44d74d5ae
Merge: d401348 4f76769
Date:   Fri Oct 20 16:27:18 2017 -0500

    Merge pull request #2563 from RosettaCommons/roccomoretti/compound_filter_details
    
    Permit CompoundFilter to give more info about which subfilters are failing/succeeding.
    
    To do this with minimal user-facing perturbation, I had to reorganize how the confidence value was treated in FilterFactory (basically, remove the usage of CompoundFilter there).
    
    This also involved overhauling the StochasticFilter -- the semantics of StochasticFilter were messed up as a side effect of how the confidence value was being treated. I regularize/rationalized the StochasticFilter interface, then added the ability to run a subfilter on StochasticFilter success/failure, and re-did the FilterFactory to use that directly, rather than the StochasticFilter/CompoundFilter approach it used before.
    
    Unit tests for StochasticFilter and FilterFactory were added, to make sure I got things right. Some slight trajectory changes in integration tests, as this change reduces the number of random number draws in the `confidence="0"` case.

commit d401348297bf53da64a5ad7de6c7b66939d77872
Merge: f251fb4 9598b31
Date:   Fri Oct 20 14:51:42 2017 -0400

    Merge pull request #2623 from RosettaCommons/BYachnin/set_catalytic_respack_behavior_xsd
    
    Added XSD info for SetCatalyticResPackBehavior
    
    Failed tests are almost surely due to other commits to master that have changed several integration tests.

commit f251fb45de855c63c72732adaca6c6c602c47ea4
Merge: d4ba49d b36261a
Date:   Fri Oct 20 10:14:16 2017 -0400

    Merge pull request #1987 from RosettaCommons/dougrenfrew/nterm_proline_hydrogens
    
    Change ICOOR for Nterminal hydrogens for proline and proline-analogs.
    
    This results in quite a few integration test changes, 35 on my machine and 38 on the test server. All of them are either cosmetic changes from the modified patches, trajectory changes as a result of having Nterminal prolines in input files or allowing them during the trajectory (e.g. during design), or are round off differences.

commit d4ba49d86cd699e34cee232161c3b75e0857a366
Merge: 3ab8e95 7cd5fcf
Date:   Thu Oct 19 18:52:24 2017 -0700

    Merge pull request #2645 from RosettaCommons/fordas/ndarray_const_fix
    
    Fixup ndarray const -> numpy writable flag conversion.

commit 3ab8e9578ccdf89c13d1df094dc6891bbdbf6222
Merge: d2ee9c8 046efae
Date:   Thu Oct 19 17:09:55 2017 -0700

    Merge pull request #2641 from RosettaCommons/danpf/ninja_test
    
    Fix release_static build for cmake

commit d2ee9c8378b838a5c302545a1085c480d1ad9731
Merge: a9b5e8f 35db640
Date:   Thu Oct 19 14:37:18 2017 -0700

    Merge pull request #2619 from RosettaCommons/hahnbeom/iterhyb_update
    
    Hahnbeom/iterhyb update

commit a9b5e8f23430a5b99185d305e9b64c5c60bcd4ae
Merge: 435da8e 3ea6139
Date:   Thu Oct 19 12:06:13 2017 -0700

    Merge pull request #2638 from RosettaCommons/bfrenz/no_lower_glycan_term_w_MissingDensityToJump
    
    don't add lower terminus types glycans when using missing density to jump.

commit 435da8e18ebdfd7ae9edcc8f747ce3d73a3737cf
Merge: a0a8514 f70b881
Date:   Thu Oct 19 11:54:06 2017 -0700

    Added a few minor fixes to the BOINC build.

commit a0a8514b07a4be6970dc1db73325037232841efe
Date:   Thu Oct 19 11:52:15 2017 -0700

    Added a few minor fixes to the BOINC build.

commit afd5dcfe3d4d1807e754ca693b4720bb10ce4c2f
Merge: 3afebce 4b0d732
Date:   Wed Oct 18 15:14:57 2017 -0600

    Merge pull request #2639 from RosettaCommons/sergey/binder
    
    Refactoring PyRosetta build so it now avoid copying database files. Updating PyRosetta package, adding symlink creation for pyrosetta and rosetta dirs so PyRosetta and scripts(like self-test.py) could be run in package unpacked location in-place, without need to install PyRosetta first.

commit 3afebce18f835f0815f602e47266b7564302980b
Date:   Wed Oct 18 14:12:38 2017 -0400

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

commit 57ab09b04ac7a81a50256cfecc15f7abce9c8cbe
Merge: 017d70a df82161
Date:   Wed Oct 18 11:10:52 2017 -0700

    Merge pull request #2528 from RosettaCommons/vmullig/oligourea
    
    Add support for oligoureas in Rosetta peptide design and structure prediction
    
    These resemble beta-amino acids, but with a urea linkage to the next amino acid instead of a simple amide bond.
    
    @twcraven
    
    Tasks:
    - [x] Add `OLIGOUREA` property.
         - [x] Convenience functions in `ResidueType` class.
         - [x] Torsion specifications in `Pose` class.
         - [x] Add to the horrible `Conformation::backbone_torsion_angle_atoms()` function... ugh.  (At least I'll have it call another function for oligoureas, so that it's not more mess in that function.)
         - [x] Some new unit tests for `Conformation`.
    - [x] Update relevant patches:
         - [x] NtermProteinFull.
         - [x] CtermProteinFull.
         - [x] N-terminal acetylation.
         - [x] C-terminal methylation.
         - [x] Cutpoint variants.
    - [x] Update `SmallMover` to support oligoureas.
         - [x] Unit test.
         - [x] Document this.
    - [x] Update `pro_close` energy to support OU3_PRO.
         - [x] Unit test.
         - [x] Document this.
    - [x] Update `OmegaTetherEnergy` to support oligoureas.
         - [x] Unit test.
         - [x] Unit test: minimization.
         - [x] Document this.
    - [x] Update CycpepSymmetryFilter to support oligoureas.
         - [x] Document this.
    - [x] Add oligourea mainchain potentials.
         - [x] Update mainchain potential class so that it can be applied to a subset of mainchain torsions.
         - [x] Unit test.
    - [x] Add oligourea params files.
         - [x] OU3_ALA.
              - [x] Update peptide bond geometry.
         - [x] OU3_PHE.
         - [x] OU3_ILE.
         - [x] OU3_LEU.
         - [x] OU3_PRO.
         - [x] OU3_VAL.
         - [x] Update peptide bond geometry in all of the above.
    - [x] Add oligourea mainchain potentials.
         - [x] For OU3_ALA.
         - [x] Unit tests for mainchain potential with 3 mainchain torsions.
         - [x] For OU3_PRO.
    - [x] Add oligourea rotamer libraries to Git LFS repository.
    - [x] Update `simple_cycpep_predict` to allow oligourea prediction.
    - [x] Integration test: `simple_cycpep_predict`.
    - [x] Integration test: oligourea design.
    - [x] Address points in comments below: make it possible for rotamer libraries to be dependent on a subset of mainchain torsions.
    - [x] Documentation: `simple_cycpep_predict`.
    - [x] Beauty.
    
    Put off to a future pull request:
    - Unit test: cyclic geometry.
    - Unit test: mirroring.
    - Add additional oligourea params files.
         - OU3_AIB.
         - OU3_CYS.
         - OU3_ASP.
         - OU3_GLU.
         - OU3_GLY.
         - OU3_HIS.
         - OU3_LYS.
         - OU3_MET.
         - OU3_ASN.
         - OU3_ORN.
         - OU3_DAB.
         - OU3_DAP.
         - OU3_GLN.
         - OU3_ARG.
         - OU3_SER.
         - OU3_THR.
         - OU3_TRP.
         - OU3_TYR.
         - Update peptide bond geometry in all of the above.
    - Add additional oligourea mainchain potentials.
         - For OU3_AIB.
         - For OU3_GLY.
         - Symmetry unit tests for OU3_GLY, OU3_AIB.

commit 017d70acf70552f753b3bd051280bdc3a8a62b86
Merge: cfc97a6 be8819d
Date:   Wed Oct 18 08:48:12 2017 -0400

    Merge pull request #2635 from RosettaCommons/JackMaguire/MPIWorkPoolJobDistributor_refactor_corrections
    
    Increased std::string usage efficiency in MPIWorkPoolJobDistributor

commit cfc97a69b5f9576c6f606e3d32ad2c4c2a335f8a
Merge: 1e388b8 754f919
Date:   Tue Oct 17 16:30:11 2017 -0600

    Merge pull request #2627 from RosettaCommons/sergey/binder
    
    Adding function to set/get Path* options in PyRosetta. Refactoring PyJobDistributor so it works more reliably on filesystem with caching. Adding option to write compressed PDB files. Adding JD unit tests.

commit 1e388b8004e2f8eaef85e023905217d8cec7610a
Merge: cd901cc 3665aab
Date:   Tue Oct 17 09:16:07 2017 -0700

    Merge pull request #2633 from RosettaCommons/xingjiepan/fix_loop_modeling_build_levels_problem
    
    Quick and ugly fix of the build level bug caused by loop modeler

commit cd901cc3762375c4e6f11f8a600011eda74c0d99
Merge: 3de1fa7 015df1a
Date:   Tue Oct 17 10:10:06 2017 -0500

    Merge pull request #2629 from RosettaCommons/jadolfbr/fix_glyco_unit_test
    
    Jadolfbr/fix glyco unit test

commit 3de1fa7cb415f85aef76bb26206ff2e7485493b1
Merge: 3dc12e5 e33fb9a
Date:   Tue Oct 17 09:51:24 2017 -0400

    Merge pull request #2628 from RosettaCommons/aleaverfay/fix_invrottree_atom_indexing_bug
    
    PDB I/O from the InvrotTree indexing-from-0 bug
    
    The InvrotTree code was constructing a PDB file counting from atom index 0,
    but large sections of PDB writing assumes that atom indices start from 1.
    
    This bug was recently uncovered by the (several) fixes to the behavior of
    CONECT record creation in PDB writing with PR #2595 and disrupted the behavior
    of the cstfile_to_theozyme_pdb integration test

commit 3dc12e512eae6660dc512fd402cc9bac966f29e6
Merge: c0af4a4 c7099a7
Date:   Tue Oct 17 09:49:04 2017 -0400

    Merge pull request #2613 from RosettaCommons/aleaverfay/jd3_distributed_output
    
    Aleaverfay/jd3 distributed output
    
    To further reduce the work performed by the head node in MPI job-distribution schemes, output from the JobQueen is separated into three steps:
    
    1) The head-node job queen (JQ0) creates an OutputSpecification object that contains everything that describes how an output file should be generated for a particular JobResult and gives this OutputSpecification to the JobDistributor, and
    
    2) The JobDistributor gives the OutputSpecifiation to a (perhaps different) JobQueen asking the JobQueen for a ResultOutputter for this job, after first perhaps having added an output suffix to the OutputSpecification. This output suffix ensures that no two nodes write to the same file. The JobQueen then returns a ResultOutputter that respects the JD's output suffix.
    
    3) The JobDistributor then gives the JobResult to the ResultOutputter so that the ResultOutputter can write the result to disk / database / whatever.
    
    The division between step 1 and the rest is to allow the ResultSpecification to be shipped to another node to perform the output while still giving JQ0 the opportunity to give the output structure a particular name based on its history / standing.
    
    The division between step 2 and step 3 is so that output may be performed by multiple threads simultaneously by a (future) MPIMultiThreadedJobDistributor.
    
    HT: @jadolfbr for identifying the I/O bottleneck in JD3.

commit c0af4a427db5df0965d267d53c511ea1e2f55854
Merge: cd91c8a 299b8b5
Date:   Tue Oct 17 02:28:18 2017 -0700

    Merge pull request #2634 from RosettaCommons/vmullig/fix_thread_local_test
    
    Adding THREAD_LOCAL keyword to tracer that was missing it.

commit cd91c8a3f01ebe205c5b3994f71b8bd89902fc42
Date:   Mon Oct 16 12:42:04 2017 -0700

    adding try/catch block to the pilot app pad_helices

commit 919c1366434eabfa85748041e10c3ad15100b337
Merge: ebb009e cefcd75
Date:   Mon Oct 16 10:33:05 2017 -0700

    Merge pull request #2551 from RosettaCommons/everyday847/pocket_grid
    
    Break up large files into more sensible units
    
    ^ This will be absolutely the first pass of MANY; notably, I split out some too-aggressive changes to PocketGrid that had functional effects, and there are SO MANY files that I could do this to. Ultimately, this just involved creating 3 new subclasses of specific pose utils.

commit ebb009e1bbe658929ba07940378a4ecccb6633ff
Date:   Mon Oct 16 10:00:56 2017 -0400

    Big oops! Disabling out the failing unit test in TestAutoDetectGlycanConnections.cxxtest.hh
    meant there were no non-failing tests! CxxTest got grumpy :'-(

commit 00da7c62f598e8c29f5221cfe54e5236308f118c
Date:   Mon Oct 16 08:45:18 2017 -0400

    Disabling Jared's unit test until he gets back from vaction

commit 7c0f75faa4caa7b5cd5c6c0b9c4b15cb3708a0e5
Merge: b1eb0ea 7b4f657
Date:   Sun Oct 15 21:53:50 2017 -0600

    Merge pull request #2625 from RosettaCommons/sergey/f
    
    Refactoring integration.compare(...) so it always marking test as 'script failed' when .test_did_not_run.log or .test_got_timeout_kill.log files present in test output

commit b1eb0eae2c1c2118105f3bab38a218ef384a3bb4
Merge: ce46617 c869546
Date:   Sun Oct 15 09:27:15 2017 -0700

    Merge pull request #2624 from RosettaCommons/everyday847/working_native_Fix
    
    Working native fix
    
    Integration test failures are due to an inexplicably early merge base chosen for the comparison in re: CONECT record output. If you look at my code diff, that's just not affected by these four lines of code.

commit ce466173d8df70d57b5d4344469c136a7fcdf290
Merge: da52352 2cf9fc5
Date:   Sun Oct 15 07:49:03 2017 -0400

    Merge pull request #2626 from RosettaCommons/JackMaguire/fix_mpi_unit_tests
    
    Fix MPIWorkPoolJobDistributor Unit Tests

commit da52352fb09b634dc6f620a148be21e363516591
Merge: 4d9e5da cc0e04a
Date:   Sat Oct 14 12:22:51 2017 -0400

    Merge pull request #2569 from RosettaCommons/aleaverfay/spades_performance_bugfix
    
    Moving forward with a non-inner-loop-disrupting Spades implementation
    
    Spades introduced a read into the options system in the inner-inner-innermost loop, looking at the options system billions of times. This is slow, yes, but it also disproportionately slowed down the multithreaded build.
    
    The goal that spades is seeking is to have water not desolvate. That's actually easier to implement by adjusting the LK parameters of a new atom type used only by water: "OW". When the Spades flags are on the command line, OW's LK_DGFREE and LK_VOLUME are set to 0. This commit removes billions upon billions of read accesses into the options system -- but I understand from @jklai that there are others that ought to be removed. In particular, the reads in inline_atom_pair_energy.hh really need to be removed.
    
    Be warned: if previously you looked for the atom whose atom-type was "OH" in a water residue, that atom's type is now "OW"
    
    There are a lot of cosmetic integration test changes caused by the addition of a new atom type. There are two integration test changes where a full-atom pose is being scored by the centroid "vdw" term, and the addition of a new fullatom atom type causes this centroid score to change. These are weird tests.
    
    There are two trajectory changes for the hydrate protocol that I can explain quite easily: before, the fa_sol term was turned off for water scoring, but now water derivatives. Oops! Now fa_sol is off for both scoring and derivatives.

commit 4d9e5da1f5ec929208e52a5204919df37f28ff0d
Date:   Sat Oct 14 12:10:39 2017 -0400

    Adding two missing semi-colons to help the beautifier

commit 35684edf531eef6a17ee49115e831b6651be8f36
Merge: aaaa22a be1e2ac
Date:   Fri Oct 13 19:09:28 2017 -0700

    Merge pull request #2621 from RosettaCommons/xingjiepan/loop_hash_kic
    
    Xingjiepan/loop hash kic

commit aaaa22a2422a5c48dbf0243a6d195d4f21ea9bbd
Merge: d9a9391 5afa481
Date:   Fri Oct 13 18:58:50 2017 -0500

    Merge pull request #2616 from RosettaCommons/roccomoretti/skip_compile_benchmark
    
    Add '--skip-compile' option to the benchmark.py script. This allows you to skip the compilation phase of the benchmark.py script if you already have things compiled locally.

commit d9a939186f0a57804768652d17197c34ef222479
Date:   Fri Oct 13 15:53:20 2017 -0700

    adding a pilot app that does helical bundle heptad repeat stitching

commit 4768e51c0f5b018227cee53144a43571204b79ad
Merge: 48fbbfc 40a9dcd
Date:   Fri Oct 13 16:39:43 2017 -0400

    Merge pull request #2611 from RosettaCommons/sboyken/mchbnet_updates2
    
    Sboyken/mchbnet updates2 (resubmission)

commit 48fbbfcf97521d5d2e3eaf5620fe2c0adc22b9d3
Merge: 82718e2 bee5788
Date:   Fri Oct 13 16:29:20 2017 -0400

    Merge pull request #2595 from RosettaCommons/aleaverfay/pdb_conect_performance_bugfix
    
    JD3 bottleneck / PDB output taking too long
    
    Attempting to fix a pretty serious performance bug in PDB writing that spent O(N^2) time trying to determine the CONECT records. This impacts JD3 protocols quite heavily in that it creates a bottleneck on node 0 when outputting the results from other nodes.
    
    Fixing a few bugs in the way CONECT records were written out at the end of PDBs. For this reason, lots of integration tests change, but not coordinates of structures written out -- only the record of which atoms are bonded to which other atoms.

commit 82718e2c9ab53e38095c71abb5e79117e17abe1f
Date:   Fri Oct 13 11:41:47 2017 -0700

    Fixed the text rendering code in the R@h graphics app.

commit b8e58652751be064a15c1b0390842fb8a97ec2fd
Merge: 2d4add5 3918c16
Date:   Fri Oct 13 12:23:09 2017 -0400

    Merge pull request #2620 from RosettaCommons/JackMaguire/improved_jd3_archiving
    
    Archiving Refactor for JD3's MPIWorkPoolJobDistributor

commit 2d4add5760f905a54da645321a011e7d051c9440
Date:   Wed Oct 11 23:40:44 2017 -0400

    beautifying

commit 1279aff19117b1c1fd0c6f1781c7bb689fe7d0dd
Merge: 75a8ed2 99ba1b4
Date:   Wed Oct 11 21:18:46 2017 -0600

    Merge pull request #2608 from RosettaCommons/sergey/binder
    
    Updating PyRosetta so it uses Binder compatible with Pybind11-2.2

commit 75a8ed249b64c713c8caf146e3ed1a2c945f95e4
Merge: 709336a f74599a
Date:   Wed Oct 11 21:17:23 2017 -0600

    Merge pull request #2618 from RosettaCommons/sergey/f
    
    Updating PyRosetta build script (was broken on some Mac's)

commit 709336a0e4fe551429d14d20e16534b6708bf33b
Date:   Wed Oct 11 18:55:09 2017 -0400

    Explicitly specify for which branch we setting upstream

commit 16cd2bbc6c8cb6c75c58899206a67ef3384a9734
Date:   Wed Oct 11 18:52:44 2017 -0400

    Updating `beautify` test so it explicitly set upstream for beautifying branch

commit 23fa0ef5e12339ca59b1b831f219d30eb9ec401f
Merge: 63767f2 227debe
Date:   Wed Oct 11 10:30:58 2017 -0700

    Merge pull request #2614 from RosettaCommons/egurapha/remodel_cutpoint_fix
    
    Remodel: fixing broken cutpoint assignment

commit 63767f20b998c18946dea62d7350bddb1cf5dcd2
Date:   Tue Oct 10 23:35:56 2017 -0400

    beautifying

commit a31cc2c37c0dd9fff7bf41a78975ef1cba1a6477
Merge: 7e40929 a83ca77
Date:   Tue Oct 10 22:06:57 2017 -0400

    Merge pull request #2575 from RosettaCommons/aleaverfay/jd3_output_structure_naming
    
    JD3: output indices change
    
    The JobOutputIndex is a 4-tuple of integers representing a primary- and a secondary-index
    as well as an upper bound on the number of primary- and secondary-indices.
    
    The interface to the PoseOutputters changes slightly.
    
    Derived job queens of the SJQ may override the assign_output_index method to give the just-about-to-be-output Poses different indices if she wants. This is particularly necessary for multi-stage jobs, where there might be more than one InnerLarvalJob (and so the nstruct index is not unique!).
    
    This pull request is a launch point for PR #2613 which further changes the way the JobQueen interacts with generating output. The changes in this PR are not overridden by PR #2613, but if you are writing a new JQ and this PR is disruptive, then you will possibly find the next one disruptive too. Please email me if this affects you.

commit 7e409298cfc25edaa4555f9dbc813ee0b82cc527
Merge: b895481 28ad3c0
Date:   Tue Oct 10 18:03:50 2017 -0700

    Merge pull request #2606 from RosettaCommons/everyday847/fmi_segid
    
    Full segment ID support in RNA applications

commit b895481b9a8ecc9b378dda54cc5bf66d2d180774
Merge: 12eabc5 ef35fc2
Date:   Sun Oct 8 18:56:11 2017 -0500

    Merge pull request #2601 from RosettaCommons/jadolfbr/glycan_fixes
    
    Jadolfbr/glycan fixes
    
    This PR has a bunch of bug fixes, mainly in `GlycanTreeRelax's` quench mode found during benchmarking.  I'll list them below.
    
    - Fix `GlycanTreeRelax` issues if not modeling all glycans in the PDB.  Improve the logic of `ResidueSelector` masking for quench mode.
    - Add logic to exit if `GlycanTreeRelax` has no glycans to work on.  Set mover failure, which can be picked up and passed through the JD machinery.  Makes us waste less time benchmarking something that does not need to be benchmarked (for example short glycans where the layer size is equivalent to the number of glycans being modeled - this then is just basic `GlycanRelax`.
    - Make some 'Error' output be 'Debug' in carbohydrate util functions as they are not actually errors if you are checking the return values.
    - `Fix GlycanTreeRelax quench mode logic`
    - __Fix `GlycanRelaxMover` where the MonteCarlo object was being set at the wrong place.  This potentially caused input models to be output as final models and was not seen earlier, as up until this point we have been primarily building glycans from scratch and modeling them or loading very low-res models that have huge potential for improvement. __
    - Add `min_rings` and `cartmin` options to `GlycanTreeRelax`

commit 12eabc5d191af35e7022475ce7b9c179a8fa1e96
Date:   Sun Oct 8 17:26:36 2017 -0400

    beautifying

commit f738797cbab648ef8be6057b269220812c972c26
Date:   Sun Oct 8 17:04:06 2017 -0400

    Updating beautify test so beautification for master beautify all files regardless of origin of changes.

commit 9f764e1e367522fc3553f1a9687218180a378361
Date:   Sun Oct 8 16:53:28 2017 -0400

    Updating beautify test, adding more logging

commit 8922618be12f24bf0fc7c3307bc940b8e49668e2
Date:   Sat Oct 7 15:48:09 2017 -0700

    One more minor fix.

commit 79b85003545732db759d29c6df39f0f12e1a3944
Merge: e1cff9e bf5749c
Date:   Sat Oct 7 14:07:34 2017 -0700

    Minor fix for build test failures.

commit e1cff9eaa23865ab5e4b3f5599717da826d9870f
Date:   Sat Oct 7 14:04:53 2017 -0700

    Minor fix to an issue which is causing a bunch of build test failures.

commit 166bb7b67fb452d7dbe216e1706c12eec289304f
Date:   Fri Oct 6 14:39:46 2017 -0700

    Fixed linux build settings for the BOINC graphics build.

commit 8b5501ab2efde89bf2881fb21a3cee5158729b5e
Date:   Fri Oct 6 11:09:42 2017 -0700

    Added a fix to handle a bug in the recently released Windows BOINC client
    version 7.8.2.  Also added the option to revert back to the original
    black background in the graphics app in response to R@h users. The client
    bug allows dirty slot directories causing the R@h app to crash due to a
    failure to create shared memory for graphics. The fix just ignores the
    graphics if shared memory can't be initialized.

commit 4f69c5e4d7ba9b970a6749db5aa9fdcf3c04f8f6
Merge: 5ecad7c 5c50abe
Date:   Fri Oct 6 11:01:19 2017 -0500

    Merge pull request #2535 from RosettaCommons/JWLabonte-patch-1
    
    Carbohydrates: adding another xylose .pdb 3-letter code to list (Labonte) and increasing range of auto_detect_logic detection. Updated glycan auto detect unit test.

commit 5ecad7c2d2d52561011182a2dddcb9d4bfe8aa62
Date:   Fri Oct 6 11:16:56 2017 -0400

    Fixing Mac PyRosetta build

commit a4bbdaedc17fec35dda3edad91f9e72512e9dfb3
Merge: f1d4e15 17c73f9
Date:   Fri Oct 6 10:56:10 2017 +0200

    Merge pull request #2600 from RosettaCommons/jaumebonet/index_selection
    
    fixed selection error for ranges from inside the pose to values outside of it when specified as PDB numbering

commit f1d4e157176bd36227318f832292739c6137a190
Merge: 76889fe 5e16dd7
Date:   Thu Oct 5 19:15:52 2017 -0700

    Merge pull request #2596 from RosettaCommons/raemisch/symdef_multi_chain
    
    update make_symdef_file_denovo.pl

commit 76889fe2703e24790f264e4da0274942666a675c
Merge: fc46926 cc42e81
Date:   Thu Oct 5 17:30:52 2017 -0600

    Merge pull request #2603 from RosettaCommons/fordas/pyrosetta_macos_cmdline_fix
    
    Update pyrosetta build to support macos commandline developer tools.

commit fc469267efc5d186db20254df7a21fcb5c2138ba
Merge: d2f4283 265d333
Date:   Thu Oct 5 16:17:55 2017 -0700

    Merge pull request #2605 from RosettaCommons/fordas/pyrosetta_binder_update
    
    Update Binder submodule: per class include support.

commit d2f4283b22ca58efacaa87ec8c42763a82700617
Merge: 89265a5 617fc96
Date:   Thu Oct 5 15:42:03 2017 -0700

    Merge pull request #2581 from RosettaCommons/bfrenz/glycan_hydrogen_fixes
    
    Bfrenz/glycan hydrogen fixes

commit 89265a5d9478e284cd4d0a6186fda90b3dbb7d0d
Merge: 4c40c58 a8f646a
Date:   Thu Oct 5 08:27:26 2017 -0700

    Merge pull request #2602 from RosettaCommons/fordas/cmake_hdf5_support
    
     Add hdf5 support to cmake build, extend cmake YCM support.

commit 4c40c58e8a8012419be8ac64aa22cb2b379d2d97
Merge: b688dc7 1447732
Date:   Thu Oct 5 08:26:25 2017 -0700

    Merge pull request #2604 from RosettaCommons/fordas/ndarray_stride_fix
    
    Fixup ndarray stride calculation in pybind11 type converter.

commit b688dc701c6565e233264a66cd6820aa47732082
Merge: da7a749 ac63431
Date:   Wed Oct 4 18:18:17 2017 -0400

    Updating checkout procedure of 'beautify' so it more robust

commit da7a74970f6c372c8f3aa4ba3c9c9240076b2252
Merge: 23c605b 7c1c4a0
Date:   Wed Oct 4 15:08:56 2017 -0600

    Merge pull request #2599 from RosettaCommons/benchmark
    
    Enabling beautification of master branch

commit 23c605b576cc2f32e7ab1b17e7f673fe4fd9530f
Merge: d62aaaf 2c275f3
Date:   Tue Oct 3 16:04:25 2017 -0600

    Merge pull request #2598 from RosettaCommons/sergey/binder
    
    Updating Binder submodule: refactoring to improve performance.

commit d62aaaf2ca17ed1f15e1a2a80d5ba683e76834f1
Merge: 267b4ca 16b9df5
Date:   Tue Oct 3 08:33:38 2017 -0700

    Merge pull request #2591 from RosettaCommons/fordas/vim_ycm_completion_update
    
    Update ycm_extra_conf to support files without compilation db entries.

commit 267b4ca2ab01c981f58c068f0f149e22ab30c1d6
Merge: 1b869a4 7b17a9b
Date:   Mon Oct 2 23:05:42 2017 -0700

    Merge pull request #2590 from RosettaCommons/fordas/feature/extern_updates
    
    Add external external libraries ndarray & tinytimer. Update boost 1_55 library coverage.

commit 1b869a4cc1f8c0c4a1a4ab6126ae16e9940f1e91
Merge: 61b0ece 75627fc
Date:   Mon Oct 2 15:58:38 2017 -0400

    Merge pull request #2594 from RosettaCommons/ewrenbeck/mutation_scanning
    
    Adding filterscan scripts that do not remove mutations with low PSSM …

commit 61b0ece44a83dce163657cc0d100fd3d07a02023
Merge: bac373f 0c8b019
Date:   Sat Sep 30 23:36:40 2017 -0500

    Merge pull request #2592 from RosettaCommons/darwinyfu/minor-ligand
    
    New scoring grid for ligand docking, addition of two grid based unit tests

commit bac373f7c59fd7bba1db8f4248afc8265d2bea5b
Merge: 475a8e6 b6f257d
Date:   Fri Sep 29 11:20:23 2017 -0500

    Merge pull request #2586 from RosettaCommons/jadolfbr/fix_jd3
    
    Fix MPI-JD3 overwrite behavior
    
     The MPIWorkPoolJD was not properly checkpointing in order to continue the run, and overwriting already-complete files.  This fix is from @aleaverfay.
    
    Thanks Andrew!

commit 475a8e69b1b612020fdb838e10a4a09b84a37200
Merge: 623325f 9b658b1
Date:   Fri Sep 29 11:00:53 2017 -0400

    Merge pull request #2582 from RosettaCommons/jkleman/domains
    
    Jkleman/domains:
    Adding mp_domain_assembly protocol

commit 623325f6eb004afb472ac2e66bb1122c827f32dc
Date:   Thu Sep 28 17:07:37 2017 -0400

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

commit 514306d6a7f1d2b2665c4dadffbb408c6c04de2f
Date:   Wed Sep 27 18:06:45 2017 -0700

    Removing the check for canonical amino acids in the DumpSingleResidueRotamers mover. It appears to be unnecessary and I want to use this with NCAAs.