commit 3bdf9bac7adff473e5595c6c2a3af65df046bb8b
Merge: 557098e a378612
Date:   Wed Jan 28 12:59:52 2015 -0500

    PyRosetta adding bindings for int, Size, SSize and Real std::pair's.

commit 557098e2d9d22a93229b42c47b5058a5d344ae22
Merge: a059c58 218a20c
Date:   Tue Jan 27 15:01:13 2015 -0500

    Merge pull request #284 from RosettaCommons/lqtza/pyrosetta_pymol_energy_labels_fix
    
    PyRosetta: Fixed bug for sending energies from pyrosetta to pymol as ca-labels

commit a059c5859d8760ce77f161cb670dd91b554eec72
Merge: ff43d87 6f351d3
Date:   Tue Jan 27 10:22:14 2015 -0800

    Merge pull request #289 from RosettaCommons/hahnbeom/refinement
    
    Hahnbeom/refinement

commit ff43d87ac05cead06c9e76336d777a350501a446
Merge: 2e9e982 09accb2
Date:   Tue Jan 27 11:26:22 2015 -0500

    Merge pull request #275 from RosettaCommons/JWLabonte/utilities
    
    A few years back, I added what I consider a couple helpful convenience methods to vectorL. I had never written unit tests for them; now I have.
    
    This merge also introduces a third convenience method for appending one vector into another, which would be really helpful for some sugar code I'm working on.
    
    There is a simple carbohydrate code fix as a rider to this merge, so carbohydrate integration test changes are expected. All other tests pass.

commit 2e9e9823fdbeba9faa244807f8b499440c26d0fd
Merge: ffbe765 09033a4
Date:   Mon Jan 26 18:17:55 2015 -0600

    Merge pull request #292 from RosettaCommons/justinrporter/env_devel
    
    Multiple small bug fixes to the broker (see commits 9854a39, 13d49bd, and 09033a4). No broken integration tests outside the usual failures or unit tests outside of the Windows pyrosetta build, which seems to be broken for everybody at the moment (and it wouldn't really make sense for what I've done to break it...).

commit ffbe7650b15ba1a012d6fb31bc5d484ba9f29416
Merge: 11b69ef 184303e
Date:   Mon Jan 26 11:21:18 2015 -0600

    Fix issues with reading waters from silent files
    
    Thanks to Per for pointing it out.

commit 11b69ef4755595817ccb39cb00dd349f9f7ebd28
Merge: 3683b8e d187f61
Date:   Mon Jan 26 12:49:41 2015 -0500

    Merge pull request #293 from RosettaCommons/revert-280-jkleman/mp_updates
    
    Revert "Jkleman/mp updates"
    reverting merge for now until I figure out what's going on with the windows.PyRosetta build.

commit 3683b8e5d51c7582f15a05094d982668f49ddfa1
Merge: 9f05b89 f9dfd7e
Date:   Mon Jan 26 07:36:47 2015 -0800

    Merge pull request #281 from RosettaCommons/phbradley/tiny_hbscale_bugfix
    
    tiny hbond-scale bugfix: the per-atom hbond scale factors were applied to the derivatives but not to the function values for the chi score.

commit 9f05b89c45997fcad1288209801cca6371b5d00d
Merge: 37afbf6 1238884
Date:   Sat Jan 24 21:31:10 2015 -0500

    Merge pull request #280 from RosettaCommons/jkleman/mp_updates
    
    = corrected MPDocking weights from incorrect weights and added smooth terms and weights: mpframework_docking_<fa/cen>_2014.wts; these should be used from now on
    = changed instances from using OP as args to &
    = AddMembraneMover:
            * switched SSize for membrane residue to regular Size
            * spanfile is not a required input any more: if flag -membrane_new:setup:spans_from_structure <bool> is passed, it calculates the topology from the structure => this requires the structure to be transformed into membrane coordinates
            * reading in MEMs got better: AddMembraneMover will automatically detect MEMs without a flag; flag can be used if multiple MEMs are present
            * one of the constructors can now also use the anchor residue as input, default is 1 throughout
    = SpanningTopology:
            * adjusted method fill_from_structure so that it can be used from outside the class
    = compute_structure_based_membrane_position:
            * renamed to compute_structure_based_embedding
            * overloaded functions to also take SpanningTopology as input: this is more useful for Symmetry or computing embedding for parts of the pose where the topology isn't necessarily for the whole pose
    = protocols/membrane/geometry/util
            * added split_topology_by_jump method and unit test for it
    = span_from_PDB:
            * changed default thickness from 12.5A to 15A
    = core/pose/util.hh
            * added function nres_protein that counts protein-only residues in the pose
    = MEM / EMB params files:
            * made all of them consistent to match the fa MEM params file, numbers didn't change except thickness is now consistently 15A for both low-res and high-res
            * order of atoms in EMB changed, but this shouldn't affect any calculations
    = MPDockingMover:
            * reorganized code to be able to add stuff easier
            * constructor now takes a jump number for docking
            * added option to read in scorefunctions for both low-res and high-res steps
    = FlipMover:
            * added and unit tested: flips a pose element in the membrane, given a jump number

commit 37afbf66a8a069ef2286ca97cd11f97b56a9fd57
Date:   Sat Jan 24 13:47:04 2015 +0200

    warnings as errors correction

commit 94972480ecec4c750b7810c7ff28b045fc2b14c2
Merge: 64500f6 88151b6
Date:   Sat Jan 24 13:05:36 2015 +0200

    Merge pull request #291 from RosettaCommons/sjf/InterfaceAngle
    
    reducing verbosity

commit 64500f686bde26b9cd4542454e1ee95150444f3d
Merge: 1a2944e b05f2ee
Date:   Sat Jan 24 13:01:35 2015 +0200

    Merge pull request #288 from RosettaCommons/sjf/InterfaceAngle
    
    Sjf/interface angle
    Compute the angle between a small molecule and a predetermined vector. This is very ad hoc; not sure it will be of general use...

commit 1a2944e2a5b3c7ae205815e3fc9ab02291b94c75
Date:   Fri Jan 23 13:21:33 2015 -0600

    In integration tests, ignore lines about updating an outdated Dunbrack binary.

commit bd9558c70947fda77a7f989154e51b96e5370be3
Merge: 0ba1402 c93ff5a
Date:   Fri Jan 23 10:07:45 2015 -0600

    Merge pull request #263 from RosettaCommons/justinrporter/env_release
    
    Commiting fixes to Broker framework, small updates to syntax, renaming claiming mover to client mover, NullMover is now a MovemapMover (it doesn't do anything with the movemap it gets).
    
    Integration test changes for a) broken tests and b) unstable performance tests. Otherwise clean.

commit 0ba1402f64619b4f47193eb3137fbac0924689ca
Date:   Fri Jan 23 09:37:38 2015 -0600

    Fix PyRosetta MPIJobDistributor.

commit 97b99fe383f45d0b12c6d629644f77867e43dfe0
Merge: 1453c95 b1ba365
Date:   Thu Jan 22 21:00:55 2015 -0800

    Merge pull request #287 from RosettaCommons/vmullig/fix_metal_issues
    
    Fixed a bug in automatic metal setup when patches are applied.
    
    (The name order was incorrect.)
    
    No integration or unit test changes expected. Since this is a very minor change, I will merge immediately.

commit 1453c9599b82886d76ea4da725e8369c04197bca
Merge: b14a1f5 d87cce8
Date:   Thu Jan 22 16:42:01 2015 -0500

    Merge pull request #90 from RosettaCommons/everyday847/everyday847/disulfides
    
    Adding support for disulfides including homocysteine and D-homocysteine

commit b14a1f5cbc29d763e87046c2c22c61107718d9e7
Date:   Thu Jan 22 12:22:33 2015 -0600

    Fix DockingTest:test_DockingProtocolFunctions
    
    Change the UTracer results for this test.
    
    The difference is a small change in the fa_dun term in one instance
    (and resulting change in total score). This is easily explained by
    the Dunbrack binary issues we've seen recently.

commit 927458584a05f23fc0a37dd47bc66fc0f3ee7b5b
Merge: 0adfb8e ffdc40e
Date:   Thu Jan 22 10:55:55 2015 -0600

    Merge pull request #277 from RosettaCommons/roccomoretti/rotlib_cmp
    
    Add Dunbrack binary validation tests
    
    We've had issues with changes to the codebase which alter the contents of
    the Dunbrack-library-as-read-from-ASCII versus the Dunbrack-library-as-read-
    from-a-previous-version's-binary. There's a version number in
    core/pack/dunbrack/RotamerLibrary.cc which is supposed to control for this,
    but people don't always realize that their changes require a version number bump.
    
    This commit adds unit and integration tests which attempt to compare the ASCII
    and binary versions of the Dunbrack library, and see if they're different. Note
    that this integration test is looking at a single version, rather than a version
    comparison.
    
    The test is also not foolproof, as there is a delta in the real number
    comparisons, but hopefully it should catch the major changes.
    
    New unit tests and integration tests - they shouldn't (cross fingers) be failing,
    due to the previous commit which bumped the version number and forced
    binary regeneration.

commit 0adfb8eb9adef32bad10b240a2e4ad457f3ecc7b
Date:   Thu Jan 22 09:35:41 2015 -0600

    Bump version number on Dunbrack binary.
    
    There's been a number of changes which have changed the contents of the
    ASCII-loaded Dumbrack library versus what's loaded from a binary
    generated by a previous version. These should have come along with a
    version number increase for the binary, but weren't always. This commit
    number increase should reset any remaining old binaries, and going
    forward we can hopefully keep on top of increments. (A separate commit
    will introduce a unit/integration test for changes.)
    
    Known changes which changed the binary:
    2015-01-13 - resolution fix for rotlibs (prob <= 1e-6, not prob == 0)
        57550 (test) c7ce5fe8d820cb13 (merge) f8ce0ac3bc65c8 (change)
    2014-12-01 - Fixing an error in SingleResidueDunbrackLibrary::rotno_2_rotwell
        57471 (test) 5b0686ce58de4832 (merge & change)
    * There may be others as well, which weren't noticed.
    
    Possible integration test changes on the server as old Dunbrack binaries
    are flushed.

commit 66a2609ef3632beefb1a33a4a42b6c3ac3dab38d
Merge: 0d6cd80 438cdbb
Date:   Tue Jan 20 07:31:32 2015 -0800

    Merge pull request #274 from RosettaCommons/phbradley/tiny_minpack_bugfix
    
    tiny min_pack bugfix

commit 0d6cd80a79d2153316e1e1f2f159b91a8f700630
Merge: ee475ab 06d5615
Date:   Mon Jan 19 07:20:09 2015 -0800

    Merge pull request #272 from RosettaCommons/phbradley/residue_datacache
    
    Phbradley/residue datacache

commit ee475ab090ea0d0e83c69fcd23304bc0058afe42
Merge: 0f82242 dd88f69
Date:   Sat Jan 17 16:56:53 2015 -0800

    Merge pull request #252 from RosettaCommons/rhiju/trace_assert
    
    updating assert() to print backtraces
    
    tests look OK.
    [one unit test failed; same as in master (I see that sergey is doing some fixes).]
    Will do global find/replace of assert() to debug_assert() in a separate pull request.

commit 0f82242b10c434513626d072241dd03b6d9fb873
Date:   Wed Jan 14 20:29:08 2015 -0500

    Disabling folding and part of refinement PyRosetta unit tests until issues with Abinitio stability is resolved

commit 93f34d41449a5cbd451a2b39d6059a8bcf3020c3
Merge: 872ca32 438e1ce
Date:   Wed Jan 14 09:12:48 2015 -0800

    Merge pull request #266 from RosettaCommons/hahnbeom/refinement
    
    Hahnbeom/refinement

commit 872ca320415bba38f7f3e0f6f6e4118df50678e4
Merge: c7ce5fe 3c090f5
Date:   Tue Jan 13 23:32:26 2015 -0800

    Merge pull request #267 from RosettaCommons/vmullig/for_chris
    
    Very minor bugfix to BundleGridSampler (taking out some unnecessary restrictions on input).
    
    Test changes are only those integration tests that are already failing.

commit c7ce5fe8d820cb134d93da7ca4ba635ad3301b56
Merge: 911cda0 4c3f69c
Date:   Tue Jan 13 13:30:39 2015 -0500

    Committing the resolution fix for rotlibs (prob <= 1e-6, not prob == 0)

commit 911cda0c282147191da7d641a4b3df1cd95d89aa
Merge: 3f65b7c 231ae7e
Date:   Tue Jan 13 13:29:04 2015 -0500

    Merging in fix to rotamer library resolution (should be 1e-6)
    No test changes expected

commit 3f65b7c953a57a0570465e01e2448c5313b38280
Merge: db2d031 52d68f0
Date:   Mon Jan 12 10:31:27 2015 +0100

    Merge pull request #198 from RosettaCommons/wpotrzebowski/fiber_diffraction
    
    Merging Fiber Diffraction scoring and derivatives calculation
    
    There are three separate Fiber Diffraction modules (energy terms).
    FiberDiffractionEnergy – all-atom scoring and derivatives
    FiberDiffractionEnergyDens – low-resolution (centroid) scoring based on electron density of subunit
    FiberDiffractionEnergyGpu – all-atom scoring and derivatives performed on GPU.
    This module is based on NVIDIA Cuda library and was developed before OpenCL standard was introduced. To compile it extras=cuda flag has to be used. One has to uncomment two lines (71 and 72) in tools/build/nvcc.py file. This will pass arch=sm_20 flag to nvcc.  I’ve also added #define BOOST_NOINLINE statement to external/boost_1_55_0/boost/config/compiler/nvcc.hpp  so the module compiles in debug mode. The corresponding line has to be uncommented too.
    
    #UNIT TESTS:
    Fiber Diffraction tests have been added.
    Unit tests status: All pass
    
    #INTEGRATION TESTS:
    fiber_diffraction and fiber_diffraction_fad Integration tests have been added.
    Integration test results as expected: database_jd2_compact_io, database_jd2_io,  features and sweep_respair_energies are changed because new score terms are added.
    
    #PyRosetta:
    FiberDiffractionEnergy, FiberDiffractionEnergyDens works with PyRosetta, while FiberDiffractionEnergyGpu was excluded from these builds (src/python/bindings/exclude.py)

commit db2d031fe9ef5724f8f19cab5ef8bd84783b4deb
Date:   Sun Jan 11 11:43:11 2015 -0500

    Set use_centroid_dg to False in InterfaceFeatures.  It is unused and unreported.  Having it true makes pdbs fail with modifications or other ligands without centroid params.  Thanks to Jordan Willis for finding this

commit 8628cf4143cbd167e139f5b82fab1a8cda05c8f3
Merge: 7fff3e0 18b82ea
Date:   Sat Jan 10 23:27:48 2015 -0700

    Merge pull request #262 from RosettaCommons/revert-261-hahnbeom/refinement
    
    Revert "Hahnbeom/refinement" until issues with Windows PyRosetta build is fixed

commit 7fff3e0be19b071fced8b709275691b66c410831
Merge: d401c6e b639958
Date:   Sun Jan 11 00:18:01 2015 -0600

    Merge pull request #255 from RosettaCommons/justinrporter/env_release
    
    Merge miscellaneous bug fixing related to Environment, except a bug in FoldTree::insert_fold_tree_by_jump that creates an invalid fold tree when the inserted fold tree is a single, one-residue peptide edge. This is fixed by commit 90120df.
    
    Integration test failures are expected from antibody_graft and inverse_rotamer_remodel for unrelated reasons, as well as "core_scoring_Score_10000x_fa_cust_pair_dist," which seems to be failing these days.

commit d401c6ed9f27e8b42f1fd5afe11ef5939e6150ff
Merge: 45f3fbf a67d0d8
Date:   Sat Jan 10 11:04:25 2015 -0800

    Merge pull request #261 from RosettaCommons/hahnbeom/refinement
    
    Hahnbeom/refinement

commit 45f3fbfa6668a609b5e336c080197fcd168805be
Merge: 1321f34 c32bd95
Date:   Fri Jan 9 17:12:36 2015 -0800

    Merge pull request #259 from RosettaCommons/revert-257-vmullig/turn_off_smoke_detector
    
    Revert "Temporarily turning off an integration test that no one has seen...

commit 1321f34fb10e7276eb71621483605b74cc382cc6
Merge: 5ce229f 2259ee2
Date:   Fri Jan 9 16:53:22 2015 -0800

    Merge pull request #258 from RosettaCommons/vmullig/for_chris
    
    Adding a pre_selection_filter option to the BundleGridSampler.
    
    This adds one option to the BundleGridSampler (a pre-selection filter that filters out gridpoints that don't pass some criterion).
    
    Tasks:
        Add the filter option.
        Add RosettaScripts support.
        Have it do something in the apply() function.
        Tweak the bundlegridsampler_design integration test to use a filter. (Changes to this integration test expected).
        Update the documentation.
    
    Incidental changes:
        Tweaked my design_cycpeptide_MPI.cc app.
    
    Expected test changes:
        Only the bundlegridsampler_design integration test should change (a bit more logfile output, a few fewer pdb files written since some are filtered out by the new filter).
         I didn't wait for the Windows PyRosetta build test, since it's very slow.  I'll chance it -- there's no reason that this should cause that build to fail when the Mac and Linux PyRosetta builds are fine.

commit 5ce229f53ebf4e992b45a718911390e41e1e2d64
Merge: dd65b53 dbd9329
Date:   Fri Jan 9 16:49:58 2015 -0800

    Merge pull request #257 from RosettaCommons/vmullig/turn_off_smoke_detector
    
    Temporarily turning off an integration test that no one has seen fit to fix in some time
    
    Moving the antibody_graft integration test to disabled_tests to turn it off. This integration test, along with inverse_rotamer_remodel and pcket_suggest_targets, have been broken for some time (though the latter two work in at least one of release_debug or release, so I'll leave them). A smoke detector that rings continuously is worse than useless; it masks actual alarms and trains people to ignore the alarm. I'm switching the antibody_graft integration test off until someone sees fit to fix it (and I hope someone will also fix the other two). I don't know whose tests these are because there are no observers. If they're yours, fix them and put them back in tests, please.
    
    Update -- I see that pocket_suggest_targets was fixed.  Thank you!  The debug_release integration test should give a green light, now, with antibody_graft disabled.  (Whoever wrote antibody_graft, please fix it and re-enable!)

commit dd65b53417b5fedce9be0f9e877dbbb2bedfb71d
Date:   Fri Jan 9 12:29:35 2015 -0500

    remove hardcoded pose dump statement from AnchoredGraft unit test

commit 08b5eab9759f841feb6048a653af5874d724b740
Date:   Fri Jan 9 09:08:07 2015 -0600

    Fixed failed assertion in pocket_suggest_targets debug build integration test