commit 9005cc64587b4189882337bc87783ab96ead263f
Merge: c3b824c d8b8520
Date:   Tue Aug 9 07:33:18 2016 -0700

    Merge pull request #1513 from RosettaCommons/rhiju/reconcile_bps_input_pdb_farna
    
    Rhiju/reconcile bps input pdb farna
    
    + this was needed to model eterna switches in 3D
    + changed behavior of bps_moves ("base_pair_step moves") to not move residues inherited from input PDBs. Makes SRP modeling cases (e.g. in integration test) worse, but more consistent with other conventions that we've used for, e.g., stepwise.

commit c3b824ce6c1288f2af11019e79c5e845a16575fe
Merge: 30eba8b 51ef1a3
Date:   Mon Aug 8 20:00:10 2016 -0700

    Merge pull request #1514 from RosettaCommons/tlinsky/bridge_chains
    
    Fix scorefxn parse_my_tag option in BridgeChainsMover, and add integration test

commit 30eba8b50dc0fe3ecd20c466af0a8e3a5d3866f4
Merge: 3dcad50 7e3f841
Date:   Mon Aug 8 11:36:45 2016 -0700

    Merge pull request #1271 from RosettaCommons/rfalford12/fix-fa-pH-test
    
    Fix Membrane Fa pH Score Function Fingerprint Test - Adding missing atoms to 1qd6_tr_C.pdb which caused problems with the score function fingerprint test.

commit 3dcad5010aa2f1da62f2576a71b939cb696e64ff
Merge: 10c6242 3aeb03d
Date:   Mon Aug 8 07:34:46 2016 -0700

    Merge pull request #1509 from RosettaCommons/rfalford12/energy-method-code-templates
    
    Code Templates for Energy Methods:
    
    Adding code templates for one body, two body, and whole structure energy methods to the collection. These interfaces are based off of the base class interfaces. I don't have a pressing energy term to implement right now as a better test, but I will adjust these as I go in the next few weeks.

commit 10c6242c068791232e1bd8644f97acd55545fab3
Merge: e9c3daa 68938b4
Date:   Sun Aug 7 21:57:59 2016 -0700

    Merge pull request #1512 from RosettaCommons/vmullig/noisier_flipping_tests
    
    Make flipping tests noisier
    
    About eighteen integration tests are showing weird "flipping" behaviour on the test server, and no one knows why. Making two of these tests noisier (-out:level 500) to try to track down the problem. (It would be good to know at least what Rosetta modules were being invoked when the trajectory changes start to appear.)

commit e9c3daaaae51f93fabf82d6fd2de061023ef48b3
Merge: 38bae42 7882a7a
Date:   Fri Aug 5 10:14:48 2016 -0700

    Merge pull request #1505 from RosettaCommons/rhiju/fix_amw_ribosome_tether_example
    
    Rhiju/fix amw ribosome tether example
    + @everyday847 the bug is fixed in master.
    + some integration tests change, but they look like the 'usual' ones that are sensitive to floating point inaccuracies.

commit 38bae42cd4a95f94f5719261ddc2928bf52ca0c9
Merge: 8cc4d21 790e43a
Date:   Fri Aug 5 07:21:17 2016 -0700

    Merge pull request #1501 from RosettaCommons/tlinsky/atom_pair_constraint_generator_update
    
    Quick update to AtomPairConstraintGenerator

commit 8cc4d21adc9d95afe493036d3f35e81c09d6fc45
Merge: 627c210 bd41cac
Date:   Thu Aug 4 19:52:28 2016 -0700

    Merge pull request #1504 from RosettaCommons/vmullig/fix_mpi_tests
    
    Fix error in MPI-mode integration tests introduced in Documentation XRW
    
    The tests were failing to run due to a small error in integration.py. Fixed now.

commit 627c210eec1d6d1230e8a661fc61a54623c619a6
Merge: bd7c756 288980e
Date:   Wed Aug 3 18:36:20 2016 -0700

    Merge pull request #1499 from RosettaCommons/rpavlovicz/fastsaxs_fix
    
    fastsaxs scoring was failing in centroid mode and when dealing with symmetric poses due to virtual atoms and virtual residues being considered during COM calculations. these changes fix this issue.

commit bd7c7567d8d1742cf85dd5c8b25cd3625df7e58c
Merge: 9f72dca 737bbc3
Date:   Wed Aug 3 15:42:41 2016 -0700

    Merge pull request #1487 from RosettaCommons/yhsia/sc_residue_selector
    
    Adapting SC filter to take ResidueSelectors

commit 9f72dcacd7c67121fcf57746091e7a6e6a61b712
Merge: 4a9b8bd 78785f6
Date:   Wed Aug 3 08:39:09 2016 -0400

    Merge pull request #1494 from RosettaCommons/jkleman/mp_updates_stats
    
    Jkleman/mp updates stats
    
    adding small app for lipid accessibility
    
    14 integration tests change, these are the unstable ones, this can only be because I added new options and Rosetta was rebuild from the ground up as I am not changing anything that could cause these tests to fail

commit 4a9b8bd24685304ac9761ee46100a4a1a31866aa
Merge: f1ef907 a61954a
Date:   Mon Aug 1 16:04:18 2016 -0700

    Merge pull request #1491 from RosettaCommons/yhsia/sym_residue_selector
    
    added integration_test for symmetrical_residue_selector.