commit f7ed5793479fe7814557fb0423e4be40f4b4d9ab
Merge: b502141 a06e68e
Date:   Tue Aug 16 12:38:14 2016 -0400

    Merge pull request #1533 from RosettaCommons/rfalford12/extend-mpdock-rscript-interface
    
    Extend the MPDock parse_my_tag function
    
    Add options to MPDock's parse_my_tag to set alternate low & high resolution score functions from the RosettaScripts interface

commit b5021419965d872899c875908ef496d280d47608
Merge: 9ac15ec b3c8646
Date:   Mon Aug 15 19:45:19 2016 -0700

    Merge pull request #1536 from RosettaCommons/jkleman/mv_app
    
    moving app

commit 9ac15ec04b88b3e5974b9ba867f4c45d2ceb17c0
Merge: 5e13982 3c491c8
Date:   Mon Aug 15 18:38:29 2016 -0700

    Merge pull request #1538 from RosettaCommons/vmullig/cycpep_predict_jd
    
    Adding integration test for 4-level job distribution with simple_cycpep_predict.

commit 5e139824de605b27811fdc532a4f5420ac7bbe2e
Merge: f0ba5c1 3a66979
Date:   Sun Aug 14 19:37:57 2016 -0700

    Merge pull request #1498 from RosettaCommons/hahnbeom/cartbonded_and_hxltors
    
    Hahnbeom/cartbonded and hxltors

commit f0ba5c1abdef0a589bbee44186d812d9dd86c70c
Merge: 2d51ccb f820d70
Date:   Sun Aug 14 13:19:30 2016 -0700

    Merge pull request #1522 from RosettaCommons/tlinsky/cst_score_filter
    
    update constraintscorefilter to work with symmetry
    Unit tests originally failed, but passed on resubmission (http://benchmark.graylab.jhu.edu/revision?id=4523&branch=)

commit 2d51ccb39469668ef3a01e46717915f6c61e20c3
Merge: 121efcf 2a65642
Date:   Sat Aug 13 16:48:33 2016 -0700

    Merge pull request #1521 from RosettaCommons/tlinsky/consensus_loop_design
    
    Updates to consensus loop design
    
    Linux gcc unit test failed on the first try, but passed when I rescheduled the test (http://benchmark.graylab.jhu.edu/revision?id=4520&branch=).  Merging, fingers crossed.

commit 121efcf7a34b3b439d06cebc6dc17081056bc7be
Merge: 7c1a29c e46eeb0
Date:   Sat Aug 13 14:11:11 2016 -0500

    Merge pull request #1515 from RosettaCommons/bazzoli/sho-lk-hybrid-for-merge
    
    Merge SHO–EEF1 hybrid model

commit 7c1a29c65ff73e905943a4ae0381cfa815764b1a
Merge: 0e1c17b 3b9caca
Date:   Sat Aug 13 09:22:40 2016 -0700

    Merge pull request #1531 from RosettaCommons/xingjiepan/LoopBuilder_bug_fix
    
    Fix edges cases for loop modeling

commit 0e1c17bc86c91af4cfd4d1911855c6967bfd2cb2
Merge: 55b08e5 48914dd
Date:   Sat Aug 13 09:22:23 2016 -0700

    Merge pull request #1511 from RosettaCommons/xingjiepan/fix_Werror_gcc6
    
    Fix new Werrors from GCC6

commit 55b08e5ba7f6bc685b5b0b6aeabb8b735e57065e
Merge: 60e6446 4101f6c
Date:   Fri Aug 12 16:08:01 2016 -0700

    Merge pull request #1500 from RosettaCommons/tlinsky/ssene_remove_state
    
    Remove state information from SetSecStructEnergies mover

commit 60e6446da43610b3a0ad3035b01d3ebf12025068
Merge: dc83811 defd9b2
Date:   Thu Aug 11 16:55:10 2016 -0700

    Merge pull request #1526 from RosettaCommons/tlinsky/restore_ignore
    
    Tlinsky/restore ignore

commit dc83811516f64ba532e2f2b1bfeeff5b70c68816
Merge: 92f5147 c9877d0
Date:   Thu Aug 11 13:13:54 2016 -0700

    Merge pull request #1525 from RosettaCommons/everyday847/gatekeeper_clarification
    
    Clarifying Readme to list the one existing gatekeeper

commit 92f5147b9641d715fd08a2d6be50a65910e43c90
Merge: 605d7ae efa6047
Date:   Thu Aug 11 10:04:45 2016 -0700

    Merge pull request #1520 from RosettaCommons/tlinsky/delete_region_rechain
    
    Add rechain option to DeleteRegionMover

commit 605d7aed7e7c9bb624a275dff1046c8fbde26c04
Merge: 991e3f9 857135d
Date:   Wed Aug 10 16:34:57 2016 -0700

    Merge pull request #1518 from RosettaCommons/tlinsky/constraint_generator_update
    
    Updates to DistanceConstraintGenerator and HydrogenBondCstGenerator

commit 991e3f9302e90fce5e8a03aec72feeb69d0d042f
Merge: c77ea6d 5be9adf
Date:   Wed Aug 10 12:55:19 2016 -0700

    Merge pull request #1507 from RosettaCommons/tlinsky/secondary_structure_filter
    
    Fix how secondary structure corrects for strand residues

commit c77ea6d92dd0127d004217e2ade046890e769337
Merge: 0446c53 5f5b9b6
Date:   Wed Aug 10 12:44:49 2016 -0700

    Merge pull request #1519 from RosettaCommons/tlinsky/fix_bridge_test
    
    fix bridge_chains integration test

commit 0446c53353fe7b201830fd7ac553274ef52737fe
Merge: 8b9b312 623b30b
Date:   Tue Aug 9 23:03:29 2016 -0700

    Merge pull request #1516 from RosettaCommons/rhiju/fix_syn_anti_south_north
    
    Rhiju/fix syn anti south north
    
    @fdimaio I used your CircularSplineFunc for this, to set up a dihedral restraint. However, I had to update the function so that when it accepts `x` from a DihedralFunc ,it knows to convert radians to degrees; the flag is 'convert_to_degrees'. I saw in hybridize/HybridizeProtocol that you didn't have the conversions in ... might be worth a quick look.

commit 8b9b3123e14f2c1e65d02b85a9f613b6f512f385
Merge: 9005cc6 57972b4
Date:   Tue Aug 9 19:00:03 2016 -0700

    Merge pull request #1506 from RosettaCommons/tlinsky/paired_sheet_residue_selector
    
    Add residue selector to select residues involved in strand-strand pairings
    
    Integration test change expected for code templates due to slightly modified Template files

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.

commit f1ef90776046d74e50d6434cac53507d6e68a805
Merge: c135f27 b46c0f4
Date:   Tue Aug 2 06:35:50 2016 +0800

    Merge pull request #1497 from RosettaCommons/dimaio/dens_tools_avgFSC_fix
    
    Fixing build error

commit c135f273df631b0fc1efa3079c7923ba3b67beed
Merge: 1a4afa4 428b440
Date:   Mon Aug 1 16:26:40 2016 -0500

    Merge pull request #1457 from RosettaCommons/jadolfbr/fix_seed_ensemble
    
    Fix Seed Ensemble integration test
    
    This should properly run the integration test for seed ensemble JD2.  Thanks for @roccomoretti for the find!
    
    This also properly reinstates certain protocol movers to work better with multiple different poses - AKA calls proper Mover functions to tell JD2 what to do.  Most were already coded this way, but this explicitly says what to do.

commit 1a4afa4bb9a0feeca5383ea282b3218c20435188
Merge: 6fa655d d881802
Date:   Tue Aug 2 05:19:57 2016 +0800

    Merge pull request #1496 from RosettaCommons/dimaio/dens_tools_avgFSC_fix
    
    Modifying the way integrated FSC is calculated in density_tools …

commit 6fa655dcd903e9f9024225db438efb822ecb8913
Merge: e4ed189 e214619
Date:   Mon Aug 1 13:46:32 2016 -0500

    Merge pull request #1275 from RosettaCommons/jadolfbr/pyrosetta/setup_pyrosetta
    
    Add PyRosetta Setup Script
    
    
    
    
    Add a script for setting up PyRosetta -  ```setup_pyrosetta.py```.  This has been needed for years.  Thanks to @raemisch for the suggestion.   It runs SetPyRosettaEnvironment (which is now updated), and creates a new file for PyRosetta paths (which are usually exported at the end of the shell file). This file should then sourced in your profile, which this script can append for you if it is not already present in the file.
    The script interactively asks you if you would like to add this to your profile if not already present
    ```
    ## PyRosetta ##
    source /Users/jadolfbr/.pyrosetta_env
    ```
    
    The new file looks like this:
    ```
    # PyRosetta Paths.  Source this within your profile.
    # Date Created: 04/13/2016
    
    
    export PYROSETTA=path/To/PyRosetta.namespace.mac.release
    export PYTHONPATH=$PYROSETTA${PYTHONPATH+:$PYTHONPATH}
    export DYLD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${DYLD_LIBRARY_PATH+:$DYLD_LIBRARY_PATH}
    export export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
    export PYROSETTA_DATABASE=$PYROSETTA/database
    
    ```
    
    You can either use SetPyRosettaEnvironment or setup_pyrosetta.py script. The setup_pyrosetta.py script should be run anytime directories are changed (Which is now actually able to be done through the dylib - this never actually worked before).
    
    Here is the help output of the python script:
    
    ```
    usage: This file adds a file to your home directory, .pyrosetta_env, and by default adds a line to your bash or zsh profile (if not already present) to source this file.   After running this script, you will no longer need to run anything before using PyRosetta or add anything to your profile.
           [-h] [--source SOURCE] [--outname OUTNAME] [--outdir OUTDIR]
           [--shell_profile_path SHELL_PROFILE_PATH]
    
    optional arguments:
      -h, --help            show this help message and exit
      --source SOURCE, -s SOURCE
                            The file to source in order to set the environment.
                            Default is SetPyRosettaEnvironment.sh
      --outname OUTNAME, -o OUTNAME
                            Name of the output file we will eventually source.
                            Default is .pyrosetta_env
      --outdir OUTDIR, -d OUTDIR
                            Output directory of the env file. Default is $HOME
                            directory
      --shell_profile_path SHELL_PROFILE_PATH, -p SHELL_PROFILE_PATH
                            If your shell profile path is different than the
                            common ones, please set the path here.
    ```

commit e4ed189eb7c3e2a820175665b86ab927df716de2
Merge: 3fab378 8d0364c
Date:   Sat Jul 30 18:53:17 2016 -0600

    Merge pull request #1490 from RosettaCommons/sergey/binder
    
    Fixing ScoreFunction show methods so they work correctly in PyRosetta

commit 3fab37892d80f5606533ba7bc8007646ae67e0a3
Merge: cc78bbd 399db48
Date:   Fri Jul 29 11:09:01 2016 -0700

    Merge pull request #1485 from RosettaCommons/jadolfbr/singleton_code_template
    
    Add code_template for Singletons
    
    Thanks to @JWLabonte for some great singleton examples and tips.
    Now, we have almost full coverage of common Rosetta classes!!!

commit cc78bbd5705375ebceda393e18020b5ebd3bd7f5
Merge: cfa9f71 2011d3c
Date:   Fri Jul 29 11:05:14 2016 -0700

    Merge pull request #1486 from RosettaCommons/jadolfbr/jadolfbr/h3_camelid
    
    Fix H3 model camelid integration test
    
    It turns out that camelid antibodies NEVER actually worked in AntibodyModelerProtocol.  So my simple addition of an integration test and simple fixes for what I thought I had broken while working on antibody design, was not enough.
    
     Adding the integration test caused a failure, which I thought was due to adding the test.
    
    This fixes that.

commit cfa9f71519f144d31d11607ccb3b04a894adc9d1
Merge: c466fb4 0b5bc6d
Date:   Fri Jul 29 09:11:24 2016 -0700

    Merge pull request #1444 from RosettaCommons/tlinsky/setup-symm
    
    Add option to ExtractAsymmetricUnitMover to keep/not keep virtual atoms

commit c466fb496a30ddcd6f13a2b811e9009813057d78
Merge: b0bbd02 2fdfd96
Date:   Thu Jul 28 14:38:06 2016 -0700

    Merge pull request #1488 from RosettaCommons/yhsia/sym_residue_selector
    
    ResidueSelector: Selects input residues + all of its symmetrical cloned residues

commit b0bbd02a9da2c0e8c2ed4b3ee358f320a9df9d3a
Merge: c52e57a ae374e8
Date:   Thu Jul 28 08:01:59 2016 -0700

    Merge pull request #1482 from RosettaCommons/tlinsky/tag_quote
    
    Add non-default option to tag to quote options when the tag is written

commit c52e57a0660c7aefef7a4748e11a6ce7af3d5232
Merge: ae16351 f8b8329
Date:   Thu Jul 28 07:59:57 2016 -0700

    Merge pull request #1481 from RosettaCommons/tlinsky/stream_util
    
    Add std::set operator<< in stream_util.hh
    
    Cosmetic integration test changes expected for symm_disulfidize and dcys_disulfidize, due to disulfidize mover now using std::pair operator<< found in stream_util.hh

commit ae163518e1880caaa7f067c7c9826539f83f3c47
Merge: fb7cd48 69fb7f8
Date:   Tue Jul 26 15:20:31 2016 -0700

    Merge pull request #1477 from RosettaCommons/everyday847/DMS_valgrind
    
    Avoid accessing the -1st position of a string

commit fb7cd482a1f2d42f06eab2ea5f97e2c1173061e5
Merge: e6f38b8 7e67de1
Date:   Tue Jul 26 14:14:58 2016 +0300

    Merge pull request #1438 from RosettaCommons/orlypolo/fix-namespace-location
    
    Orlypolo/fix namespace location

commit e6f38b84cceb581bd5e78e2d8c656b2ba5ba5287
Merge: d4662ab a5a9906
Date:   Tue Jul 26 09:35:05 2016 +0800

    Merge pull request #1479 from RosettaCommons/dimaio/cart_smpler_rama_fix
    
    Fix a few bugs with rama mode for cart sampler

commit d4662abb70731bf39ac1a4f3b9488496393c7e1f
Date:   Mon Jul 25 15:31:48 2016 -0400

    Moving Krishna "pH_protocol" to public apps

commit 3abecf1beb0e51f45878b127afcf9413c271439b
Date:   Mon Jul 25 10:04:20 2016 -0700

    adding observers files to tests

commit d5a8b07e60892ddd921fd629c26c337ef258dc98
Merge: 7e1e880 624ea8a
Date:   Sat Jul 23 17:24:29 2016 -0700

    Merge pull request #1474 from RosettaCommons/hahnbeom/fa_intra_elec
    
    Hahnbeom/fa intra elec

commit 7e1e880855f42127f0cfbd742f82613edc8187df
Merge: 7ce9d5b f332425
Date:   Sat Jul 23 14:40:54 2016 -0700

    Merge pull request #1476 from RosettaCommons/everyday847/fix_windows_build
    
    Don't look for sys/resource.h on Windows

commit 7ce9d5bf5174d497560ce1624761e0c166dc30c3
Merge: c68d507 d11bc3c
Date:   Fri Jul 22 16:07:06 2016 -0700

    Merge pull request #1475 from RosettaCommons/vmullig/aspartimide
    
    Add a score term to penalize sequences that are likely to result in aspartimide during peptide synthesis
    
    In designing peptides, we're having to throw away or redesign a heck of a lot of designs because of DN, DS, DT, Dx, DG, dn, ds, dt, dX, or dG sequences, which often result in the unwanted aspartimide side-product during peptide synthesis. My Thursday night project will be to add a score term to penalize these two-residue sequences during design, so that the packer simply doesn't put them in. (There are several other things that we're also having to filter for, and each one cuts down our viable designs by an order of magnitude, greatly increasing the number of designs that we have to do in order to get one that we can synthesize. This is the easiest and quickest thing for me to fix with a non-filter-based solution, increasing our good design rate by an order of magnitude or so.)
    
    Tasks:
    
    -   Add the score term.
    -   Have it only apply itself to pairs of residues that are conventionally connected (i.e. residue i is connected to residue j at residue i's C-terminus and residue j's N-terminus).
    -   Have it penalize the sequences in question.
    X  Double-check which sequences should be penalized. (Some also say DC, DD, and DR [and their mirrors]. DP and Dx', where x' is N-methylated, should be immune to aspartimide formation, though.) @gbhardwaj --> If there's a need to tweak what's penalized in the future, or to add general user controls, we can do this when we need it.
    -    Unit test.
    -    Beauty.
    -    Documentation.

commit c68d5070724eb4e1b6c1b5ee9c91bc1de6d1dfa2
Merge: 62063d8 dfec261
Date:   Thu Jul 21 19:24:29 2016 -0700

    Merge pull request #1146 from RosettaCommons/everyday847/rna-dev
    
    Cleaning up and troubleshooting ERRASER a bit; also, some non-natural residues

commit 62063d837652235ed85a376b5bac0c8f0dc39474
Merge: ef9dd4d 005326e
Date:   Wed Jul 20 11:23:28 2016 -0700

    Merge pull request #1372 from RosettaCommons/jadolfbr/antibodies/fix_h3_ab_protocol
    
    Camelid and antibody protocol fix
    
    This PR enables camelid antibodies for the antibody protocol, specifically, antibody_H3. I don't think this ever actually worked as the test for camelids was never being checked. This also adds an integration test for camelid antibodies and antibody_H3.

commit ef9dd4d294f4310252543e507083cb3c4849d65f
Date:   Tue Jul 19 18:57:59 2016 -0700

    Removing an extraneous file, and taking the opportunity to beautify master while I'm at it.

commit 0028baa6259ff5598dcf35623f6782537a4df5c4
Merge: 892dc6f 2f520dc
Date:   Tue Jul 19 18:52:35 2016 -0700

    	deleted:    source/src/protocols/cyclic_peptide/dVdPN_A.pdb

commit 892dc6f7fb355ad662847c82dc6bff29d39e2943
Merge: 3dfda33 19e4da7
Date:   Tue Jul 19 16:44:02 2016 -0700

    Merge pull request #1472 from RosettaCommons/jadolfbr/jadolfbr/carbohydrates/val_fix
    
    Fix simple glycosylation
    
    Fix an uninitialized variable in the copy constructor of glycan relax that was causing the simple glycosylation unit test to fail in valgrind. Thanks to @roccomoretti for actually debugging this and finding where the variable was uninitialized in the first place.

commit 3dfda3335774295a5053d685bb45c83c4b442446
Merge: fadb0ac 54f14ff
Date:   Wed Jul 20 07:19:14 2016 +0800

    Merge pull request #1473 from RosettaCommons/dimaio/symm_density_fixes
    
    Two small fixes for elec_dens_fast with symmetric complexes.

commit fadb0ac28d8eddd38c7703ca740510bff901f03e
Merge: 2d13982 5c1aaeb
Date:   Tue Jul 19 14:03:59 2016 -0700

    Merge pull request #1470 from RosettaCommons/hahnbeom/fa_intra_elec
    
    this is "just adding fa_intra_elec term".

commit 2d1398245393eb68d21773cbf8544100146755e3
Merge: 11809c5 97e11b1
Date:   Mon Jul 18 19:05:21 2016 -0700

    Merge pull request #1469 from RosettaCommons/jadolfbr/demo_scripts
    
    add scripts moved from demos.

commit 11809c546db6832427f0221e61b93f3201376b3f
Merge: 109f0a2 277e4b9
Date:   Tue Jul 19 04:43:49 2016 +0800

    Merge pull request #1471 from RosettaCommons/dimaio/app_bugfixes
    
    Fixing two bugs in hybridize/cartesian_sampler. Thanks @roccomoretti for finding these.

commit 109f0a264ed196f738e2583bb1d2b8ca62ccdde9
Merge: 811632d d33e40b
Date:   Mon Jul 18 10:46:06 2016 -0500

    Merge pull request #1467 from RosettaCommons/roccomoretti/valgrind_benchmark_fix
    
    More integration.py fixes
    
    
    
    Fix integration.valgrind -- slightly different flags are needed. (--skip-comparison messes it up.)
    
    Also, fix the integration test execution time ordering. (The extra directory in the test name messed things up.)

commit 811632d136667bad5c75a65e59bc0ef6faa940a9
Merge: ef059b4 98c2f3b
Date:   Sat Jul 16 23:07:20 2016 -0700

    Merge pull request #1466 from RosettaCommons/tlinsky/constraint_generator_nonglobal
    
    Add serialization support to ConstraintsMap

commit ef059b4c5486a97789e55fea41a75d0e29d3cc2f
Date:   Sat Jul 16 15:13:10 2016 -0500

    Small change to hts_io integration test.
    
    The test doesn't actually produce a screening_features.db3 file, so remove the analysis of that file.

commit ad3252184b328423ea6f575ffc06266f144889c0
Merge: ba861e0 8035a40
Date:   Sat Jul 16 14:01:05 2016 -0500

    Merge pull request #1454 from RosettaCommons/roccomoretti/alignVectorSets
    
    Fixes for numeric:alignVectorSets
    
    numeric:alignVectorSets() had some edge conditions (zero vectors, co-linear vectors) which resulted in utility_exits. Add special cases to catch these conditions and do something reasonable instead.
    
    Unit tests for alignVectorSets() added. There's some integration test changes observed (KIC_with_fragments, density_denovo), which look to be due to changes in optimizations w/r/t this inlined function. (The changes don't happen locally with a debug build.)

commit ba861e0c30adc65bf6b45695071e3c34a8243c0d
Merge: 4c3be7c 99239ed
Date:   Sat Jul 16 11:45:59 2016 -0500

    Merge pull request #1465 from RosettaCommons/amelie-stein/ddG_with_ligands
    
    On behalf of Amelie, merge in some fixes to the ddg_monomer applicaition to allow it to work with non-amino acid residues.

commit 4c3be7cd05e33361cdbdd1f7bfbb666530440f85
Merge: a49b29d 0588286
Date:   Thu Jul 14 18:33:24 2016 -0700

    Merge pull request #1458 from RosettaCommons/vmullig/ncaa_betanov
    
    Fix loading of NCAA rotamer libraries when using beta_nov15
    
    The problem turned out to be that beta_nov15 turns on the Shapovalov rotamer libraries, which have a slightly different file format (an extra column in the middle of the file, which is irritating). When an NCAA library is loaded, it is therefore misinterpreted: Rosetta assumes that the extra column is there when it is not. The solution is to count the columns in the first line and to determine whether a file is a Shapovalov-format file or not.
    
    Tasks:
    
    -    Fix the bug.
    -    Merge the latest master into branch.
    -    Fix the fix so that it doesn't break the loading of gzipped rotamer libraries.
    -    Beauty.

commit a49b29d96564db596b09f5a6e72239dc797b8ba1
Merge: 98ae263 e319077
Date:   Thu Jul 14 15:44:29 2016 -0700

    Merge pull request #1455 from RosettaCommons/tlinsky/constraint_generator_nonglobal
    
    Remove global data from ConstraintsManager

commit 98ae2632f27254659d148005391190df046f57e2
Merge: 4069494 fb3b467
Date:   Thu Jul 14 08:32:00 2016 -0700

    Merge pull request #1459 from RosettaCommons/tlinsky/tlinsky/ss_filter_selector
    
    Add residue selector support to SecondaryStructureFilter

commit 40694948a6960c135c0cf53d381f5bee569690f2
Merge: 196fc44 fc9d964
Date:   Wed Jul 13 21:36:31 2016 -0400

    Merge pull request #1453 from RosettaCommons/lqtza/prepack_centroid_fix
    
    Docking Prepack Outputs Full-Atom Poses Only

commit 196fc442ba8b95d82325bf539612ff458ddc9254
Date:   Wed Jul 13 20:51:00 2016 -0400

    Fixing PyRosetta build on Ubuntu 16.04

commit 2ed6b8e4427473c98bd7a4ca47ad9fc92439ae84
Merge: 892c812 baf8c2e
Date:   Mon Jul 11 14:32:32 2016 -0700

    Merge pull request #1446 from RosettaCommons/bfrenz/denovo_density_point_selection
    
    Bfrenz/denovo density point selection

commit 892c8123fdeea22b6119abecf2ea6de9edda8e5d
Merge: 0f120c1 b81112d
Date:   Mon Jul 11 13:32:53 2016 -0700

    Merge pull request #1448 from RosettaCommons/xingjiepan/LoopBuilder_bug_fix
    
    Remove the idealize_loop() function in LoopBuilder::do_apply()

commit 0f120c1d363716d95e0ab07af64388db5c3998db
Merge: 6f2c615 5b2c6c5
Date:   Mon Jul 11 15:43:01 2016 -0400

    Merge pull request #1452 from RosettaCommons/Cyrus/mergetarget
    
    Cyrus/mergetarget
    
    Included in this PR:
    
    PR Cyrus 35: add comment clarifying pilot_apps.src.settings.release (there was some list traffic here)
    
    PR Cyrus 31: global replace old UNC address with gmail address in doxygen tags (smlewi@unc->gmail)
    
    PR Cyrus 33: Tweaks SSPredictionFilter (actually PsiPredInterface) to automatically allow for a second type of name mangling from a different version of runpsipred
    
    PR Cyrus 32: Smlewis cyrus/beta nov15 score catcher: Catches the problem where you pass a beta weights file without the accompanying required flag to activate the params overrides. (exit from ScoreFunctionFactory in the (in)appropriate circumstance).
    
    Also PR Cyrus 29, which got caught in a time vortex, and was merge -X theirs overwritten because Rhiju was forced to duplicate the code itself instead of taking it from its original crossfork PR.

commit 6f2c615bc0ae0effe0c8dcc30fc5cf9bb182fd6e
Merge: 6e1fba8 ea775dc
Date:   Sun Jul 10 17:54:27 2016 -0700

    Merge pull request #1449 from RosettaCommons/vmullig/small_genkic_tweak
    
    Adding option to the GeneralizedKIC mover ("dont_fail_if_no_solution_found=true") to NOT set mover status to failure if no solution is found.  (The default is false, which means that the mover WILL exit with failure status if no solution is found, aborting a trajectory.  There are some cases in which one might not want this, though.)
    
    Tasks:
    
    -    Add option, setter function, and parsing in parse_my_tag().
    -    Have it control mover status.
    -    Update documentation.
    -    Beauty.

commit 6e1fba8ddaff1dd266a9d2886f5755dda4a4f037
Merge: 7575a41 579bbba
Date:   Sun Jul 10 14:53:45 2016 -0700

    Merge pull request #1433 from RosettaCommons/everyday847/n3_adenine_prot
    
    Adenosine protonation variants

commit 7575a419bd978497b411db00240c2622d5d9480d
Merge: 679718a 6608372
Date:   Sun Jul 10 10:22:11 2016 -0500

    Merge pull request #1447 from RosettaCommons/bazzoli/ignore_waters_by_default
    
    Ignore waters by default.

commit 679718a25282a2bc8c5f2601a57af3f706afb541
Merge: 4fa8a7c 3a0b68a
Date:   Sat Jul 9 22:16:36 2016 -0600

    Merge pull request #1450 from RosettaCommons/sergey/binder
    
    Adding bindings for ObjexxFCL

commit 4fa8a7c2566212456f87ba925d74c89d37390a03
Merge: d6e5143 ebe9685
Date:   Fri Jul 8 18:45:21 2016 -0700

    Merge pull request #1441 from RosettaCommons/tlinsky/symmetry
    
    Add simple unit test and doxygen for core::pose::symmetry::symmetrize_fold_tree

commit d6e5143553a5ce5eaa3f4dc02231fb89eae59f02
Merge: b0fa12d fe66630
Date:   Sat Jul 9 02:40:56 2016 +0800

    Merge pull request #1443 from RosettaCommons/dimaio/multichain_hybrid_bugfixes
    
    A bug in my previous checkin with multichain hybridize

commit b0fa12d5047586049e2ed40a42094f117eae2c8d
Merge: e0e867a e1d6361
Date:   Thu Jul 7 21:15:40 2016 -0700

    Merge pull request #1431 from RosettaCommons/tlinsky/helix_pair_filter
    
    Update and clean up HelixPairingFilter, add unit test

commit e0e867ae858c66ff32f9754069ad631b9cbfe2a7
Merge: c384a55 416785f
Date:   Thu Jul 7 20:16:22 2016 -0400

    Removing unneeded include to fix release’s

commit c384a555794a9577971b5b0503f5a0fe9a99514f
Merge: da19bd8 1152fe7
Date:   Thu Jul 7 08:39:48 2016 -0700

    Merge pull request #1439 from RosettaCommons/tlinsky/delete_region_pdb
    
    Make DeleteRegion parse_my_tag congruent with documentation

commit da19bd82721e0d78c06fb3888483bdfaa3a13769
Merge: 02cecca 37c4103
Date:   Thu Jul 7 11:10:12 2016 -0400

    Merge pull request #1442 from RosettaCommons/rhiju/rna_denovo_setup
    
    + hotfix to FARNA integration test that includes VRT residue
    + also removing some unnecessary verbiage from rna_denovo_setup
    + restoring rna_puzzl5_P15P3P8... test which used virtual residue & rigid body docking of all segments.
    + tests look OK

commit 02ceccaa92244b8c096a4e2a38b59e4ca5b90907
Merge: 5f0a431 60919f2
Date:   Thu Jul 7 08:29:50 2016 +0800

    Merge pull request #1436 from RosettaCommons/dimaio/multichain_hybrid_bugfixes
    
    Fix a few bugs in hybridize with multichain poses.
     - Run a bit faster when DetailedControls are enabled by skipping unnecessary calcs.
     - Move some output to Trace level.
    hybridize/mr_protocols integration test changes expected.

commit 5f0a4310ff9d47a33afca4c7a8eca7d867f4881f
Merge: 5cdaa7a ada631c
Date:   Wed Jul 6 13:42:28 2016 -0400

    Merge pull request #1437 from RosettaCommons/rhiju/rna_denovo_setup
    
    fix getcwd() compile bug in ubuntu.
    standard tests look OK (except profile, not yet complete), and separately ran ubuntu builds

commit 5cdaa7aefea25017eb4ba68f34c6e4c9deec17b7
Date:   Tue Jul 5 19:00:35 2016 -0400

    PyRosetta, decreasing runtime of Workshop5test.py test

commit bc361c50ee2051250ea236870f25e5a88258ffcd
Merge: 5209f47 2251974
Date:   Tue Jul 5 06:14:59 2016 -0700

    Merge pull request #1434 from RosettaCommons/rhiju/rna_denovo_setup
    
    Rhiju/rna denovo setup
    Some small updates to input & help in rna_denovo
    • iccbuild is failing due to license issue on test server
    • in integration tests, new test `rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation` is having a problem -- will fix in a separate pull request.
    • `hybridization` test was broken previously.

commit 5209f47ba636688f3470733c4c5bc878d2f022ab
Merge: 55ba4c3 2da458d
Date:   Mon Jul 4 12:09:28 2016 -0700

    Merge pull request #1432 from RosettaCommons/rhiju/rna_denovo_setup
    
    Rhiju/rna denovo setup
    + integration tests for `rna_denovo` give cosmetic changes -- all confirmed/checked locally.
    + some new integration tests `rna_puzzle_*`.
    + other integration tests that change only do so in linux.release_debug or mac.clang but not both, suggesting uninitialized variables or other stochastic choices depending on system state.
    + icc build broken on Hojo3, but error message is about license problem, so i don't think that's this pull request.
    + profile  may have changed in 1-2 tests, but getting timeout on test server. 1-2 profile test changes in previous build appear within bounds of variability of these tests.

commit 55ba4c3a290fdf4e54ccc02a6b0a9e628c881614
Date:   Sun Jul 3 18:40:05 2016 -0400

    Increasing run time for PyRosetta4 test. Increasing profile tests tolerance.

commit 680b8217792076090e9199f7946de6ec3a5bbd3f
Date:   Sat Jul 2 19:58:35 2016 -0400

    Adding PyRosetta4 release tests

commit 8439cb3a2493c8f243d6178797c1d060c138ed9f
Merge: ff77e15 d3818bb
Date:   Sat Jul 2 17:52:04 2016 -0400

    Merge remote-tracking branch 'origin/master' into sergey/binder

commit ff77e156480078151619850a066217ceb148ff96
Date:   Sat Jul 2 17:51:33 2016 -0400

    Updating PyRosetta4 package to include demo and tests

commit 8e0a129e628ed0ac0f308b3c71df0fb0d9b6c49f
Date:   Fri Jul 1 20:04:18 2016 -0400

    Adding PyRosetta4 release tests

commit 2e6f3507baba16db564a0507209450964e1224c4
Date:   Sat Jun 25 19:37:16 2016 -0400

    Refactoring PyRosetta generation procedure to make results more reproducible on different os/compiler/filesystems

commit 442254b23335349ada054fe847d4561628a117aa
Date:   Sat Jun 25 12:47:59 2016 -0400

    disabling deprecated code

commit 97869caeaf0dd23a1484f88020a62967b5401331
Merge: d8d0ecd 0142294
Date:   Fri Jun 24 21:31:17 2016 -0700

    Merge pull request #1419 from RosettaCommons/vmullig/better_errors
    
    Add some more informative error messages

commit d8d0ecd7982d60b7494207740747fcc33c2a569d
Merge: afeafd3 ccb5ba9
Date:   Fri Jun 24 18:11:03 2016 -0600

    Merge pull request #1416 from RosettaCommons/sergey/binder
    
    fixing PyRosetta SubClassing* tests

commit afeafd30570a2eb1d0b353527e1edb7a009f6772
Merge: fa97b18 dbe4249
Date:   Fri Jun 24 11:33:54 2016 -0400

    Merge pull request #1413 from RosettaCommons/Cyrus/mergetarget
    
    Cyrus/mergetarget
    
    Four changes here:
    
    README.md: a minor informational change, originally meant to test these cross-fork PRs
    
    source/src/apps/pilot/smlewis/LoopAnalyzer.cc: bitrot repair in a disabled pilot app
    
    source/src/protocols/constraints_additional/BindingSiteConstraint.cc: adding comments gleaned from a deep SVN archaeology dive
    
    source/src/protocols/constraints_additional/BindingSiteConstraint.hh
    
    source/src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc: fixing a bug introduced by 543ed88 (a two year old refactoring)
    source/src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc
    
    No test changes expected. The only compiled code change prevents a crash, so this code path was perforce untested before.

commit fa97b18fe8f8daca1444cd6600061db516c5e146
Merge: 3a6815b 29345d3
Date:   Thu Jun 23 00:53:17 2016 +0200

    Just updated my old pilot app and merged with master

commit 3a6815b8ab0333ba6a457c4d2f39ef8777616450
Date:   Wed Jun 22 14:34:46 2016 +0200

    a small fix to my pilot app