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