commit a2a641bc30be678f9c06dae2a56f43ad493a15ac
Merge: 38fb1e6 ab9f597
Date:   Mon May 9 10:55:56 2016 -0700

    Merge pull request #1323 from RosettaCommons/tlinsky/random_residue_selector_rg
    
    Replace instance of std::random_shuffle with Rosetta's random_permutation

commit 38fb1e6fee3d3ccfd4cf35912bbd5f28b2b08a78
Date:   Sun May 8 23:22:04 2016 -0700

    Update README.md

commit acb160bc4541f485a32ae3ea7341dee4ad2562a5
Date:   Sun May 8 23:21:22 2016 -0700

    Update README.md

commit 7e3aa18d15737ae03a763739e8360a2ee33548eb
Merge: b76784e 5b41c26
Date:   Sun May 8 22:13:17 2016 -0700

    Merge pull request #1326 from RosettaCommons/vmullig/write_template
    
    Adding option to rosetta_scripts to print a template script
    
    I often find myself going to the help wiki to find the template RosettaScript whenever I sit down to write a new script. If I'm working on a laptop without an Internet connection (e.g. on a train or a plane), this is a particular pain in the neck. This pull request adds a flag, -print_template_script, to the rosetta_scripts application that lets the application print out a blank, template RosettaScripts script and then exit. This should be handy for quick reference when sitting down to write a new script.
    
    Tasks:
    --    Add the feature.
    --    Documentation.

commit b76784e4dfab959256a5f240f5fc004d92544d92
Merge: 27e3028 582c547
Date:   Sun May 8 22:08:45 2016 -0700

    Merge pull request #1325 from RosettaCommons/vmullig/fix_rama_power
    
    Tweaking recent implementation of power scaling of rama values greater than zero
    
    -- Removes repeated call to options system whenever rama scoring occurs.
    -- Makes the option a Real instead of an integer (since fractional power values might be useful).
    -- Adds a unit test for the option.

commit 27e3028731ce3f957abcea7505fb39a6ab1690c8
Merge: aaaca21 4f7e5f3
Date:   Sat May 7 15:46:04 2016 -0700

    Merge pull request #1324 from RosettaCommons/vmullig/std_random_begone
    
    Remove other instances of std::random_shuffle() from the code.
    
    There are one or two places where std::rand() and std::random_shuffle() are used with good reason. In all other instances, Rosetta's random number generating system should be used (which means random_permutation() instead of std::random_shuffle()). This pull request is a complement to #1323, removing other instances of std::random_shuffle().
    
    It would be very interesting if this resolves the current integration test instabilities on the test server.

commit aaaca21077d8c8b91572952c0acbeb999e304c7e
Merge: 9bb8be9 9756ada
Date:   Fri May 6 15:51:50 2016 -0700

    Merge pull request #1318 from RosettaCommons/vmullig/rosettascripts_include
    
    Add inclusion to RosettaScipts
    
    Users want to be able to do something like the following:
    
    <ROSETTASCRIPTS>
         <xi:include href="my_common_residueselectors.xml" />
         <xi:include href="my_common_taskoperations.xml" />
         <xi:include href="my_common_filters_and_movers.xml" />
         <PROTOCOLS>
              <Add mover="fastrelax" />
         </PROTOCOLS>
    </ROSETTASCRIPTS>
    
    Where the included files might be something like:
    
         <RESIDUE_SELECTORS>
              <... selector definition 1 ... />
              <... selector definition 2 ... />
              <... selector definition 3 ... />
         </RESIDUE_SELECTORS>
    
         <TASKOPERATIONS>
              <... taskoperation definition 1 ... />
         </TASKOPERATIONS>
    
         <FILTERS>
              <... filter definition 1 ... />
              <... filter definition 2 ... />
         </FILTERS>
         <MOVERS>
              <... mover definition 1 ... />
              <... mover definition 2 ... />
         </MOVERS>
    
    All of this would automatically and naïvely (i.e. saving error-checking and interpretation for later) be concatenated, with the included files inserted in place of the INCLUDE statements, to give:
    
    <ROSETTASCRIPTS>
         <RESIDUE_SELECTORS>
              <... selector definition 1 ... />
              <... selector definition 2 ... />
              <... selector definition 3 ... />
         </RESIDUE_SELECTORS>
         <TASKOPERATIONS>
              <... taskoperation definition 1 ... />
         </TASKOPERATIONS>
         <FILTERS>
              <... filter definition 1 ... />
              <... filter definition 2 ... />
         </FILTERS>
         <MOVERS>
              <... mover definition 1 ... />
              <... mover definition 2 ... />
         </MOVERS>
         <PROTOCOLS>
              <Add mover="fastrelax" />
         </PROTOCOLS>
    </ROSETTASCRIPTS>
    
    This pull request aims to implement this. Note that there is existing <INCLUDES> block functionality, but this only allows users to append XML to a script, which isn't very useful -- it doesn't let them insert XML at the point of inclusion, which would be far more useful.
    
    Tasks:
    -    Add <xi:include href="" /> parsing prior to the rest of script interpretation.
    -        Debug.
    -    Unit test.
    -    Improve circular inclusion detection logic.
    -    Unit test for detecting circular inclusion.
    -    Integration test.
    -    DOCUMENTATION.
    -    Beauty.

commit 9bb8be98df23f7c3c84f9ff1c3119de8ac2bbca2
Date:   Fri May 6 10:28:34 2016 -0700

    Option for adjusted rama scoring function (steeper penalties for bad rama; this has been useful in Foldit design).
    
    No changes in integration tests.

commit e932e5600cd8c3fe38bf192ddf5d9963423fdc59
Merge: 1c2facc 947108a
Date:   Fri May 6 07:35:33 2016 -0700

    Merge pull request #1319 from RosettaCommons/tlinsky/random_residue_selector
    
    Add residue selector that selects random residue(s)

commit 1c2faccbb32d36c39e91aa298e1f0e67fd28c09d
Merge: 41fa410 2c01594
Date:   Fri May 6 00:13:16 2016 -0700

    Merge pull request #1320 from RosettaCommons/tlinsky/constraint-generator
    
    Add option to CoordinateConstraintGenerator to force native alignment

commit 41fa4103d448823648a19eb2b8d3d3d7c437d2b9
Merge: 19fa678 bff1159
Date:   Wed May 4 18:46:18 2016 -0600

    Merge pull request #1313 from RosettaCommons/antibody
    
    Update antibody app

commit 19fa678ec02f692c4d8cc667f755bb9c0d17fa38
Merge: 1ab7679 8447742
Date:   Wed May 4 16:37:46 2016 -0700

    Merge pull request #1317 from RosettaCommons/vmullig/tweak_bettercluster2
    
    Tweaking a pilot app
    
    Enclosing bettercluster.cc pilot app's main() function in a try/catch block. Will merge without testing.

commit 1ab7679f797325c44bfcf84ebbbddb334c86b5a5
Merge: 63b9853 59a78b7
Date:   Wed May 4 16:14:15 2016 -0700

    Merge pull request #1316 from RosettaCommons/vmullig/rosetta_bluegene2
    
    Fixing the Blue Gene build now that libxml2 has been added
    
    Since this only affects a build that's not tested on the test server, I'm merging without testing.

commit 63b98534d1fd974949ef9cb481e0fef0faab6c06
Merge: 71ea838 fce0390
Date:   Tue May 3 16:53:10 2016 -0700

    Merge pull request #1312 from RosettaCommons/hahnbeom/normalmode_update2
    
    Fixing issues with extra_res in NormalMode

commit 71ea838051cc64c2442b6ecf5aa75f20cbb0e984
Merge: 3ba9874 bcb0237
Date:   Tue May 3 15:25:23 2016 -0400

    Merge pull request #1230 from RosettaCommons/aleaverfay/libxml2_to_master
    
    Adding a new external library to Rosetta: libxml2.  This allows for the automatic validation of an XML file against an XML Schema, so that we can detect badly formatted input files.
    
    Improving the API for the definition of XML Schemas. It is now substantially easier to define schemas for elements that themselves contain subelements.
    
    Defining XML Schemas for TaskOperations, ResFilters, and ResLvlTaskOperations in addition to ResidueSelectors. In addition, the factories for each of these four kinds of classes now have unit tests to ensure that each class that is registered with the factories needs to define a valid XML schema. (Note: for a schema to be valid is not the same thing as for the schema to be correct. A valid schema is merely recognizable to something that parses xml schema; a correct schema accurately describes the language read by those classes trying to parse the input XML files).
    
    Thanks, Andy @everyday847 for all your help in writing these schemas.

commit 3ba9874e6ce43024c7abfe36b9a043d0f0d86eaf
Merge: e7364f2 bd7e489
Date:   Tue May 3 09:30:05 2016 -0400

    Merge pull request #1276 from RosettaCommons/JWLabonte/sugars/docking
    
    Carbohydrates: Bug fixes for sugar docking
    
    This fixes a miscellany of bugs related to docking that affected sugar-docking, some mine, some other people's.
    
    All tests pass; sugar-related integration tests expected. 2 other tests show changes because of high tracer volume.

commit e7364f2e3a1c0f96052a37607e15f35409765ec1
Merge: edf4261 88b12be
Date:   Mon May 2 14:55:19 2016 -0700

    Merge pull request #1297 from RosettaCommons/tlinsky/rotamer_boltzmann_residue_selector
    
    fix uninitialized value in RotamerBoltzmannWeight filter

commit edf4261c200b16d1700765d3eff4c06cca9c5dda
Merge: 5e610c8 e89b74a
Date:   Mon May 2 14:55:04 2016 -0700

    Merge pull request #1293 from RosettaCommons/tlinsky/constraint-generator
    
    Add modules for generating constraints (e.g. sheets, hbonds, etc)