commit 557d20a0ffd23ea37bf785dd0f8038cf402ad8ae
Merge: 996f1cd 8d3ac8c
Date:   Tue May 31 11:25:00 2016 -0700

    Merge pull request #1366 from RosettaCommons/hahnbeom/residue_depth
    
    Adding residue depth filter

commit 996f1cd1879fe7c9036aec41208375f03f5727a9
Merge: 1fdd40a cfa826b
Date:   Sun May 29 17:38:26 2016 -0700

    Merge pull request #1365 from RosettaCommons/vmullig/fix_rama_uninit
    
    Trying to fix uninitialized var issue flagged by Valgrind.
    
    Turns out that it was a couple of new variables that were initialized in the default Ramachandran constructor, but not in an alternative constructor.

commit 1fdd40a139d1fb97a3c51957a27d4d6830ff705a
Merge: bcfbf55 a466429
Date:   Sun May 29 10:10:19 2016 -0700

    Merge pull request #1367 from RosettaCommons/rhiju/magnesium_in_stepwise
    
    Code updates needed for modeling RNA residues around magnesium ions for ERRASER and stepwise modeling. Includes code for optimizing water locations and orientations around Mg(2+) during stepwise.
    
    No tests change, except for floating point issues & minor output changes to mg_modeler & number_of_residue_types, which are expected.

commit bcfbf55f0cbe140542e5afb4e2d64a597285d2d3
Date:   Fri May 27 17:37:20 2016 -0400

    Adding measurement units to profile test graphs legends

commit a170acff5b4d61dd4f301b0aa71aadd2a2307256
Merge: d1b399e 1252cf8
Date:   Thu May 26 14:33:42 2016 -0400

    Merge pull request #1356 from RosettaCommons/weitzner/ab_auto_kink
    
    Antibody: auto kink! adding the ability to generate a kink constraint on-the-fly for the H3 modeling phase of antibody_H3

commit d1b399e822e26a981c83a47d79fdba57bde5634e
Merge: 61f9e24 ea2e25d
Date:   Thu May 26 00:19:58 2016 -0700

    Merge pull request #1362 from RosettaCommons/vmullig/move_fastdesign
    
    Moving FastDesign from devel to protocols.
    
    FastDesign is very widely used, and is pretty feature-complete (I don't think anyone is developing it much), but it has been sitting in devel for some time. I want to write a protocols-level algorithm that invokes it, but can't as long as it's in devel, so I'm going to move this to protocols.
    
    Tom Linsky has also gone through this and cleaned up the FastDesign code a bit, removing some extraneous stuff.

commit 61f9e240485b755a263dda2f1dc951ce783628e3
Merge: 3dd6c2d 1e155a2
Date:   Wed May 25 11:42:33 2016 -0700

    Merge pull request #1363 from RosettaCommons/jadolfbr/make_cdr_cluster_ident_public
    
    Promote the identify_cdr_clusters app to public, as suggested by @lqtza.  This app can be used for any numbering scheme and cdr definition.  It will print the cdr cluster information and echo the info to any output PDB.
    
    Documentation is here:
    https://www.rosettacommons.org/docs/wiki/application_documentation/antibody/CDR-Cluster-Identification
    
    An integration test is currently in Rosetta.

commit 3dd6c2dedb6c5d27b4f24033127b242768d90691
Merge: 08f28fd 718807b
Date:   Mon May 23 23:02:34 2016 -0700

    Merge pull request #1360 from RosettaCommons/vmullig/countpair_issue
    
    Cache FA_Elec data that are loaded repeatedly with beta_nov15
    
    With the beta_nov15 scorefunction, certain FA_ElecEnergy data are loaded from disk every time the term is instantiated or cloned. This is a HUGE problem in protocols that copy scorefunctions in loops -- especially when they're being run on Blue Gene. This pull request aims to allow these data to be read once per process and cached as global (static) data.