commit 876e2a9469b95aa69c02d1daf3bf0d40f34d2694
Date:   Fri Jun 19 15:17:13 2015 -0400

    Update release.py
    
    Inexplicable typo from my recent merge... My apologies, Sergey!

commit 62b4114621ff4bde7dd34b8b82af31cde0f45760
Merge: 3a00193 1a3f250
Date:   Fri Jun 19 09:45:18 2015 -0400

    Merge pull request #574 from RosettaCommons/dougrenfrew/fix_tcre_tests
    
    Adding a missing param tot he TCRE methods. Changing oop_dock design to only to a single run. This should fix the instability in the ncaa_fixbb and oop_dock_design integration tests and the mm_std_fa_elec_dslf_fa13_split_unfolded score function finger print test

commit 3a00193cdb743d37589d22ae52fdf57b417dfa7a
Merge: 53eecd9 f0c1db9
Date:   Fri Jun 19 08:00:25 2015 -0400

    Branching: Various updates to branching/chemical conjugation: Part A
    
    This is a merging in of Part A of Pull Request #459
    
    NEWS: This merge...
    
    * Adds a new TorsionType for branch connection torsions, which are located at
      CHEMICAL EDGEs of the FoldTree.
    * Adds a new BRANCH TorsionType to MoveMap.
    * Adds the ability to get or set a torsion angle in the AtomTree by TorsionID
      containing a BRANCH TorsionType.
    * Allows the minimizer functionality to minimize TorsionIDs containing BRANCH
      TorsionTypes if permitted by MoveMap.
    * Has Rosetta automatically set up a FoldTree in the reverse direction for
      ubiquitin on load-in from a PDB file without resorting to Movers by using
      LINK records (as wanted by @hajosep).
    * Has Rosetta ignore LINK records defining sugar main chains that Rosetta could
      figure out on its own anyway (as wanted by @fdimaio for easier loading of
      glycoproteins for crystal refinement).
    * Automatically sets angle and bond constraints for chemical conjugation based
      on LINK records.
    
    @everyday847 also contributed to this branch.
    
    I am keeping the pull request open, as not all desired/related tasks are
    completed.
    
    ----------------------------------------
    Unit test status: Pass
    Integration test status: 20 changed tests
        carbohydrates:             expected
        c_term_conjugation:  new
        18 other tests:      output modifications regarding branches or the MoveMap

commit 53eecd97da4ed4e2e8a392bc89949c5d9b19bbe6
Merge: 68ce915 2b81d59
Date:   Thu Jun 18 16:09:50 2015 -0400

    merging in master to resolve conflicts before merging in current work in this branch/pull request

commit 68ce9158c11b888379430f52d86cc2a969acdc16
Merge: 9817e95 ef51c81
Date:   Mon Jun 8 11:39:43 2015 -0400

    merging master before testing on server

commit 9817e9587847b89a09eceb3957bec00b4192c2b1
Date:   Mon Jun 8 11:33:13 2015 -0400

    PDB Input/Output: Rosetta now ignores redundant LINK records, instead of crashing

commit 56e6bb6429a856a491d4370f0e2e38e8a74f79c0
Date:   Fri Jun 5 17:40:07 2015 -0400

    restoring carbo tests post bug fix

commit bed58f2dfe33da83d5b0fd7a011e592fc2a18a03
Date:   Fri Jun 5 17:29:00 2015 -0400

    bug fix

commit 87648c2f7180838e72dbfb9c193ebee1370f7fa2
Merge: b7c4ae9 9446eba
Date:   Thu Jun 4 17:35:12 2015 -0400

    merging in master and resolving merge conflicts

commit b7c4ae9c159d4df71f4223d8f9b948bd0654e60d
Date:   Thu Jun 4 17:16:45 2015 -0400

    namespacing bug fix

commit 74ec36907105b7b25c2ea016e41dc8b1808d559b
Date:   Tue May 19 14:32:24 2015 -0400

    Additional constraints (dihedral and angle). Inferred from linked atom name.

commit b96a4e93e962ac0c8909c25e82ae15686b3fb247
Date:   Sun May 17 21:57:51 2015 -0400

    Compilation fixed. Weird boost foreach issue

commit 1f1fe2a3d547e12b3ee0ab15bfbcaeeaf9ec9b3a
Date:   Sun May 17 17:55:49 2015 -0400

    Changing name of constraint-from-link function for namespacing issue?

commit 283c4c6b6da784743bf02faa6d826630a62490f8
Merge: 33859f7 fb3dbb3
Date:   Sun May 17 13:17:24 2015 -0400

    Merging in master; maybe it will help to debug this weird boost building issue!

commit 33859f74e10f91fb92ce1461bf46dd1c099509b6
Date:   Sun May 17 13:17:04 2015 -0400

    Simple constraints (just atom-pair for now) based on link records for sidechain conjugation

commit 8efd2b8280986b250447a82d0ebb1bbd0488c80d
Date:   Fri Apr 24 17:17:42 2015 -0400

    removing GCC warning

commit 2ece7fefc5e7454dd9ae91ffbce0e2fd78c6d50f
Merge: ea4fb84 b387389
Date:   Fri Apr 24 16:27:06 2015 -0400

    merging in master for testing

commit ea4fb840ea31aa7531981498c81cd5f1c0178ddc
Date:   Fri Apr 24 16:15:44 2015 -0400

    Branching: adding patch file for C-linked branching/conjugation

commit 28ff8781347e55a0be6fa280160d381a621bdc10
Date:   Fri Apr 24 15:38:02 2015 -0400

    changing more Tracer volumes

commit a6bc2298bcdbd18cc81424b46bedd78e7119baab
Date:   Fri Apr 24 15:32:21 2015 -0400

    Branching: C-terminal conjugation: FoldTree runs backwards on import from PDB without having to use a Mover

commit 7e8295121f41817d6f9a755d1a716361f543ad2b
Date:   Fri Apr 24 11:25:30 2015 -0400

    changing tracer volume to make deciphering itegration test changes easier

commit 04bbc91383a84400be37af623375717c58ee5671
Date:   Thu Apr 23 17:13:24 2015 -0400

    Branching: turning off un-needed checks during pose-building that make bad assumptions

commit 25b2693ab0570cda5951278c4d463cb916c06a3a
Date:   Thu Apr 23 16:41:43 2015 -0400

    squashing a warning on the test server

commit 236ce007c23887f8d5ef2a29cc12d6a74574e245
Date:   Thu Apr 23 15:46:40 2015 -0400

    Branching: refactor of set_reasonable_fold_tree() part I

commit 1e0839e5248ba606cf3de045c45e9aaa6a41c30d
Date:   Thu Apr 23 14:09:02 2015 -0400

    Branching: pilot app/integration test expansion

commit 611a25b13a29c97557a65b58de9b60b52a5567f5
Date:   Wed Apr 22 21:32:03 2015 -0400

    Branching: fixing tracers; fixing patch files

commit 16777afdabad53df9348e8ff0d1f0c80b4febcc4
Date:   Wed Apr 22 21:03:33 2015 -0400

    Branching:typo in O-linked patch

commit f4b528bd873a1388f54bbfc9df4b4ce0c6a9dbc8
Date:   Wed Apr 22 19:59:14 2015 -0400

    Branching: adding C-terminal_conjugation.txt patch file

commit 8804f3d04e03a8a0c7d3793627a4432e6e3c3bdd
Date:   Wed Apr 22 19:01:07 2015 -0400

    Branching:branch patches only read in if option is set

commit d685a1ba056608fc6142b074901d197c42c08e2f
Date:   Wed Apr 22 18:34:45 2015 -0400

    Branching: moving O-linked glycosylation patch to a more general location in the database and renaming to be the generic O-linked conjugation patch

commit b9e7504dda98251a437e968fffc81702431e0eb6
Date:   Wed Apr 22 18:03:44 2015 -0400

    Branching: adding files for testing of C-terminal conjugation

commit 3a04759a0cb5e14d6249d66960cd22b693cd7f99
Date:   Sat Apr 18 23:29:46 2015 -0400

    Carbohydrates: scoring fixes; I'm confused about L-sugar scoring....

commit 55e5a8ae9b7f11e8bb58d1f3e9889459d4b19679
Date:   Sat Apr 18 22:04:14 2015 -0400

    Branching: serious bug fixes in minimizations of rings and branches

commit c180f4a17b88cb6d1554913dd85d37c9f80d5fb4
Date:   Sat Apr 18 19:16:11 2015 -0400

    TorsionID: improving output

commit 00fde2c06a9f959c41f7b7db46a92f53b446cbc9
Date:   Fri Apr 17 20:02:40 2015 -0400

    Carbohydrates: updating carbohydrating scoring integration test, which demonstrates that the BRANCH TorsionType is working properly with the MoveMap and the MinMover, and I can minimize a CHEMICAL EDGE/branch point connection torsion

commit 6431eee1c06c9973ac828066c15eeb33f02b894d
Date:   Fri Apr 17 19:43:01 2015 -0400

    Carbohydrates: improved sugar_bb score to evaluate BRANCH TorsionTypes

commit cf199ef1f0ea345a772e6de2cdb2d9d855af08d2
Date:   Fri Apr 17 19:36:21 2015 -0400

    Branching: setting up MinMover to minimize BRANCH torsions

commit 39ee4d5c6b56a7fed810c2911bd34e9b9870594c
Date:   Fri Apr 17 18:27:52 2015 -0400

    Carbohydrates: correction to sugar scoring method when using L-sugars

commit 039e2d65453479236f656efabc2a2a06086e7e00
Date:   Fri Apr 17 17:56:15 2015 -0400

    Branching: removing commented-out code

commit 0ca0b3ceebf429f693d5acf67469bd0db7698fba
Date:   Fri Apr 17 17:32:10 2015 -0400

    bug fix

commit f1426ecd1bfb590599e13204ab5a93a61f9f90b8
Date:   Fri Apr 17 17:15:15 2015 -0400

    Branching: Conformation::torsion() and Conformation::set_torsion() now should work with TorsionIDs that have the BRANCH TorsionType

commit db130bc79950a016bfc951982cd53b5c8ca6a087
Date:   Fri Apr 17 16:37:54 2015 -0400

    making method const

commit c188112747226dfb82a20d23ccdc998c779a70f6
Date:   Fri Apr 17 16:23:44 2015 -0400

    Branching: moving helper method from pose/carbohydrates/util.cc to conformation/Residue.cc and renaming to make more general

commit a6a55f5fc356bb06afd796e6718aaa6bea9dd4b6
Date:   Fri Apr 17 13:09:45 2015 -0400

    Branching: comments/style fixes/notes to self and to Andy and the Dougs while looking around

commit 23bdecc64b98ea3add96443f54507dbb83c72cd3
Date:   Fri Apr 17 12:35:54 2015 -0400

    Branching: adding much needed comments to clarify huge difference between JUMP TorsionIDs and other types

commit 54fe90f231cbe8931eb7865e184342278cdd2eb6
Date:   Wed Apr 15 18:42:43 2015 -0400

    Branching: updating MoveMap show() methods... and fixing a bug in one of them

commit d4332d978887043c58cb61d7b6415635ac3d8d3c
Date:   Wed Apr 15 18:29:43 2015 -0400

    Branching: adding MoveMap getter for BRANCH TorsionType

commit 93478c012a8ebc82601b198d298abfd6262bc729
Date:   Wed Apr 15 18:24:53 2015 -0400

    Branching: adding MoveMap setters for BRANCH TorsionType

commit be81b19f23ef6a7416677cc728ffdb9169dd212a
Date:   Wed Apr 15 18:08:33 2015 -0400

    Branching: adding BRANCH TorsionType

commit ed487459f913e5cd71b2800462d2ee76594c5e58
Merge: 4a6e844 045b165
Date:   Wed Apr 15 17:48:31 2015 -0400

    merging in master to begin branching code work

commit 4a6e844ed8f1d0ca341425d54db2976c15f3ac24
Merge: d2fc6e7 6d98dd0
Date:   Thu Aug 8 16:39:12 2013 -0400

    merging in master for integration testing