# [ONE LINE DESCRIPTION OF CHANGE]
# NEWS: [DETAILED DESCRIPTION OF CHANGE]
# ----------------------------------------
# Unit test status: [Pass/Fail/Not Run]
# Integration test status: [Number of changed tests / Not Run]
# [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ...
# explanation of change, cont'd.
# [NAME_OF_CHANGED_TEST_2]: explanation of change
#+BugFix [BUG_NUMBER] [LINK_TO_BUG]
# Uncomment and fill in the line above to indicate this commit
# fixes a known bug.
# On branch master
# Your branch and 'origin/master' have diverged,
# and have 1 and 8 different commit(s) each, respectively.
#
# Changes to be committed:
# (use "git reset HEAD <file>..." to unstage)
#
# modified: database/chemical/residue_type_sets/fa_standard/patches.txt
# modified: source/src/apps/pilot/awatkins/hbs_creator.cc
# modified: source/src/apps/pilot/blivens/disulfides.hh
# modified: source/src/apps/pilot/chrisk/domain_assemble.cc
# modified: source/src/apps/pilot/dgront/JumpSpecificAbrelax.cc
# modified: source/src/apps/pilot/doug/rotamer_prediction_benchmark.cc
# modified: source/src/apps/pilot/jadolfbr/antibody_design/graft_design_cdrs.cc
# modified: source/src/apps/pilot/james/dp_align.cc
# modified: source/src/apps/pilot/johnk/constellation_list.cc
# modified: source/src/apps/pilot/kale/examples/kick_with_balance.cc
# modified: source/src/apps/pilot/kale/kic_refactor/original/KinematicMover.cc
# modified: source/src/apps/pilot/kale/kic_refactor/original/apply.KinematicMover.cc
# modified: source/src/apps/pilot/kale/kic_refactor/original/simple_apply.KinematicMover.cc
# modified: source/src/apps/pilot/kdrew/ld_converter.cc
# modified: source/src/apps/pilot/kdrew/oop_creator.cc
# modified: source/src/apps/pilot/kdrew/oop_dock_design.cc
# modified: source/src/apps/pilot/kdrew/scaffold_matcher.cc
# modified: source/src/apps/pilot/neil/enumeration_test.cc
# modified: source/src/apps/pilot/neil/matdes_dock.cc
# modified: source/src/apps/pilot/olli/r_assign_clusters.cc
# modified: source/src/apps/pilot/parin/parin_test.cc
# modified: source/src/apps/pilot/ralford/mpframework_integration.cc
# modified: source/src/apps/pilot/rhiju/coarse_rna_test.cc
# modified: source/src/apps/pilot/rhiju/easy_target_test.cc
# modified: source/src/apps/pilot/rhiju/legacy/stepwise_test.cc
# modified: source/src/apps/pilot/rhiju/pack_phosphates.cc
# modified: source/src/apps/pilot/rhiju/rna_graft.cc
# modified: source/src/apps/pilot/rhiju/rna_test.cc
# modified: source/src/apps/pilot/rhiju/screen_phosphates.cc
# modified: source/src/apps/pilot/rmoretti/ligand_rpkmin_jd1.cc
# modified: source/src/apps/pilot/sergey/PDBTest.cc
# modified: source/src/apps/pilot/smlewis/FloppyTail_loop.cc
# modified: source/src/apps/pilot/wendao/cenrot_jd2.cc
# modified: source/src/apps/pilot/wendao/general_pair_counting.cc
# modified: source/src/apps/pilot/will/options_will.py
# modified: source/src/apps/pilot/will/smhybrid.cc
# modified: source/src/apps/public/ligand_docking/arls_impl.py
# modified: source/src/apps/public/ligand_docking/ligand_rpkmin.cc
# modified: source/src/apps/public/ligand_docking/pdb_to_molfile.py
# modified: source/src/apps/public/noncanonical_backbones/hbs_design.cc
# modified: source/src/apps/public/noncanonical_backbones/oop_design.cc
# modified: source/src/apps/public/rna_util/rna_thread.cc
# modified: source/src/apps/public/stepwise/enumerate/rna/legacy/swa_rna_util.cc
# modified: source/src/apps/public/stepwise/monte_carlo/swm.cc
# modified: source/src/devel/denovo_design/ConnectJumps.cc
# modified: source/src/protocols/rotamer_sampler/JumpRotamer.cc
# modified: source/src/protocols/rotamer_sampler/rigid_body/RigidBodyRotamer.cc
# modified: source/src/protocols/stepwise/monte_carlo/rna/RNA_AddDeleteMonteCarlo.cc
# modified: source/src/protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.cc
# modified: source/src/protocols/stepwise/sampling/StepWiseConnectionSampler.cc
# modified: source/src/protocols/stepwise/sampling/movemap/util.cc
# modified: source/src/protocols/stepwise/sampling/rna/checker/RNA_ChainClosureChecker.cc
# modified: source/src/protocols/stepwise/sampling/rna/checker/RNA_ChainClosureChecker.hh
# modified: source/src/protocols/stepwise/sampling/rna/legacy/StepWiseRNA_PoseSetup.cc
# modified: source/src/protocols/stepwise/sampling/rna/legacy/connection/StepWiseRNA_ConnectionSampler.cc
# modified: source/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarSampler.cc
# modified: source/src/protocols/stepwise/sampling/rna/sugar/util.cc
# modified: source/src/protocols/stepwise/sampling/util.cc
# modified: source/src/protocols/stepwise/screener/AnchorSugarScreener.hh
# modified: source/test/core/chemical/carbohydrates/CarbohydrateInfo.cxxtest.hh
# modified: source/test/protocols/match/ProteinUpstreamBuilder.cxxtest.hh
# modified: source/test/protocols/rotamer_recovery/RRComparer.cxxtest.hh
# modified: source/test/run.py
#
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# source/a.out
# source/external/boinc/