Added 1 new integration test and modified two existing ones The 3 modified integration tests are: 1. Splice_in 2. Splice_out 3. Splice_seq_constraints All 3 integration test deal with the functionallity of Splice.cc in devel Unit test status: Pass Integration test status: 3 changed

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Adding a ring detection algorithm and unit test for the ring detection algorithm. Unfortunatly, this does not work for bucky balls but maybe I will fix that in the future. Added annotations to bonds to determine if the bonds are in a ring or not. If bonds are classified as undefined ringness, run ring detection algorithm to assign ringness. Added new support functions for bonds in core/chemical/bond_support.cc Add new support functions for residuetypes in core/chemical/ResidueSupport.cc Added const access to the ResidueGraph in ResidueType Added a new visitor class to BFS_prune that will hide nodes on a graph during a breadth first search. No unit test changes. No integration test changes on this side (I would assume ligand dock will change though).

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Adding exception handling to extract_motifs app.

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Merge remote-tracking branch 'origin/master'

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rewritten /src/protocols_b.5.src.settings

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GPSRosetta: New subroutines to score Pseudocontact Shift from multiple metal centers NEWS: Scoring PCSs from multiple tag sites in a manner analogous to GPS satellites. please see references for methodology Yagi, H.,et al. (2013). Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites. Structure (London, England : 1993), 21(6), 883–890.

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# [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 1 different commit each, respectively. # # Untracked files: # (use "git add <file>..." to include in what will be committed) # # source/f_compilation.log # source/src/protocols/scoring/methods/search-replace.sh # source/src/xxx

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# [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 is ahead of 'origin/master' by 105 commits. # # Changes to be committed: # (use "git reset HEAD <file>..." to unstage) # # modified: database/scoring/weights/gauss1.wts # modified: source/src/apps.src.settings # modified: source/src/apps/pilot/phil/test1.cc # new file: source/src/apps/public/motif_tools/extract_motifs.cc # modified: source/src/apps/public/vip.cc # modified: source/src/basic/options/full-options-list.md # modified: source/src/basic/options/keys/OptionKeys.cc.gen0.hh # modified: source/src/basic/options/keys/OptionKeys.cc.gen1.hh # modified: source/src/basic/options/keys/OptionKeys.cc.gen2.hh # modified: source/src/basic/options/keys/motifs.OptionKeys.gen.hh # modified: source/src/basic/options/option.cc.gen.hh # modified: source/src/basic/options/options.dox # modified: source/src/basic/options/options_rosetta.py # modified: source/src/devel/splice/Splice.cc # modified: source/src/devel/splice/Splice.hh # modified: source/src/protocols/frags/TorsionFragment.cc # modified: source/src/protocols/frags/TorsionFragment.fwd.hh # modified: source/src/protocols/frags/TorsionFragment.hh # modified: source/src/protocols/frags/VallData.cc # modified: source/src/protocols/frags/VallData.hh # modified: source/src/protocols/membrane/MembraneUnitTestMover.cc # modified: source/src/protocols/toolbox/task_operations/DatabaseThread.cc # modified: source/src/protocols/toolbox/task_operations/DatabaseThread.hh # modified: source/src/protocols/vip/VIP_Mover.cc # modified: source/src/protocols/vip/VIP_Report.cc # modified: tests/integration/tests/vip/flags # # Untracked files: # (use "git add <file>..." to include in what will be committed) # # source/PCS_pcs_edit.edit # source/compilation.log # source/compilaton.log # source/pcs_edit.edit # source/src/protocols/xxx.edit # source/src/xxx.edit # source/xxx.edit

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Add some legacy code to the old protocols/frags directory. Prep for getting an app committed. ligand_dock_script and rna_denovo showed changes in release that went away in debug.

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Removing unused variable.

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Adding application for extracting motifs from pdb files.

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fixed indentations using VI

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fixed indentations (hopefully…)

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Removing map::at calls from MembranceUnitTestMover.cc

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moved allow_all_aa up in the definitions section

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Benchmark scripts. Changing how logs got truncated for successful builds. This should allow logs for scons-failed-platform detection case to became visible on our web site.

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