Updating performance benchmark: - Decreasing individual tests runtime to 64 - Increasing failure tolerance to 16%

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Merge pull request #728 from RosettaCommons/aleaverfay/fix_coordcst_clone_w_func Adding a clone( FuncOP ) method for the CoordinateConstraint class to fix the hotspot_graft and place_simultaneously integration tests.

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Merge pull request #713 from RosettaCommons/JWLabonte/sugars/loops2 CCD Loop Closure/Carbohydrates: making CCD work with polysaccharides One of the main reasons I helped @weitzner refactor CCD last year (#51) was to set up a better framework that would allow one to close saccharide loops as well. However, there was still a collection of hard-coded assumptions deep in the code that prevented sugar loops from working with cut-point variants. This merge seeks to remove those assumptions, freeing the new CCD to do its job on carbohydrate loops, such as for the project I briefly described at the end of my talk at RosettaCON. This merge also fixes some silent bugs regarding ring conformations. All unit tests pass. CCD and carbohydrates integration test changes expected. code_duplication test is from new whitespace. cppcheck was not functioning properly at the time of this merge. hotspot_graph, place_siumltaneously, inverse_rotamer_remodel, and rs_loophash are all still broken.

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Fixing Andy's pilot app to fix the build.

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Merge pull request #730 from RosettaCommons/vmullig/bettercluster_memory Fixed bug in bettercluster.cc Fixed a segfault in a pilot app. No test changes expected (or possible, really). Skipping tests.

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Fixing app_exception_handling my bad!

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changing z1 from 1.570660756980 to 1.51 (for backward-compatibility) in the BundleGridSampler param file. No test change expected

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Merge pull request #674 from RosettaCommons/everyday847/literally_cant_even So this went a bit off-track, because the assumption in question is kind of hard to track and relies on a really good understanding of what could go wrong with pseudobonds, which I do not have. Instead, I reworked some really bad (kind of related) assumptions with the HBS patches which were causing clashes and weird geometry and other bad stuff--I think we can safely use HBS dock-design with talaris now, as long as we aren't using any NCAAs. I also fixed the hbs and a3b_hbs creators so they work... much better.

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Updating parallel.py script so it communicate with child process even if no output file was set

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Fix benchmark/util/parallel.py issue. parallel.py wasn't properly waiting for subprocesses to finish, leading to a process explosion.

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Merge pull request #711 from RosettaCommons/vmullig/fix_hotspot_graft Fixing syntax in HbondsToResidueFilter in integration tests Fixing problem with HbondsToResidueFilter in hotspot_graft and place_simultaneously integration tests due to changed syntax in this filter. Note that this does NOT fix these tests -- there was something else broken affecting them. I'll merge this fix since Rebecca closed her branch fixing these tests. We might as well solve this problem so that we know when the other problem is solved.

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Merge pull request #688 from RosettaCommons/jadolfbr/db_with_path Allow pathing to database output This merge allows -out:path:all to be used by -out:use_database and the FeaturesReporter framework. Adds another option -out:path:db to be used specifically for databases. Tested using pdb output to db via score_jd2 and a feature reporter script. Fixes bug/feature request 359: https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=359

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Merge pull request #719 from RosettaCommons/rhiju/fix_carbohydrate_patches_with_on_the_fly_residue_types Rhiju/fix carbohydrate patches with on the fly residue types carbohydrates integration test restored, confirmed by @JWLabonte. All other tests pass except ones that failed before (cppcheck, 3 integration tests; the match tests, which can give different output orders).

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Merge pull request #710 from RosettaCommons/rfalford12/cleanup_meminfo_and_addmemb Updating Documentation & Organization of AddMembraneMover and MembraneInfo Its been about a year since I've updated the in-code documentation (@brief, @detials, class description) for AddMembraneMover and MembraneInfo but a lot has changed. Its also becoming harder to figure out where to add things in terms of (1) where data gets stored and (2) at what step to initialize new data in AddMembraneMover. In this pull request, I updated the documentation for both classes. I also reorganized methods so adding new extensions to these classes is easier. I've also updated some logic in AddMembraneMover to fail if none of the current edge cases cover an input PDB which is more informative to the user Integration test Changes: Code duplication: Catches consistent initialization between constructors (this is good duplication!) and mp_relax_w_ligand is cosmetic

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Merge pull request #675 from RosettaCommons/everyday847/nu_angles_for_ncaas It isn't PERFECT, but it is a necessary step to get where we're going. A later (and longer) effort: synergize ring conformer and rotamer enumeration so the two are sampled together.

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Merge pull request #591 from RosettaCommons/rhiju/on_the_fly_residue_types Rhiju/on the fly residue types Link to preRosettaCon2015 talk on this pull request, including benchmarks showing significantly reduced load time: https://dl.dropboxusercontent.com/u/21569020/Das_preRosettaCon2015_ResidueTypeSet.pdf Yes finally all tests pass. Notes on changed integration tests: Cosmetic: fiber_diffraction_fad, fold_and_dock, rs_loophash, Enzrevert_xml, enzdes, mp_find_interface, match_1n9l Previously broken: hotspot_graft, inverse_rotamer_remodel, place_simultaneously (also mac.pyrosetta was previously broken)

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