PyRosetta. Refactoring how C++ ‘struct’ handled (now binding access to data-members by default).

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Commit without Rosetta Benchmark test (this commit will be safe though). Now I add a missed "generate_five_ss_model" option for sewing_hasher.

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More work on the hbond distance-polynomial refitting script

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Merge pull request #882 from RosettaCommons/everyday847/loop_simplify Loop structure simplification and miscellany

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Merge pull request #883 from RosettaCommons/kimdn/master_sew [what has been updated for beta-sandwich_analysis] * Add a more rule so that two parallel short strands can be "sheet" for Tim-barrel [what has been updated for SEWING] * [model generation update] - sewing::hash_tag_only_terminal_Es is possible - User can provide an option (generate_five_ss_model) so that 'db -> node (model)' can generate '3_or_5_secondary_structure_based models' - added unit test (SewingHasherTests.cxxtest) for "db -> node (model/substructure) can generate 5_secondary_structure_based models" * [Model_trimmer update] - becomes little faster (don't care rest trimming steps if any preceding trimming decides to erase the model) - can do 'leave_models_with_E_terminal_ss' - can do 'leave_parallel_way_H_bonded_models_by_terminal_strands_only' - can do 'leave_antiparallel_way_H_bonded_models_by_terminal_strands_only' - can do 'model_should_have_at_least_one_E' - can do 'model_should_have_at_least_one_E_at_terminal_segment' * [hashing update] node (model) -> edge (score) can handle 'any number of secondary_structure' based models * [model assembly update] - User can choose between 27 and 125 boxes for neighborhood_lookup (-sewing:box_length), both scoring and assembly should use same box numbers * [ExhaustiveAssemblyMover newly added] - Enumerate every possible assembly exhaustively - User can choose 'dump_every_model_for_devel_purpose' option * [MonteCarloAssemblyMover update] - User can choose not to stick to best_score if specified 'min_assembly_score' as an option in parser - User can choose 'offset_bump_dsq' as an option [beautified some other's files] beautified except File utility/json_spirit/json_spirit_writer_template.h could not be beautified File utility/json_spirit/json_spirit_error_position.h could not be beautified File utility/json_spirit/json_spirit_writer_options.h could not be beautified

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Merge pull request #878 from RosettaCommons/tlinsky/hotfix Fix gcc 5.x.y cmake build

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Merge pull request #880 from RosettaCommons/vmullig/reset_issue Fix the functionality of RESET The commutativity-breaking resfile command RESET, which is necessary for noncanonical design (since noncanonicals can only be turned ON while canonicals can only be turned off) wasn't resetting canonicals properly. This command now: - Disables all noncanonicals (as it did before). - Enables all canonicals (which it was not doing properly before). - Enables design and repacking. Which is what the documentation claimed that it was doing. I've also moved the RESET functionality to a single function in the ResidueLevelTask class, so that we don't have a lot of ways for external things to break commutativity. (Anything can call the reset() function, but it will always break commutativity in exactly this way.)

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Merge pull request #879 from RosettaCommons/vmullig/bintransition_bug Caught a mistake in BinTransitionCalculator.cc. This was affecting the setup of sub-bin cumulative probability distributions for the i+1 residue.

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Updating the refit_hbond_polynomials.py script to more robustly handle cases where the new polynomial does not reach it's requisite height (+1.1).

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Merge pull request #877 from RosettaCommons/rhiju/fix_up_to_virtual_phosphate Rhiju/fix up to virtual phosphate changes to integration tests are expected – due to virtualization of 5' phosphates of RNA that should have been happening anyway.

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Merge pull request #870 from RosettaCommons/vmullig/peppredict_boinc Add checkpointing to simple_peptide_predict app David Kim rightly pointed out that my peptide structure prediction app isn't checkpointing itself properly. While results would still be returned on BOINC, trajectories would likely be repeated if users stopped a work unit and re-started it. This will address that. Tasks: - Figure out how the BOINC stuff currently talks to the classic ab initio JobDistributor and to JD2. (I'll probably want to use the nstruct-level checkpointing of JD2, but first I want to understand how everything currently works.) - Figure out whether JD2's nstruct-level checkpointing somehow knows to skip jobs that failed. (I'll definitely need this, since my app heavily filters, so that many trajectories return no result.) - Get simple_cycpep_predict to checkpoint. (It was simpler to add checkpointing than to get it to use an existing JobDistributor, and I was able to time the checkpointing to my short jobs rather than the over-frequent checkpointing that I'd have if I relied on the BOINCJobDistributor). - Get the minirosetta with the simple_cycpep_predict protocol to talk properly to the text overlays in the BOINC graphics. - Test with the text overlay on the graphics (not tested yet). - While I'm at it, tweak the energy and RMSD updating in the graphics display. - Beauty - Documentation Cosmetic change to simple_cycpep_predict integration test expected (one extra line of output).

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Merge pull request #875 from RosettaCommons/indigogo/hbscan Indigogo/hbscan

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The big green button somehow did me wrong. This should fix the build.

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Merge pull request #872 from RosettaCommons/everyday847/remove_ncaa_rotlibs Remove most NCAA rotlibs from RosettaCommons/main

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Merge pull request #862 from RosettaCommons/revert-860-revert-676-tjacobs2/sewing_motifs Merge of the SEWING framework for de novo protein design. Thanks to Sergey for fixing an issue with the Windows PyRosetta build. All tests pass. Expected changes to features and features_database_schema integrations tests. Also, two new tests for the continuous and discontinuous sewing hasher.

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Merge pull request #871 from RosettaCommons/roccomoretti/valgrind_mpi Fix integration.py w/r/t valgrind and MPI Not all test directories have non-MPI command files - don't fail if one isn't present

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