Merge pull request #732 from RosettaCommons/sergey/f Adding specialized operator<< with visibility check for Tracer and TracerProxy (Thanks to @roccomoretti for the idea!)

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Fix a few new cppcheck issues.

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Merge pull request #700 from RosettaCommons/vmullig/gellman_helix The main purpose of this merge is to fix packing when mainchain chiral centres switch their chirality (e.g. design with both D- and L-amino acids). This also introduces a subset of the L-gamma-4 amino acids with canonical side-chains. The following integration test changes are expected: - flexpepdock (There really was an HA atom in a wonky place in this integration test, which this change fixes.) - dcys_disulfidize (Expected changes to HA placement when designing with D and L residues -- the major bugfix that this merge introduces.) - cyclization (Very small changes to post-relaxation geometry with peptoid residues. Tracked this down to the swapping of 1HA and 2HA atoms that were in the incorrect relative arrangement. So that's good.) - oop_design (No changes to structure, but minor changes to some output information. Also not surprising.) - d_workflow (HA atoms are now in the correct positions after design. Yay!) - cluster_alns (Very minor changes to side-chain rotamers. Curious.) - oop_dock_design (No structural changes; minor changes to output information.) - ncaa_fixbb (Different non-canonical side-chain no longer chosen after fixing HLU. The only difference is that 1HA2 and 2HA2 in the "601" residue, which were staring out in swapped positions, are now correctly swapped back by the packer. So that's good.)

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Merge pull request #729 from RosettaCommons/roccomoretti/cppcheck_output Cppcheck output fix This is accomplished by splitting the stdout and stderr streams in parrallel.py, and ignoring the stdout one from the cppcheck runs.

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Fixing library levels in Frank's recent commit.

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Fixing the build -- Frank left an unused variable in LK_BallEnergy.cc.

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LKball now works with nblist_auto_update

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Beautifying master. This is a large commit and will undoubtedly produce conflicts with everyone seeking to merge into master. The merge process for advancing past this commit is as follows: > git pull && git checkout 3f02864 > git merge 6d44fcf00 dismiss them cd into Rosetta/main/source run the python beautifier script: > python ../../tools/python_cc_reader/beautify_rosetta.py -j 40 --overwrite (or leave off the --overwrite flag to write the beautified X.cc file to X.cc.beaut, if you'd first like to see what the beautifier does) The -j flag tells the script how many processors to use. It takes about 5 minutes. SHA-1 in this commit log message because this commit log message goes into determining the SHA-1!) using the -Xours flag: > git merge -Xours <thissha1> and must be carefully handled.

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Merge pull request #727 from RosettaCommons/sjf/parse_resnum_in_PreventResiduesFromRepackingTaskop PreventResiduesFromRepacking task operation will now allow specifying…

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Merge pull request #724 from RosettaCommons/vmullig/gaurav_dcys Adding support for D-cysteine disulfides to the Disulfidize mover. In the process, I caught a major bug in the DisulfideMatchingPotential that was greatly limiting its usefulness for finding new disulfides (e.g. in Remodel or in Disulfidize). I recommend that users who use these protocols to place disulfides update to the latest master after this merge. Tasks: - Add interface items to mover. - Alter mover's process_pose() function. - Alter find_possible_disulfides() function. - Alter construct_poly_ala_pose(). - Alter check_disulfide_score and build_and_score_disulfide(). - Alter core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(). - Track down and fix weird DCS "atom doesn't exist" bug. - Integration test. - Update documentation. - Tweak unit test appropriately, since it now finds far more disulfides and could actually run out of time/RAM. Changes to integration tests expected: - dcys_disulfidize (Just added; expected to fail.) - rs_loophash (Failing to run on test server.) - remodel_disulfides (Previously found no disulfides; with the fix to DisulfideMatchPotential, it now finds a decent-looking one, so that's good.) - hotspot_graft (Was failing to run on test server.) - minimize_with_electron_density (As far as I can tell, this is related to the preservation of Residue information since cysteines are not being rebuilt unnecessarily any more. Very subtle numeric differences.) - place_simultaneously (Was failing to run on the test server.) - make_symdef_file (Identical PDB output, but the CYS residues, which had 0 in their temperature column before, now have values. All other residues had temperature factors that were nonzero before and after this merge. This is an unanticipated but now-expected benefit of the changes to change_cys_state(), which no longer replaces CYS residues with new Residue objects (lacking the attached data) unless it's actually switching CYS to CYD or CYD to CYS.) - database_jd2_io (Like make_symdef_file -- identical output, but values in the temperature column for CYS.) - repack_with_electron_density (Same thing again -- temperature factors for CYS.) - resource_database_locator (Same thing again -- temperature factors for CYS.) - symmetry_data_resource (Same thing again -- temperature factors for CYS.) - resource_database_tables (Same thing again -- temperature factors for CYS.)

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Further increasing failure threshold for performance tests

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Merge pull request #714 from RosettaCommons/aleaverfay/prebeauty_cleanup Merging branch aleaverfay/prebeauty_cleanup into master (pull request #714). Modifying files ahead of beautification that contain un-scoped if blocks and other statements all on a single line. The beautifier now flags such lines as sources of possible bugs. However, it demands that if you want to put several statements on one line, that you should scope the if block. This commit goes through all the cases in the code that the beautifier flags and scopes them appropriately.

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Merge pull request #720 from RosettaCommons/roccomoretti/stored_rotamers Add the ability to load rotamers from the SDF files passed to -extra_res_mol By default, all the entries in an SDF file with the same molecule name (the first line) will be loaded as rotamers, using (indirectly) SingleLigandRotamerLibrary. To facilitate usage, if the name line is blank, it's assumed that the entry is a rotamer for the previous entry. Note that like molfile_to_params.py, only the first entry of a given name will control the ResidueType layout - all the additional entries are used for coordinates *only*. Behavior is undefined if the atom indexes of the multiple entries used for rotamers don't match up. I think *cross fingers* that this is the major outstanding issue for using SDF files directly, rather than passing them through (standard) molfile_to_params.py. (mol2 files, polymeric residues, and controlling non-default behavior are still not implemented.)

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Merge pull request #725 from RosettaCommons/rhiju/remove_override_rsd_type_limit removing rsd_type_limit warning to encourage folks to check in patches… All changed tests are the expected ones (the ones which displayed the rsd_type warning), ones that are broken (cppcheck), or ones that have been unstable recently (match & cst_to_theozyme in mac but not linux integration tests).

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Merge pull request #723 from RosettaCommons/rhiju/remove_backtrace_in_pose_from_annotated_sequence removing print_backtrace from disulfide backwards compatibility code … only changes are in expected test (rs_loophash) and broken tests (hotspot_graft, place_simultaneously). Some match tests are giving change in output order on mac.clang.integration (but not linux) -- this appears to date to my on_th_fly_residue_types merge, and I am looking into it separately.

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Merge pull request #715 from RosettaCommons/everyday847/who_knows_torsion_stuff A couple of fun demos of noncanonical functionality. Integration test changes are all prior failures or cosmetic changes (indeed, changes to tracer output I had added in the first place, or a bit of TR.Trace output). New vancomycin integration test, too!

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