Temp. fix as second attemp to restore master

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restoring master; sorry, all

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Merge pull request #769 from RosettaCommons/vmullig/muteall_issue Fixing B3V.params. Somehow, I managed to delete a line in B3V.params in my previous commit. Weeeird.

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Merge pull request #745 from RosettaCommons/rhiju/remove_RNA_residue_type_set Getting rid of RNA residue type sets Last full set of tests: http://benchmark.graylab.jhu.edu/revision?id=2377&branch= (ran a few more after that, but cancelled after unit & integration. They were just to check merge conflicts.) Tests look good: + Cosmetic change: removal of line loading in rna_residue_type set. But no further changes, as desired. + Cosmetic changes: removed unnecessary packer initialization when pack_missing_sidechains() is called but there is nothing to pack. (In a couple tests, exposes warnings about unused options like -packing:use_input_sc.) Sorry, this changes one line in a lot of tests, but I figure folks wouldn't mind removing this extra unnecessary step. + cstfile_to_theozyme_pdb, match_1n9l is unstable in integration, unfortunately, despite my prior attempt to fix. Those still run stably in integration.release_debug. Will be setting up a separate branch to try to resolve remaining instabilities.

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Merge pull request #763 from RosettaCommons/vmullig/hydrophobic Adding a HYDROPHOBIC property to the properties table. This is needed because some residues that are not polar (e.g. glycine, alanine, proline, cysteine) are not really hydrophobic (insofar as they're not major contributors to a well-packed hydrophobic core), either. POLAR: DEHKNQRST HYDROPHOBIC: FMILYVW Neither POLAR nor HYDROPHOBIC (for our purposes): ACGP

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Merge pull request #721 from RosettaCommons/tlinsky/tomponents Connection now has option to extend ss element or simply build a loop

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Merge pull request #718 from RosettaCommons/JWLabonte/sugars/CAPRI_redux CAPRI Round 27 Target 57 Redux This merge introduces the `.params`, patch, and apps files required to hopefully recapitulate and improve on our CAPRI Round 27 Target 57 results using the new carbohydrates framework. All unit tests pass. carbohydrate test changes expected; all other integration tests failing on the test server were either unstable or broken prior to my changes.

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Merge pull request #746 from RosettaCommons/hybrid_pdbinfo_alignment Hybrid pdbinfo alignment

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commenting out non-running membrane integration tests until I fix them

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Merge pull request #760 from RosettaCommons/everyday847/all_patches All patches activated and working, Cosmetic integration test changes.

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Merge pull request #764 from RosettaCommons/vmullig/fix_compile Fixing the build. Sergey Ovchinnikov just discovered that the existing build is actually a broken build, despite passing all build tests on the test server and on my machine. The problem is that I removed the sole member of an option group, so that that option file is no longer generated by the options.py script. There are a few files that include it, though. The file is there if it has ever been generated (e.g. in all test server builds, and on any existing checkout of Rosetta), so Rosetta compiles happily, but it is missing on new checkouts, so compilation fails there. I test-built this after deleting all of the auto-generated options files and regenerating them. Will merge without testing, to get master building properly as quickly as possible.

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Merge pull request #757 from RosettaCommons/vmullig/fix_invrotremodel Fix the inverse_rotamer_remodel integration test This seems to be failing due to a bunch of missing mm_std bond angle parameters. It bothers me, though, that this was NOT failing on the Linux builds. There was an option for ignoring missing bond angle parameters, but (a) this was set to false, and (b) even if this were set to true, you should end up with a segfault on any system if you ignore the missing parameters. Instead, the segfault was only happening on Mac. I don't know why missing bond angle parameters were being ignored, or why the segfault was only on Mac. I've removed the option (so there should ALWAYS be an error thrown and an abort if there are missing bond angle parameters), and have added the missing bond angle parameters to the database (copying similar bond angle parameters and adding comments indicating that these are copies).

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Fix cppcheck tests Delete cached cppcheck output files if the corresponding source file is no longer present. This fixes issues in the commits branch on the testing server where spurious cppcheck errors are being reported.

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Merge pull request #708 from RosettaCommons/jkleman/mp_updates2 Jkleman/mp updates2 = protocols/membrane/util: added functions pose_tm_com, rsd_closest_to_pose_tm_com, create_membrane_foldtree_anchor_pose_tmcom added unit tests for them = MembranePositionFromTopologyMover: cleaned up foldtree code and created new foldtree likely to cause integration test changes in mpfastrelax and depending protocols = OptimizeMembranePositionMover: cleaned up foldtree code and created new foldtree likely to cause integration test changes in depending protocols transformed pose into membrane first instead of computing membrane from topology, this is much more correct because the center and normal search depends on it = TransformIntoMembraneMover: removed the option of optimizing the embedding within the mover, this is much cleaner and doesn't lead to circular calling of OptimizeMembraneMover and TransformIntoMembraneMover = TranslationRotationMover: added checks = integration tests: added normalize_to_thk flag to integration tests! added integration test for mp_interface_statistics added integration test for mp_transform_optimize added integration test for visualizing embedding Apps = mp_transform: debugged version where the membrane position is optimized in addition to just transforming it into the default membrane this is now not in JD2 any more because the protocol differs and I need to access MEM after optimizing the membrane this also depended on leaving optimization and transformation more or less independent = helix_from_sequence: removed option to optimize embedding, was incorrect and will be added back soon integration test changes: mostly cosmetic, otherwise expected

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Merge pull request #758 from RosettaCommons/rfalford12/make_meminfo_default_constructor_private Making the default membrane info constructor private The MembraneInfo object relies on data initialized in the AddMembraneMover#apply() function. For this reason, it doesn't make sense to create a default MembraneInfo() object so I'm making the constructor private.

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Merge pull request #749 from RosettaCommons/phbradley/lk_ball_packing_fix Better handling of residue-cached data during LK-Ball scoring

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