Merge pull request #178 from RosettaCommons/justinrporter/env_release Fix Environment/Broker 2.0 unit tests and turn them back on.

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Merge pull request #176 from RosettaCommons/vmullig/betahelix Vmullig/betahelix This merge adds support for non-ideal mainchain bond angles and bond lengths to the MakeBundle mover. Small deviations from ideal mainchain bond angles/lengths permit more perfect long helices of helices. The mover is now fully documented on the Gollum wiki. In addition, this merge does the following: - Changes "delta_omega1_all" option to "delta_omega1" in the RosettaScripts syntax for the MakeBundle mover. - Adds an integration test for MakeBundle with nonideal bond angles/lengths. - Updates the C-terminus patch for beta-3-amino acids. Expected integration test changes: - helical_bundle test should change (though output should not) since "delta_omega1_all" is now "delta_omega1". - new helical_bundle_nonideal integration test (since it's new).

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Merge pull request #83 from RosettaCommons/sheffler/place_motifs Adds beta version of residue pair motif search and scoring mechanism. Not yet recommended for general use, but some protocols people want to have in master to rely on it, so I guess it's going in. Please feel free to contact willsheffler@gmail.com if you are interested in using this code.

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Merge pull request #172 from RosettaCommons/grocklin/gabe_devel added new options to remodel for building disulfides based on score rather than match_rt

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Merge pull request #170 from RosettaCommons/daslab All changes related to constraint_set use, mainly to get them working for stepwise applications. All changes are 'cosmetic', as noted in comments to pull request, with removal of warning "core.scoring.ConstraintSet: ERROR: HUH?!? weird stuff is going on. ConstraintSet is hearing disconnection voices that it shouldn't" Also changed back option constraints::exit_on_bad_read to true rather than false -- this would have caught several of my jobs that were silently reading through constraints in the wrong format. In cases where a pose is deleted or copied, and the constraint set then is checked -- there's actually a flag conformation_pt_.expired() that says the constraint set is out of date -- now check that before printing warning. See notes on pull request for changes to a few tests that do not run or appear unusually sensitive to small changes.

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Merge pull request #171 from RosettaCommons/roccomoretti/runtime_assert Fixes for runtime_assert w/r/t pointers Our runtime_assert macro was having problems with asserting on OPs with C++11. This looks to be due to an implicit conversion of the OP to a bool. While explicit conversions to bools work, implicit conversions give an error under C++11 and certain compilers. The implicit conversion wasn't really needed. I re-wrote the macros to skip an unneeded intermediary function call, and also the implicit conversion. Coincidentally, this also avoids a double evaluation of the parameter to the macro, which means that Rosetta should crash just a little bit faster.

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Pull of updated master after merge of pull request 166 into old master. Pull request 166 just corrected a couple of lines that were causing our compiler at KU to issue a warning (see the pull request for details).

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Changing a warning in the Xcode template that only affects executables. Now they should all build.

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Updating Xcode project template to support C++11 and to include the preprocessor directives we have defined for Rosetta. Additionally, this revision updates the flags that are used when building with Xcode to more closely match the flags used when building with SCons. This means that you will see the same set of warnings when using SCons or Xcode. No more '999+ Warnings! To use the new template, go to Rosetta/main/source/Xcode and delete Rosetta.xcodeproj/project.pbxproj. Then run the project generation script (python make_project.py all) and you will be set!

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Merge pull request #173 from RosettaCommons/benchmark Updating release.PyRosetta.namespace build. Plus various small PyRosetta fixes.

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Merge pull request #148 from RosettaCommons/justinrporter/env_release Incorporating numerous bug fixes and additonal unit testing to the Environment farmework. No unit test changes expected, no integration test changes expected.

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Fixed pose serialization in pyrosetta. Replaced ProteinBinarySilentStruct for BinarySilentStruct in pose serialization.

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Update CMake unit test build for new CMake build scheme. Also, fix a missing std::endl I saw.

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Merge pull request #168 from RosettaCommons/dougrenfrew/fixing_cxx11_mpi_build Dougrenfrew/fixing cxx11 mpi build

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Merge pull request #169 from RosettaCommons/weitzner/mac-default-build Weitzner/mac default build All Mac+Clang builds use C++11 by explicitly adding the preprocessor directives instead of adding extras=cxx11. This should simplify using other extras, e.g. mpi.

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Merge pull request #159 from RosettaCommons/daslab Daslab -- score function updates All test changes are cosmetic (due to changes in EnergyMethodOptions output or ScoreType order) except: cs_rosetta_rna fix to intra_RNA terms ddG_ensemble, ddG_of_mutation, enzdes ligand_*, sdf_reader, UBQ_E2_thioester floating point deviations (note that ligand integration tests that use the PDB 7cpa change the last digit of some hydrogen) rosetta_scripts_hbond_options -- is this being maintained? test was broken previously all swa_rna tests The changes here are due to an update of rna_bulge to be computed over non-instantiated residues, and turning off of 2'-OH virtualization. vip @bborgo, @havranek there was a mistake in how ref weights was being set by ScoreFunction before -- now fixed, but this changes the integration test...

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