This should fix all of the newline erros that were added. If it does not resolve the issue, I will revert. Sorry about this

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Adding missing newline that broke the build

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RosettaMembrane Framework Update - Library Reorganization News: The membrane framework code is now split accross three namespaces. Below is the new organization: core/conformation/membrane: Includes all code involved in defining a membrane protein. Includes: - Spanning Topology - Lipids Accessibility - Membrane Info object in conformation core/membrane: Includes all code required for making and working with a memrbane protein at the core level. Includes: - All resource manager classes - All geometry definition classes - Membrane protein factory protocols/membrane: Top level interface for creating a membrane protein. Includes: - Membrane Unit test mover (mover for unit/integration testing) - Create Membrane Pose Mover (simple mover with Rosetta Scripts hook) This commit should fix the library level build. library_levels.py passes in master. Unit Test Status: All pass on Linux GCC Integration Test Status: None expected, other than currently failing tests Added: 3/21/14

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Comment out the KIC unit tests. These are my tests, and for some reason they're failing on mac and not linux. I'll debug this issue once I get access to a mac, but in the meantime I'm just going to turn them off.

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[minor update of SandwichFeatures] - further differentiation of automatic generation of resfile like surface-heading residues at core strands - more int than Size to reduce Xcode warnings - better tracers [integration tests comment] - should not change other than features and features_database_schema (if any)

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This update should fix the pyRosetta build. Library level stil broken - that fix is in progress

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Fix build If you don't want people to call your default constructor (for example, you're storing a data member by reference) all you need to do is declare the constructor as private, and then omit the definition. This will prevent the compiler from automatically making a default constructor. Additionally, src/basic/options/options.py was adjusted to allow the older version of Python on the performace benchmark computer to work.

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RosettaMembrane Framework Updates Updated: 3/20/14 Updates: New MembraneInfo Object - Replaces previous MembraneConformation subclass - Contains placeholders for lowres and highres scoring members - Includes new corresponding unit test - Removed all previous MembraneConformation code + tests Unit Tests: All Pass on Linux GCC Integration Tests: No changes expected, other than the ones that sometimes currently have trouble

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I should really compile before pushing and work in my own branch. Intense shame. Sorry again!

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Unintentionally commited a piece of non-working code. This fixes that... Sorry.

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getting NativeClient to compile

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GPSRosetta: New functions to score Pseudocontact Shift (PCS) data generated from multiple metal binding tags/centers. NEWS: [DETAILED DESCRIPTION OF CHANGE] The distance restraints are implemented in a manner analogous to finding locations uisng GPS satellites. The current implementation is directed via usage of a broker file and can be used to setup atmost 4 different tags. GPSRosetta is an extension to previously implemented PCSRosetta which uses PCS data Ref: PCSRosetta: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 GPSRosetta: Yagi H et.al Structure, 2013, 21(6):883-890 Unit test status: [Pass]

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Fixing clang build (tested with 3.5-1ubuntu1). Attempt #2.

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Fixing clang build (tested with 3.5-1ubuntu1).

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Adding MultiplePoseMover and MultipleOutputWrapper (merging branch luki-mbi/rosetta_scripts). NEWS: The MultiplePoseMover allows a multi-step "distribute and collect" protocol to be implemented in a single RosettaScript. First, it collects all poses from the previous mover in the protocol. Next, poses are selected from the complete set using Pose Selectors, some of which use Pose Property Reporters. The sub-protocol, if any, is then run on all selected poses. Poses for which the protocol succeeds are output to another mover for further processing, or to the Job Distributor for output to persistent storage. This mover can also be used to "branch out" without any selection criteria (i.e. generate many diversified poses) or purely as a selector to trim down the set of poses based on some criteria. MultipleOutputWrapper is a simple wrapper that will execute the mover or ROSETTASCRIPTS protocol it wraps to generate additional output poses from the original pose. This commit disabled RosettaScripts resume support, since it's interfering and needs a better implementation. Unit test status: Pass All test pass except SpanFileIOTests, which fails to run on my machine (Linux, gcc 4.8.2) with: core.test: src/ObjexxFCL/DynamicIndexRange.hh:103: ObjexxFCL::DynamicIndexRange::DynamicIndexRange(int): Assertion `legal_static()' failed. Integration test status: 37 test changes (all cosmetic) Cosmetic changes are expected in the following tests due to the clean-up of empty protocol reports. Additionally, there's a new message about deprecation of the <dock_design> tag in favor of <ROSETTASCRIPTS>. Enzrevert_xml add_job_pair_data dock_with_hotspot_place_simultaneously favor_native_residue grid_scores_features hotspot_graft hts_io hybridization inverse_rotamer_remodel kinemage_grid_output ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking loop_creation make_symmdef_file nonideal_rtmin place_simultaneously posttranslationalmod_io ppk rosetta_scripts_setup rotamer_probability rs_flexbbmoves rs_loophash score12_docking score_only_silence splice_in splice_out splice_seq_constraint startfrom_file symmetry_data_resource The JD2 now outputs additional poses generated by a mover, thus the following test now produces multiple PDBs: rs_loophash The pose tag is now at the end of the PDB file name (for clarity), hence some output file name changes in: AnchoredDesign antibody_designer broker_membrane docking_prepack jd2test surface_docking

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Benchmark scripts. Adding ‘ignore’ file list. This should break all regression tests.

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