Refactoring performance benchmark so individual tests at different times instead of being run continuously. Refactoring LigandDockScript to allow multiple runs. Setting benchmark scale to 2 for Testing Server performance tests.

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Merge pull request #216 from RosettaCommons/kylebarlow/general_dev Minor change to minimize_with_cst.cc Input files can now reside in a directory other than the current working directory, as beginning of input paths are stripped when determining the input tag. Before, if input list pdbs were in a different directory, path construction would fail.

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Merge pull request #215 from RosettaCommons/rfalford12/mprelax_mover Membrane Framework Updates: 12/9/14 AddMembraneMover Updates: = Adjusted setup to create a fold tree anchored at the membrane residue by default and will fold from N--->C = Added additional test cases to the unit test to check the correct setup foldtree topology and initialization of spanning topology & lipophilicity objects Print Compatibility for PyRosetta = Modified getters in SpanningTopology and Span objects to be const correct - allows passing of const data to other rosetta and PyRosetta methods = Added << operator to all membrane framework objects (MembraneInfo, SpanningTopology, Span, no lips yet) so they can be called by print in PyRosetta = Modified the pose.show() method to print some membrane information (specifically, position, nspans, etc), Also useful for the print method in PyRosetta Scoring Bugs = Fix a bug in MPNonHelix Penalty that didn't center the membrane around the position used by the membrane framework. This calls for a better implementation of the centroid potentials & terms in general, but for now this fix suffices Relax Mover = Added a new mover, MPRelaxMover, which constructs a foldtree rooted at the residue-level center of mass, preserves existing jumps between chains, and creates an additional jump downstream of the COM to the membrane residue. This mover also sets some important settings for the relax protocol including a jump specific movemap (i.e. don't make all jumps moveable, just the membrane) and initializes the score function (mpframework_smooth_fa_2014) = MPFastRelaxMover plugged into Rosetta scripts, updated integration test mpframework_relax to use this new mover. = Added unit test for initializing the new foldtree (tested on single and multi chain cases) Test Status: =================== Score Regression: Change due to updated score for mpnonhelix penalty Unit: all pass Integration: All mpframework changed due to add membrane mover creating a different fold tree

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Fixing build

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Merge pull request #214 from RosettaCommons/roccomoretti/copyright_boilerplate Fix editor modelines and copyright boilerplate Normalize the first lines of all the .cc and .hh to the current official version. No new test changes introduced. (The issue with build.headers has been fixed in master.)

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Commenting out seg-faulting Score_geom_sol_ test. Updating performance benchmark script.

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A few bugfixes to a pilot app

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Adjusting performance benchmark tests running time

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Fixing header benchmark script so it now call scons to update options and residue types before each run. Thanks to Rocco for help on discovering this!

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Merge pull request #211 from RosettaCommons/rhiju/swm_csa Rhiju/swm csa - population-based stepwise monte carlo (using a variant of conformational space annealing) Only cosmetic changes, and some floating-point deviation in KIC_with_fragments. Note that broken unit tests for BinarySilentStructs will be fixed by me in a separate branch & pull-request.

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Merge pull request #200 from RosettaCommons/cyucheng/LarmorD Cyucheng/larmor d no changes except new integration test (cs_rosetta_rna) and a few tests that did not run before.

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Merge pull request #199 from RosettaCommons/daslab Daslab -- minor updates to stepwise constraints Integration test changes are cosmetic, or are in tests that appear to have failed in master (?).

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Merge pull request #187 from RosettaCommons/kalekundert/loop_modeling Add a rosetta-scripts front-end for the recently refactored loop modeling code. Documentation for the new scripting interface has already been pushed to the documentation wiki. The main takeaway is that the process of building and refining loops of unknown structure can now be handled using the very flexible LoopModeler tag.

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Merge pull request #209 from RosettaCommons/vmullig/fix_silent_read Adding unit tests demonstrating current major bug with silent files I'm not sure how to fix this, since I don't understand the recent changes that someone added that created the problem in the first place. Here are the symptoms, though: - If you import a PDB file, run a Rosetta protocol that changes its size (adding residues to the pose), write the pose out to a silent file, and then try to read the silent file, the read fails with a cryptic error message. - Binary silent files no longer have REMARK lines for every structure in the file. Instead, there seems to just be one REMARK line at the top of the file. I suspect that this means that information is being lost in multi-pose silent files. - Related to both, if you import multiple PDB files, add residues to all but the first pose, write out the poses to a silent file (ensuring that the first one written is the one that has NOT had any residues added), then try to read them in, the read is fine. Failure only occurs if the first entry in a silent file has had residues added. The problem seems to lie with the FULL_MODEL_PARAMETERS part of the REMARK line, which is repeated only once per silent file and stores information only relating to the first model in the silent file. (I doubt that this is what whoever added this intended, so he/she should revisit this. I can't, because the creator of this commented nothing, so I have no idea what functionality I'm supposed to be preserving while fixing this bug.) I'm therefore adding two unit tests. The first is for the first case (import a PDB, modify the pose length, write a silent file, and read it in), and the second is testing write and read of multi-pose silent files (where the poses are very different). These tests currently fail. This pull request is NOT introducing any bugs (or any changes) to the main code; it is ONLY illustrating a current bug not previously covered by tests.

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Fixing release.PyRosetta.monolith script

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Merge pull request #207 from RosettaCommons/justinrporter/env_release Fix variant-matching issue in RigidChunkCM. Buildbot showed two unit test failures, but I suspect these are test instability. Otherwise, no unit test breaks or integration test changes expected.

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