Removing unused test blocks. Should hopefully fix the ninja build

• Summary

Merge pull request #121 from RosettaCommons/rfalford12/rosetta_membrane3 Rosetta Membrane Framework Updates (October 2014) -------------------------------------------------------- This merge includes a series of bug fixes, updates, and new Rosetta membrane framework applications. Summary of Changes: (1) Loading in Membrane Models: Add capability to load in a membrane PDB. This could be a PDB output by another framework application or something created manually. Two ways to do this: (a) Search the PDB for a membrane definition (pass -in:membrane) (b) Specify the position of the membrane residue on the command line (2) Membrane residues: (a) Adding residue property MEMBRANE for EMB and MEM residue types. (b) Similar to (a): adding back Is_membrane() methods in residue type (c) Updated membrane and embedding residue param files (defaults) in fa_standard and centroid (3) Library reorganization: Moved io (resource manager) and geometry (utilities) code to the protocols level (protocols/membrane). (4) Changed default membrane fold tree behavior: Adds membrane residue by jump to the center of mass residue of the protein instead of just appending to the end. (5) PyMOL Viewer: Fixing a ton of bugs, making the implementation more generalizable (a) Removed old membrane planes class (not needed) (b) Computing plane positions on the python side (more lightweight, flexible with other Rosetta protocols) (c) When the membrane position changes, pymol will now dynamically redraw the planes. (d) Removed the extra -view_in_pymol flag. If the framework is on and pymol viewer is on, membrane planes will automatically be drawn during visualization. (6) Updating score_jd2: Score_jd2 compatibility with the membrane framework. Can score a new membrane protein or rescore a pdb output from another framework application (7) Rosetta scripts hooks for all membrane movers. (a) AddMembraneMover (b) MembranePositionFromTopology (c) SetMembranePositionMover (d) VisualizeMembranePlanesMover (e) SetupForMembraneSymmetry (8) Membrane Relax Protocol: Application for refinement of membrane protein structures using membrane min cycles. Still in pilot apps. (9) Symmetric Membrane Protein-Protein Docking Protocol: Application for symmetric protein-protien docking with the membrane framework. Includes a generic SetupForMembraneSymmetry mover. Still in pilot apps. (10) Integration tests for load time, symmetric membrane protein-protein docking, and membrane relax (11) Support for demos (in Rosetta/demos directory) for all 5 membrane framework applications Test Status ------------------- Mac build: All Pass Unit Tests: All pass Score Regression: Expected changes due to PDB info for MEM residue updates (no numerical changes, just PDB differences) Integration Tests: - mpframework integration tests - changed due to add - membrane_relax - changed due to deprecation message in old membrane energy methods - assemble_domains_jd2, broker, metalloprotein_broker, others - fixing rms print in scorefile with Luki's patch - score_jd2 - change due to adding membrane functionality in this application The linux tests have not yet completed on the test server - seems backed up quite a few commits. If there are any concerns or issue I will be sure to watch out for them and address as they come up. Please let me know if you have any concerns.

• Summary

Remove unused function with highly questionable logic.

• Summary

Merge pull request #135 from RosettaCommons/calebgeniesse/cmake_debug Fixed slowdown in cmake + ninja build

• Summary

Adding the correct version numbering for OS X Yosemite (10.10) to setup_platforms.py

• Summary

Merge pull request #133 from RosettaCommons/weitzner/unit-test-cleanse Weitzner/unit test cleanse Removing the #define private public. Get ready for me to get on my high horse!

• Summary

Merge pull request #136 from RosettaCommons/JWLabonte/molfile_to_params Minor Improvement to `molfile_to_params.py`: one can now specify the root and neighbor atoms from the command line. This merge also includes some rider changes related to carbohydrates and lipids in the database: * corrections to bond order in lipid topology files * expansion of `dock_glycans.py` carbohydrates integration test expected to change due to corrections in lipid bond orders. molefile_to_params integration test expected to change due to output change.

• Summary

Merge pull request #130 from RosettaCommons/daslab Daslab -- minor bug fixes in stepwise the 9 integration test changes are expected. (match_1n9l is always changing.)

• Summary

PyRosetta. Adding special handling for classed derived from utility::SingletonBase so bindings for them could be created.

• Summary

Merge pull request #134 from RosettaCommons/indigogo/imm_pub Indigogo/imm pub

• Summary

Fixing PyRosetta imports, this should fix most of the PyRosetta unit tests.

• Summary

Removing yet another place in the matcher where residue types are stored in a data structure by their address and then accessed by iterating across that data structure; such code leads to instability since it relies on residue types being allocated at the same location in memory in each execution. Hoping against hope that this finally fixes the matcher instability once and for all.

• Summary

Bugfix to cartesian sampler for helical symmetry

• Summary

Merge pull request #129 from RosettaCommons/PyRosetta Fixing Rosetta Windows build. Fixing minor bug in MinMover.

• Summary

Merge pull request #122 from RosettaCommons/daslab Daslab Reverting a prior revert, and making these changes compatible with new pointer system. All tests pass or have cosmetic changes due to fixes in spacing and format of silent files, or additional score term. (The cxx11_thread and pyrosetta builds aren't working, but that's true of master.)

• Summary

Add a new pilot app

• Summary

Legend: