fixing unit tests

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Merging in fix to the Windows PyRosetta build!

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Merge pull request #576 from RosettaCommons/mlnance/fold_tree_chemical_edge Added a getter function to return a list of chemical edges from the fold tree because I needed it for setting constraints at branch points.

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Merge pull request #571 from RosettaCommons/rhiju/mg_hires Rhiju/mg hires • There are a few integration test changes that are cosmetic (#residues in rna_phenix go up a little). • A couple of stepwise tests change due to last-decimal-point numerical differences during minimizing.

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Merge pull request #573 from RosettaCommons/rotamer_library_rebase Rotamer library improvements

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Merge pull request #570 from RosettaCommons/dimaio/envdep_elec Adding new options to control environment-dependent hbonding/electrostatics. Integration test failures due to additional output in EnergyMethodOptions.

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Updating benchmark unit test script so it save build log even on successful builds

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Updating release_debug_no_symbols build mode by adding -ffloat-store compilation flag. This should make this mode more ‘debug-like’. Adding this flag also lead to hard failure of previously passed fragmentpicker_integration_demo integration test.

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Merge pull request #569 from RosettaCommons/phbradley/set_atomic_charges_from_cmdline add -set_atomic_charge flag for modifying atomic charges from the cmd…

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Merge pull request #568 from RosettaCommons/phbradley/lk_ball_flags Phbradley/lk ball flags -- add some flags to modify lk_ball per-atom wts from cmdline

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Merge pull request #567 from RosettaCommons/rfalford12/cleanup_pilot_apps Rfalford12/cleanup pilot apps Cleaning up my pilot apps folder - organizing previous versions of membrane framework applications. Also updated the README.txt file in the apps/pilot/membrane folder.

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trying to restore my reverted commit

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Merge pull request #463 from RosettaCommons/vmullig/jd2_joblist_memory_issue Trying to get the JobDistributor working on Blue Gene with ridiculously large nstruct values. On Argonne's Blue Gene/Q system, RosettaScripts now works, but the app fails before any jobs are distributed if nstruct is set too high (~10,000,000 or higher). It seems that the GenericJobInputter creates a list of jobs at the start of its run, and this list fills up memory and causes Rosetta to crash. I'm going to try to fix this (though I might need some guidance on this). Update: In the interests of getting this out for the largest number of users, I'm going to merge this at this stage (the current features are stable and usable), and complete the unchecked tasks later. Tasks: -- Implement a new LargeNstructJobInputter (based on the GenericJobInputter) that generates an initial list of jobs, then clears this and generates new lists as needed. -- Hmm... I'll need a way of managing the jobs_ list in the JobDistributor intelligently as jobs are added or removed... So implement a new JobsContainer class for this purpose. -- Let the JobsContainer work with the JobInputter to add or remove jobs. -- Add an option to determine the nstruct value over which the LargeNstructJobInputter is used. -- Fix the cxx11thread build. -- Ensure that all integration test changes are expected, or fix them if they're actual problems. -- Address the const-access problem in all get_new_job_id() functions (the JobsContainer object needs non-const access since it has to update the jobs list). -- Check that the MPIWorkPoolJobDistributor is also properly marking jobs as deletable, and work properly with the LargeNstructJobInputter. -- Get the MPIWorkPoolJobDistributor to do the following: -- Mark jobs as deletable on the master node. -- Synchronize the marking of jobs as deletable across slave nodes. -- Only synchronize when strictly necessary (since the synchronization information takes significant bandwidth). TODO Check that the MPIFileBufJobDistributor is also properly marking jobs as deletable, and work properly with the LargeNstructJobInputter. TODO Get the MPIFileBufJobDistributor to do the following: TODO Mark jobs as deletable on the master node. TODO Synchronize the marking of jobs as deletable across slave nodes. -- Test this on Blue Gene before merging with master. -- Works with FASTA input, PDB output. TODO Works with FASTA input, silent file output. TODO Works with PDB input, PDB output. TODO Works with PDB input, silent file output. TODO Works with silent file input, PDB output. TODO Works with silent file input, silent file output. TODO Add integration test for non-MPI job distributor with LargeNstructJobInputter. -- Figure out how the heck to cover the MPI JobDistributor changes with tests. Also: -- Disable MPI timeout by default. As far as I can tell, this is only used by the MPIFileBufJobDistributor, and it's poorly-thought-out: it brings down the run if any job takes X times the average length of all jobs completed (where the default value for X is 3). That is, if job 2 takes more than 3 times longer than job 1 (e.g. if job 1 fails filters but job 2 passes), the whole thing comes tumbling down. This creates unexpected failures for users, and I think it should only be on if a user explicitly turns it on. -- Updated one of Lei's pilot apps so that Lei, Una, and I can use it on Blue Gene. Tasks above that are marked TODO will be completed in a future merge. This merge does not leave anything broken that wasn't broken before; it does fix job distribution with ridiculously high nstruct values in the special case of FASTA input and PDB output.

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Merge pull request #523 from RosettaCommons/rfalford12/release_mpframework Release RosettaMP Framework Applications All of these applications are described in the paper: Alford RF, Koehler Leman J, Weitzner BW, Duran AM, Tiley DC, Elazar A, Gray JJ (2015) "An Integrated framework advancing membrane protein modeling and design" PLoS CompBio Documentation is provided in the Rosetta/demos directory and on the gollum wiki (currently under construction by the XRW team). More info also provided in the README. Adding the following membrane framework applications to apps/public/membrane for release: = mp_dock: Membrane protein-protein docking = mp_dock_setup: Setup application for membrane protein-protein docking = mp_span_from_pdb: Predict transmembrane spans from the PDB = mp_transform: Transform protein into the membrane coordinate frame = mp_symdock: Assemble C-Symmetric membrane pose in the bilayer = mp_viewer: Visualize membrane planes via the PyMOL Mover = mp_relax: High resolution refinement of membrane proteins (RosettaScripts) = mp_ddG: Predict ddGs for membrane proteins (PyRosetta script) Testing: mp_dock, mp_symdock, and mp_relax have integration tests. The remaining apps encapsulate single movers and are tested via unit test. Test Changes: mp_dock and mp_symdock expected because command files changed

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Prevent warning about ambiguous order of operations in BumpGrid.cc. Add parenthesis to maintain the behavior of the code as per C++ operator precedence and associativity rules. This warning is emitted by gcc 5.1.0 and prevents compilation with scons. (This is the tweak originally intended by commit 8c0d064ab8d5f89654483308c764dc19e83a818b.)

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Revert "Prevent warning about ambiguous order of operations in BumpGrid.cc. Add" This reverts commit 8c0d064ab8d5f89654483308c764dc19e83a818b.

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