Merge pull request #274 from RosettaCommons/phbradley/tiny_minpack_bugfix tiny min_pack bugfix

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Merge pull request #272 from RosettaCommons/phbradley/residue_datacache Phbradley/residue datacache

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Merge pull request #252 from RosettaCommons/rhiju/trace_assert updating assert() to print backtraces tests look OK. [one unit test failed; same as in master (I see that sergey is doing some fixes).] Will do global find/replace of assert() to debug_assert() in a separate pull request.

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Disabling folding and part of refinement PyRosetta unit tests until issues with Abinitio stability is resolved

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Merge pull request #266 from RosettaCommons/hahnbeom/refinement Hahnbeom/refinement

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Merge pull request #267 from RosettaCommons/vmullig/for_chris Very minor bugfix to BundleGridSampler (taking out some unnecessary restrictions on input). Test changes are only those integration tests that are already failing.

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Committing the resolution fix for rotlibs (prob <= 1e-6, not prob == 0)

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Bug fix for a uncompiled pilot app. No unit or integration test changes expected.

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Merge pull request #198 from RosettaCommons/wpotrzebowski/fiber_diffraction Merging Fiber Diffraction scoring and derivatives calculation There are three separate Fiber Diffraction modules (energy terms). FiberDiffractionEnergy – all-atom scoring and derivatives FiberDiffractionEnergyDens – low-resolution (centroid) scoring based on electron density of subunit FiberDiffractionEnergyGpu – all-atom scoring and derivatives performed on GPU. This module is based on NVIDIA Cuda library and was developed before OpenCL standard was introduced. To compile it extras=cuda flag has to be used. One has to uncomment two lines (71 and 72) in tools/build/nvcc.py file. This will pass arch=sm_20 flag to nvcc. I’ve also added #define BOOST_NOINLINE statement to external/boost_1_55_0/boost/config/compiler/nvcc.hpp so the module compiles in debug mode. The corresponding line has to be uncommented too. #UNIT TESTS: Fiber Diffraction tests have been added. Unit tests status: All pass #INTEGRATION TESTS: fiber_diffraction and fiber_diffraction_fad Integration tests have been added. Integration test results as expected: database_jd2_compact_io, database_jd2_io, features and sweep_respair_energies are changed because new score terms are added. #PyRosetta: FiberDiffractionEnergy, FiberDiffractionEnergyDens works with PyRosetta, while FiberDiffractionEnergyGpu was excluded from these builds (src/python/bindings/exclude.py)

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Set use_centroid_dg to False in InterfaceFeatures. It is unused and unreported. Having it true makes pdbs fail with modifications or other ligands without centroid params. Thanks to Jordan Willis for finding this

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Merge pull request #262 from RosettaCommons/revert-261-hahnbeom/refinement Revert "Hahnbeom/refinement" until issues with Windows PyRosetta build is fixed

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Merge pull request #255 from RosettaCommons/justinrporter/env_release Merge miscellaneous bug fixing related to Environment, except a bug in FoldTree::insert_fold_tree_by_jump that creates an invalid fold tree when the inserted fold tree is a single, one-residue peptide edge. This is fixed by commit 90120df. Integration test failures are expected from antibody_graft and inverse_rotamer_remodel for unrelated reasons, as well as "core_scoring_Score_10000x_fa_cust_pair_dist," which seems to be failing these days.

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Merge pull request #261 from RosettaCommons/hahnbeom/refinement Hahnbeom/refinement

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Merge pull request #259 from RosettaCommons/revert-257-vmullig/turn_off_smoke_detector Revert "Temporarily turning off an integration test that no one has seen...

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Merge pull request #258 from RosettaCommons/vmullig/for_chris Adding a pre_selection_filter option to the BundleGridSampler. This adds one option to the BundleGridSampler (a pre-selection filter that filters out gridpoints that don't pass some criterion). Tasks: Add the filter option. Add RosettaScripts support. Have it do something in the apply() function. Tweak the bundlegridsampler_design integration test to use a filter. (Changes to this integration test expected). Update the documentation. Incidental changes: Tweaked my design_cycpeptide_MPI.cc app. Expected test changes: Only the bundlegridsampler_design integration test should change (a bit more logfile output, a few fewer pdb files written since some are filtered out by the new filter). I didn't wait for the Windows PyRosetta build test, since it's very slow. I'll chance it -- there's no reason that this should cause that build to fail when the Mac and Linux PyRosetta builds are fine.

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Merge pull request #257 from RosettaCommons/vmullig/turn_off_smoke_detector Temporarily turning off an integration test that no one has seen fit to fix in some time Moving the antibody_graft integration test to disabled_tests to turn it off. This integration test, along with inverse_rotamer_remodel and pcket_suggest_targets, have been broken for some time (though the latter two work in at least one of release_debug or release, so I'll leave them). A smoke detector that rings continuously is worse than useless; it masks actual alarms and trains people to ignore the alarm. I'm switching the antibody_graft integration test off until someone sees fit to fix it (and I hope someone will also fix the other two). I don't know whose tests these are because there are no observers. If they're yours, fix them and put them back in tests, please. Update -- I see that pocket_suggest_targets was fixed. Thank you! The debug_release integration test should give a green light, now, with antibody_graft disabled. (Whoever wrote antibody_graft, please fix it and re-enable!)

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