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Revisions №61017

branch: master 「№61017」
Commited by: Vikram K. Mulligan
GitHub commit link: 「7b20d843d84b613a」 「№3575」
Difference from previous tested commit:  code diff
Commit date: 2019-11-03 18:27:44
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration.valgrind integration performance profile release.PyRosetta4.MinSizeRel release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #3575 from RosettaCommons/vmullig/update_dump_trajectory_energy Allow easy visualization of packing trajectories A while back, Brian Coventry added a clever means of visualizing minimization trajectories: the DumpTrajectoryEnergy. This is a scoring term that sneakily writes out a PDB whenever it is called to evaluate derivatives. This pull request modifies this scoreterm so that it can also dump out scoring trajectories (e.g. to visualize the _ab initio_ application's sampling) or packing trajectories. Tasks: - [x] Correct the access to the options system. (Use proper options constructor). - [x] Add XML setup. - [x] Add option for "stride", so that we don't have to dump every function evaluation, but could do, for example, every 10th or 100th or 100th. - ~~Add separate strides for packing, minimizing, and scoring.~~ - [x] Add support for scoring. - [x] Add support for packing. - [x] Errors if we try to interrupt a packing or minimizing trajectory (since there _are_ end-of-trajectory signals). - [x] Fix unit test failure. - [x] Fix integration test failure. - [x] Integration test for packing. - [x] Documentation: added here https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/RosettaScripts#rosettascript-sections_scorefunctions_a-utility-scoreterm-for-trajectory-visualization. - [x] Beauty. This pull request also adds some configuration for the VSCode IDE, to make it work a bit more smoothly with Rosetta's massive codebase. Users should be able to navigate to the Rosetta/main/source directory and simply type "code ." to have full editing capabilities, with Intellisense and all that good stuff.

Rocco Moretti 1 week
This commit apparently perma-broke the duplicate_header_guards integration script, due to `INCLUDED_core_scoring_util_methods_DumpTrajectoryEnergy_hh`
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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
DumpTrajectoryEnergy DumpTrajectoryEnergy_packing backbonegridsampler_multiresidue bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset coupled_moves duplicate_header_guards ligand_dock_ensemble mp_find_interface mp_mutate_relax mp_mutate_repack oligourea_predict perturb_helical_bundle remodel_helical_repeat rnp_ddg_finalize simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_grafting_movers supercharge test_energy_method_options zinc_heterodimer zinc_homodimer_design
Test: mac.clang.integration

Failed sub-tests (click for more details):
DumpTrajectoryEnergy DumpTrajectoryEnergy_packing backbonegridsampler_multiresidue bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset coupled_moves duplicate_header_guards ligand_dock_ensemble mp_find_interface mp_mutate_relax mp_mutate_repack oligourea_predict pepspec perturb_helical_bundle remodel remodel_disulfides remodel_helical_repeat simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_grafting_movers supercharge test_energy_method_options validate_database zinc_heterodimer zinc_homodimer_design