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Revisions №61323

branch: master 「№61323」
Commited by: Vikram K. Mulligan
GitHub commit link: 「cd4c8de0d49b3a52」 「№4761」
Difference from previous tested commit:  code diff
Commit date: 2020-06-29 16:41:46
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-9.gcc.build.debug 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 build.ninja_debug graphics static mac.clang.static.build.release build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug linux.clang.python38.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python38.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python38.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release linux.clang.python38.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release ubuntu.clang.python38.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting scientific.antibody_h3_modeling.debug scientific.ddg_ala_scan.debug scientific.docking.debug scientific.ligand_docking scientific.ligand_scoring_ranking scientific.loop_modeling_ccd_12res scientific.loop_modeling_ngk_12res.debug scientific.mp_dock.debug scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_energy_landscape.debug scientific.mp_f19_energy_landscape scientific.mp_lipid_acc scientific.mp_relax.debug scientific.protein_data_bank_diagnostic.full scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast_5iter.debug scientific.relax_fast_5iter scientific.relax_fast scientific.simple_cycpep_predict linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan gcc-9.gcc.unit util.apps

Merge pull request #4761 from RosettaCommons/vmullig/all_to_all_pnear_analysis Add PNear analysis for many states. I'm using peptide structure prediction to train ML models that can recognize peptides that fold well. A single structure prediction run actually generates far more data than I'm using. It would be useful to compute and output PNear to all of the negative states in addition to PNear to the state that I'm designing for, to give me more data for training. This PR adds this functionality. Tasks: - [x] Add new option. - [x] Register new option. - [x] Have the new option do something: - [x] Add a new step to the `HierarchicalHybridJDApplication` class for this computation: - [x] Sends a request for each state in turn from the emperor node to all slave nodes. - [x] Each slave node broadcasts that state to all other slave nodes. - [x] All slave nodes compute RMSD to that state. - [x] Emperor collects RMSDs up the hierarchy and carries out PNear calculation. - [x] Repeat for each relevant state. - [x] Write out PNear list at end. - [x] Error if used with `-compute_rmsd_to_lowest option.`. - ~~Check and address issue #4738~~ --> separate pull request. - [x] Documentation. - [x] Integration test. - [x] Beauty.

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