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branch: master 「№60070」
Commited by: Vikram K. Mulligan
GitHub commit link: 「8f6a366c708cb747」 「№2975」
Difference from previous tested commit:  code diff
Commit date: 2018-02-23 05:46:13
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration maintenance.documentation performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2975 from RosettaCommons/vmullig/fa_dun_ncaa_mirror_scoring_hotfix Fixing a *very* subtle bug introducing minor asymmetry in NCAA fa_dun scoring When I wrote the Voronoi-based well assignment code for the NCAA fa_dun scoring, I introduced a small bug: for mirror-image types (_e.g._ D-amino acids), I was forgetting to flip the mainchain torsion values when figuring out which backbone bin I was in. This meant that the boundaries between rotamer wells could be very slightly out of place. I discovered this in the peptoids branch, since it becomes most apparent in types in which the rotamer well centres change most with backbone torsion value changes. This pull request fixes the problem.

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Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: master 「№60069」
Commited by: Jack Maguire
GitHub commit link: 「fc64acf459d38b80」 「№2966」
Difference from previous tested commit:  code diff
Commit date: 2018-02-22 21:42:05
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2966 from RosettaCommons/JackMaguire/MCHBNetCorrection This PR introduces an option to HBNet that allows HBNet's internal scores to be placed in the output poses (turned off by default). This would allow the user to access the scores using the CalculatorFilter or ReadPoseExtraScoreFilter and the scores would be included in the score.sc file.

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Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: master 「№60068」
Commited by: Sergey Lyskov
GitHub commit link: 「73be6aaed039ffad」 「№2973」
Difference from previous tested commit:  code diff
Commit date: 2018-02-22 20:53:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2973 from RosettaCommons/sergey/binder Updating Binder submodule, adding include mapping for GCC regex headers. Switching PyRosetta build script to use SSH for Pybind11 and LLVM checkout. Triggering clean build.



branch: master 「№60067」
Commited by: Sebastian Rämisch
GitHub commit link: 「ab9c79ff627163b3」 「№2969」
Difference from previous tested commit:  code diff
Commit date: 2018-02-22 15:46:36
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2969 from RosettaCommons/raemisch/BugFixSimpleGlycosylateMover SimpleGlycosylate copy constructor changed to include proper residue selector.

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Test: linux.clang.serialization.PyRosetta4.unit

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Test: mac.clang.integration

Failed sub-tests (click for more details):
farnesyl
Test: linux.clang.scripts.pyrosetta

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branch: master 「№60066」
Commited by: Andy Watkins
GitHub commit link: 「ac6e7020dbc5a246」 「№2965」
Difference from previous tested commit:  code diff
Commit date: 2018-02-22 14:24:29
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2965 from RosettaCommons/everyday847/install_sample_farnesyl_movers Install and sample farnesyl moieties using stepwise

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Test: linux.clang.serialization.PyRosetta4.unit

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Test: linux.clang.performance

Failed sub-tests (click for more details):
core_scoring_Score_100x_chainbreak
Test: linux.clang.scripts.pyrosetta

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branch: master 「№60065」
Commited by: Jack Maguire
GitHub commit link: 「29d49b005cfec62b」 「№2972」
Difference from previous tested commit:  code diff
Commit date: 2018-02-22 14:21:16
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2972 from RosettaCommons/JackMaguire/MultistageRosettaScripts There was a bug in an integration test I added to master yesterday that causes it to always fail. I did not notice it because the testing server did not have a reference to "diff" against, but now that other people are pushing to master I can see that all the diffs are backtraces. My apologies to everyone who had to deal with these useless test failures!

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Test: linux.clang.serialization.PyRosetta4.unit

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Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.scripts.pyrosetta

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branch: master 「№60064」
Commited by: Alexander Ford
GitHub commit link: 「e91aacb04ebba7da」 「№2964」
Difference from previous tested commit:  code diff
Commit date: 2018-02-21 21:21:28
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug ubuntu.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2964 from RosettaCommons/fordas/pyrosetta_wheel Add support for pyrosetta wheel distributions.

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/rna/rna_denovo.cc src/core/fragment/rna/FullAtomRNA_Fragments.cc src/core/optimization/Minimizer.cc src/core/scoring/constraints/ConstraintIO.cc src/core/select/residue_selector/SSElementSelector.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/legacy_sewing/sampling/LegacyMonteCarloAssemblyMover.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh test/protocols/rosetta_scripts/RosettaScriptsJobQueen.cxxtest.hh
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
input_and_output
Test: linux.clang.performance

Failed sub-tests (click for more details):
core_scoring_Score_100x_distance_chainbreak


branch: master 「№60063」
Commited by: Jack Maguire
GitHub commit link: 「53a8ebe8c0585f22」 「№2959」
Difference from previous tested commit:  code diff
Commit date: 2018-02-21 11:40:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Debug release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan unit.ubsan unit.valgrind

Merge pull request #2959 from RosettaCommons/JackMaguire/MultistageRosettaScripts Adding Clustering Feature in Multistage Rosetta Scripts I am adding the ability for Multistage Rosetta Scripts to increase diversity by clustering results between stages. I will talk about this more at winter rosettacon next week if you are interested. I expect it to look something like this: ``` <PROTOCOLS> <Stage num_results_to_keep="2000" > ... </Stage> <Cluster num_results_to_keep="1000"> <SomeKindOfMetric/> </Cluster > <Stage> ... </Stage> </PROTOCOLS> ```

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/rna/rna_denovo.cc src/core/fragment/rna/FullAtomRNA_Fragments.cc src/core/optimization/Minimizer.cc src/core/scoring/constraints/ConstraintIO.cc src/core/select/residue_selector/SSElementSelector.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/legacy_sewing/sampling/LegacyMonteCarloAssemblyMover.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh test/protocols/rosetta_scripts/RosettaScriptsJobQueen.cxxtest.hh
Test: linux.gcc.unit.valgrind

Failed sub-tests (click for more details):
core:NetChargeEnergyTests_packer_symm:test_energy_annealing_symmetric core:VoidsPenaltyEnergyTests_symm:test_packing_success protocols:AchiralResidueTypeTests:test_import_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_import_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_import_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:BuildDeNovoBackboneMoverTests:test_design protocols:BuildDeNovoBackboneMoverTests:test_symmetry protocols:MPFastRelaxFoldTreeTest:test_double_chain_com_anchored_foldtree protocols:MPFastRelaxFoldTreeTest:test_single_chain_com_anchored_foldtree protocols:StructureDataFactoryTests:test_silent_io protocols:StructureDataFactoryTests:test_structuredata_io protocols:StructureDataFactoryTests:test_symmetry protocols:StructureDataFactoryTests:test_xml_io protocols:SymmetricAddMembraneMoverTest:test_appropriate_foldtree protocols:SymmetricAddMembraneMoverTest:test_membrane_jump_tracking protocols:SymmetricAddMembraneMoverTest:test_preserved_symmetry protocols:SymmetricAddMembraneMoverTest:test_symm_add_postconditions


branch: master 「№60062」
Commited by: Ryan Pavlovicz
GitHub commit link: 「19ab00f908f3cef2」 「№2967」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 21:09:36
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2967 from RosettaCommons/rpavlovicz/fix_water fix variable declaration in PackPwatRotamersMover

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
duplicate_header_guards
Test: mac.clang.integration

Failed sub-tests (click for more details):
duplicate_header_guards
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: master 「№60061」
Commited by: Vikram K. Mulligan
GitHub commit link: 「352681675b0dc6ac」 「№2946」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 21:05:03
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2946 from RosettaCommons/vmullig/hbnet_energy_options Add alternative ramping options for the HBNet energy The HBNet energy currently gives a quadratically-ramping bonus for larger and larger hydrogen bond networks. @basantab observed that this results in giant hydrogen bond networks if there is any way at all to form these, at the expense of bad packing or other undesirable features. A "diminishing returns" ramping function might be better. This pull request adds options for linear, logarithmic, and square root ramping. It also adds an option for a maximum network size, beyond which there's no bonus. Tasks: - [x] Add enum for the new ramping types. - [x] Add different calculators for the bonus function. - [x] Add means for setting ramping type from flags. - [x] Add means for setting ramping type from RosettaScripts. - [x] Unit tests for different ramping types. - [x] Add option for max network size. - [x] Modify calculator for max network size. - [x] Add means for setting max network size from flags. - [x] Add means for setting max network size from RosettaScripts. - [x] Unit tests for max network size. - [x] Documentation for ramping types. - [x] Documentation for max network size. - [x] Beauty.

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branch: master 「№60060」
Commited by: Alexander Ford
GitHub commit link: 「7b9c4aa095a2d74e」 「№2963」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 19:57:40
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2963 from RosettaCommons/fordas/inline_aa_comp_constraint Add support for inline aa composition constraint definition.



branch: master 「№60059」
Commited by: Scott Boyken
GitHub commit link: 「4c9f2871afa87959」 「№2947」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 15:21:52
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2947 from RosettaCommons/sboyken/keep_info_labels_symmetric options to preserve PDBInfoLabels when detecting / generating symmetric poses; works with SetupForSymmetry and DetectSymmetry movers by simply adding keep_pdb_info_labels="true" to these movers. Longterm would be good to decide whether people want this to be default, and could be hooked into deeper symmetry code



branch: master 「№60058」
Commited by: Yang Hsia
GitHub commit link: 「80c856983f7c5c29」 「№2955」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 15:18:15
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2955 from RosettaCommons/yhsia/AddResidueLabelMover_asu AddResidueLabelMover - only label asu

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
duplicate_header_guards
Test: mac.clang.integration

Failed sub-tests (click for more details):
duplicate_header_guards


branch: master 「№60057」
Commited by: Sergey Lyskov
GitHub commit link: 「90028316834dcbca」 「№2954」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 14:28:58
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2954 from RosettaCommons/sergey/f fixing uninitialized data members in src/core/pack/rotamer_set/*

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
duplicate_header_guards
Test: mac.clang.integration

Failed sub-tests (click for more details):
duplicate_header_guards
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: master 「№60056」
Commited by: Rocco Moretti
GitHub commit link: 「560a88b76614a7c5」 「№2961」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 10:50:14
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2961 from RosettaCommons/roccomoretti/better_double_restype_message Improve the double-loaded ResidueType error message.

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
duplicate_header_guards
Test: mac.clang.integration

Failed sub-tests (click for more details):
duplicate_header_guards


branch: master 「№60055」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「14e20e12e097e665」 「№2913」
Difference from previous tested commit:  code diff
Commit date: 2018-02-20 10:46:27
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2913 from RosettaCommons/aleaverfay/layer_design_concise_logic Aleaverfay/layer design concise logic Per a discussion on slack over the difficulty in working with the layer-design residue selectors, I am creating some new code to let you combine residue selectors with boolean logic and pair those combinations with residue level task operations. This PR is not done, and I'm about to head out the door, but I wanted to give @sboyken and @cdbahl the heads up that this code is in progress. Example new syntax below: ``` <RESIDUE_SELECTORS> 
 <Layer name="surface" select_core="false" select_boundary="false" select_surface="true" use_sidechain_neighbors="true"/> <Layer name="boundary" select_core="false" select_boundary="true" select_surface="false" use_sidechain_neighbors="true"/> <Layer name="core" select_core="true" select_boundary="false" select_surface="false" use_sidechain_neighbors="true"/> <SecondaryStructure name="helix" overlap="0" minH="3" include_terminal_loops="false" use_dssp="true" ss="H" /> <SecondaryStructure name="sheet" overlap="0" minE="3" include_terminal_loops="false" use_dssp="true" ss="E" /> <SecondaryStructure name="loop" overlap="0" minH="3" minE="3" include_terminal_loops="true" use_dssp="true" ss="L" /> </RESIDUE_SELECTORS> <TASKOPERATIONS> 
 <DesignRestrictions name="layer_design"> <Action selector_logic ="surface AND ( helix OR sheet) " aas="DEHKNQRST"/> <Action selector_logic="surface AND loop" aas="DEGHKNPQRST"/> <Action selector_logic="boundary AND helix" aas="ADEIKLMNQRSTVWY"/> <Action selector_logic="boundary AND sheet" aas="DEFIKLNQRSTVWY"/> <Action selector_logic="boundary AND loop" aas="ADEFGIKLMNPQRSTVWY"/> <Action selector_logic="core AND helix" aas="AFILMVWY"/> <Action selector_logic="core AND sheet" aas="FILVWY"/> <Action selector_logic="core AND loop" aas="AFILMPVWY"/> </DesignRestrictions> 
 </TASKOPERATIONS> ``` `!` has the highest priority `AND` has the next highest priority `OR` has the lowest priority ``` x AND ! y OR z ``` would convert into a boolean-function equivalent of ``` OR( AND( x, !y ), z ) ``` Parentheses may be used to define alternate groupings: ``` x AND !( y or z ) ``` would be equivalent to ``` AND( x, !( OR( y, z ) ) ) ``` ... There is now a new top-level block for residue level task operations: ``` <RESIDUE_LEVEL_TASK_OPERATIONS> ``` that you can use in defining Actions in the DesignRestrictions task operation. These RLTOs can also be listed in the OperateOnResidueSubset task operation -- which now can take more than one RLTO (though it still takes exactly one ResidueSelector). The OperateOneResidueSubset task operation can *also* use the selector_logic attribute to construct a boolean combination of ResidueSelectors, as the DesignRestrictions TaskOp does.



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