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Revisions №60412

branch: master 「№60412」
Commited by: Vikram K. Mulligan
GitHub commit link: 「a46d8ea3fc44ca8c」 「№3477」
Difference from previous tested commit:  code diff
Commit date: 2018-09-20 11:18:05
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug 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 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

Merge pull request #3477 from RosettaCommons/vmullig/simpler_polylinear_interpolation Actually correct "as-angles" polylinear interpolation For peptoids and N-methyl amino acids, we need the polylinear interpolation used to interpolate well centres to work near the -180/180 wraparound point. Andy and I scratched our heads for a long time about little numerical problems that we were seeing in the derivatives with his approach from pull request #2851. In the end, we decided that, since the goal was to avoid weird behaviour at the wraparound point for interpolated angle values, we could achieve that just as easily by much simpler means. The basic approach here is: - Determine if the values being interpolated are generally closer to 0 or to the 180/-180 discontinuity. - If the former, interpolate as values. - If the latter, shift into the [0,360) range, interpolate as values, then shift back to (-180,180]. ~~This might break down if unusually extreme values are being interpolated, but then, interpolation isn't well suited to really extreme cases.~~ **UPDATE:** This _was_ breaking in cases relevant to peptoids, so I went back and implemented an _actually_ correct N-dimensional polylinear interpolation scheme. The new approach uses a recursive function that carries out a series of evaluations for successively lower dimensions. The 1-dimensional interpolator avoids the 0/360 or -180/180 angle discontinuities by using the shortest interpolation between two values, as described above; since higher-dimensional interpolators call the 1D interpolator, they also handle the discontinuity properly. Tasks: - [x] Implement the interpolation - [x] Check whether it solves the remaining problems in the peptoid branch (#2513). - Not all of them. But that's okay -- it's a start. - [x] Check that this works with the lysine Dunbrack test cherry-picked from closed pull request #2851. - [x] Shorten this test. - [x] Check additional unit tests pulled from that branch. - [x] Check what this does to canonical scoring. I may have to special-case the N=2 case. - I think we're okay. The generalization covers the N=2 case correctly. - [x] Beauty. - [x] Documentation. So there are a bunch of integration test trajectory changes from this branch, but no changes to scoring and no unit test failures. This tends to happen when one refactors Dunbrack or other core scoring code. Andy and I have both looked at the integration tests, and we're both pretty convinced that the failures fall into one of two categories: - Very tiny numerical differences that accumulate, since we're doing some math in a different way. - Changes to exotic noncanonicals that we actually expect (since we're interpolating Dunbrack libraries that rely on more than two mainchain torsions properly, now). **SO EXPECT A BUNCH OF INTEGRATION TEST CHANGES, IF YOUR TEST DOES PACKING OR MINIMIZATION AND USES FA_DUN.**

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AnchoredDesign KIC_refine KIC_vicinity KIC_with_fragments LayerDesign_symm SnugDock UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup antibody_H3 antibody_H3_camelid antibody_designer antibody_graft assemble_domains_jd2 batch_relax beta_strand_homodimer bin_initialization bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm classic_relax_1a19 composition_energy_layers crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal cyclization cycpep_design_pipeline d_workflow database_jd2_io database_session_resource dcys_disulfidize ddG_ensemble ddG_of_mutation density_refine density_refine_symm dock_glycans docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_site_constraints drrafter_run enumerative_sampling enzdes evolution farnesyl fast_relax features flexpepdock flexpepdock_abinitio ga_ligand_dock glycan_anomers glycan_refinment glycan_relax glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbs_design helix_from_sequence homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hybridization hydrate_relax inv_kin_lig_loop_design inverse_rotamer_remodel jrelax kinematic_looprelax ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_script match_1n9l membrane_relax membrane_relax_hbond metalloprotein_abrelax min_pack_min minimize_with_elec_dens mirror_symm motif_dna_packer_design mp_find_interface mp_range_relax mp_relax mp_relax_w_ligand mr_protocols next_generation_KIC nonideal_rtmin oligourea_design oligourea_predict oop_design oop_dock_design peptiderive pertmin pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG protocol_metric range_relax_w_cst relax_w_allatom_cst remodel_disulfides remodel_disulfides_rosettascripts repack_with_elec_dens repeat_relax resource_database_locator rna_denovo_dna_bridge rnp_ddg_calc_mut rnp_ddg_relax_command_2 rosetta_scripts_jd3 rosetta_scripts_loops sdf_reader 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_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal 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_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_glycosylation simple_metric_cache simple_metric_features simple_metrics splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter stored_residue_subset surface_docking swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swm_beta_peptide_loop swm_dna_bridge swm_protein_CCDmove swm_protein_from_scratch swm_protein_loop_sampler swm_protein_move_inside_coiledcoil_by_bond swm_protein_move_inside_helix_by_bond symm_rotamer_boltzmann task_selector threefold_symm_peptide_design torsion_restricted_sampling vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry zinc_homodimer_design
Test: mac.clang.integration

Failed sub-tests (click for more details):
AnchoredDesign KIC_refine KIC_vicinity KIC_with_fragments LayerDesign_symm SnugDock UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup antibody_H3 antibody_H3_camelid antibody_designer antibody_graft assemble_domains_jd2 batch_relax beta_strand_homodimer bin_initialization bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm classic_relax_1a19 composition_energy_layers crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal cyclization cycpep_design_pipeline d_workflow database_jd2_io database_session_resource dcys_disulfidize ddG_ensemble ddG_of_mutation density_refine density_refine_symm dock_glycans docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_site_constraints drrafter_run enumerative_sampling enzdes evolution farnesyl fast_relax features flexpepdock flexpepdock_abinitio ga_ligand_dock glycan_anomers glycan_refinment glycan_relax glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbs_design helix_from_sequence homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hybridization hydrate_relax inv_kin_lig_loop_design inverse_rotamer_remodel jrelax kinematic_looprelax ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_script ligand_water_docking membrane_relax membrane_relax_hbond metalloprotein_abrelax min_pack_min minimize_with_elec_dens mirror_symm mp_domain_assembly mp_find_interface mp_mutate_relax mp_range_relax mp_relax mp_relax_w_ligand mr_protocols next_generation_KIC nonideal_rtmin oligourea_design oligourea_predict oop_design oop_dock_design peptiderive pertmin pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG range_relax_w_cst relax_w_allatom_cst remodel_disulfides remodel_disulfides_rosettascripts repack_with_elec_dens repeat_relax resource_database_locator rna_denovo_dna_bridge rnp_ddg_calc_mut rnp_ddg_relax_command_2 rosetta_scripts_jd3 rosetta_scripts_loops rotamer_probability score12_docking sdf_reader 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_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal 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_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_glycosylation simple_metric_cache simple_metric_features simple_metrics splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter stored_residue_subset surface_docking swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swm_beta_peptide_loop swm_dna_bridge swm_protein_CCDmove swm_protein_from_scratch swm_protein_loop_sampler swm_protein_move_inside_coiledcoil_by_bond swm_protein_move_inside_helix_by_bond symm_rotamer_boltzmann symmetric_docking task_selector threefold_symm_peptide_design torsion_restricted_sampling vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry zinc_homodimer_design
Test: linux.clang.profile

Failed sub-tests (click for more details):
AnchoredDesign
Test: ubuntu.clang.python27.release.PyRosetta4.Release

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