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Revisions №60945

branch: master 「№60945」
Commited by: Rocco Moretti
GitHub commit link: 「04d3e581085629b0」 「№3770」
Difference from previous tested commit:  code diff
Commit date: 2019-09-24 11:07:52
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
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 performance profile ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source scientific.antibody_h3_modeling.debug scientific.cartesian_relax scientific.ligand_docking scientific.mp_f19_energy_landscape.debug 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 unit.ubsan util.apps

Merge pull request #3770 from RosettaCommons/roccomoretti/const_restype_split Split ResidueType into separate modifiable and "finalized" classes. Our current ResidueType layout leaves something to be desired. Right now we have an odd prefinalized/finalized state distinction in a single class, with a whole host of duplicated data which may-or-may not be valid based on the (semantic and non-queriable) state of ResidueType. To fix this, I'm splitting the ResidueType into two (three if you count the common base class). The vast majority of usage with be of the (always-finalized) plain ResidueType class, which has the conventional name-and-index implementation, with an internal struct-of-arrays layout. For most people, the interaction with ResidueTypes will be the same. What does change is the interface for people who are modifying ResidueTypes. These people don't work with the plain ResidueType class, but with a new ModResidueType class, which uses VD's (and names) as the primary accessor, with atomic information represented in a graph. (While there is an implicit atom order, accessing by index is highly discouraged in favor of the VD interface, as atoms could be added/deleted at any time, and there isn't necessarily the same bb/sc/hydro order that the plain ResidueType has.) The only way to make a (non-modifiable) ResidueType is through building and converting a ModResidueType. (You can also convert a plain ResidueType back to a ModResidueType for further alteration.) The ResidueType factory function/constructor takes over the function of the (now-removed) finalize() function. (A common base class which stores non-atom-dependent data simplifies things.) This should make working with (Mod)ResidueTypes in their modifiable form easier, as there's less redundant information, and all information there is should all be valid and up-to-date throughout the lifetime. (Versus some data/functions being contingent on being finalized.) A side effect should be that ResidueTypes become slightly smaller (as they no longer have redundant atom information), and that compilation times become shorter because ResidueType no longer has to include the highly-templated boost::graph headers. (These are limited to the ModResidueType class, which is included in many fewer compilation units.)

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Test: mac.clang.python27.build.xcode

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
autosetup_metals_centroid batch_relax carbohydrates cart_min_glycans crosslinkermover_tma cyclization ddG_of_mutation density_tools enzdes farfar_mrna fiber_diffraction_fad fold_and_dock ga_ligand_dock glycan_anomers glycan_refinment hbnet_use_input_rot helix_from_sequence hts_io hybridization ligand_database_io match_6cpa match_xml mm_params mp_find_interface mp_mutate_relax mp_range_relax mp_symmetry_load mr_protocols noe_assignment nucleobase_sample_around phosphorylation pna pna_base_pairs polyaramid_test_trivial ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG read_polymeric_components restype_converter rna_denovo_lariat rnp_ddg_finalize rosetta_scripts_jd3 sdf_reader simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_tma simple_metrics_per_residue small_molecule_lattice_dock swa_rna_gagu_03_append_to_silent swa_rna_gagu_07_prepend_dinucleotide swa_rna_gagu_08_append_dinucleotide swa_rna_gagu_09_sample_virtual_ribose swa_rna_gagu_10_prepend_and_ccd_close swa_rna_gagu_11_append_and_ccd_close swa_rna_gagu_12_helix_addition swa_rna_gagu_13_chunk_combination_and_closure swa_rna_gagu_15_combine_long_loop_sampling swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide swa_rna_gagu_18_rebuild_bulge swa_rna_gagu_19_prepend_floating_base_by_jump swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump swa_rna_gagu_22_prepend_and_kic_close swa_rna_gagu_23_append_and_kic_close swm_beta_peptide_loop swm_build_full_model 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 swm_protein_preminimize tna_base_pairs torsion_restricted_sampling vancomycin
Test: mac.clang.integration

Failed sub-tests (click for more details):
AnchorFinder Enzrevert_xml KIC_with_fragments SnugDock antibody_H3 antibody_designer antibody_designer_camelid app_exception_handling autoNOE_rosetta autosetup_metals_centroid backrub_interface_ddG bridge_chains carbohydrates cart_min_glycans crosslinkermover_tma cyclization ddG_of_mutation density_tools doug_dock_design_min_mod2_cal_cal farfar_mrna features fiber_diffraction_fad fold_and_dock ga_ligand_dock glycan_anomers glycan_refinment hbnet_use_input_rot helix_from_sequence hts_io hybridization inverse_rotamer_remodel ligand_database_io match_6cpa match_xml mm_params mp_find_interface mp_mutate_relax mp_range_relax mp_relax_w_ligand mp_symdock mp_symmetry_load mr_protocols next_generation_KIC noe_assignment nucleobase_sample_around pepspec phosphorylation pna pna_base_pairs read_polymeric_components remodel remodel_disulfides residue_energy_breakdown restype_converter rna_denovo_lariat rosetta_scripts_jd3 rotamer_recovery rs_loophash sdf_reader simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_tma simple_metrics_per_residue small_molecule_lattice_dock swa_protein_combine_loops swa_rna_gagu_03_append_to_silent swa_rna_gagu_07_prepend_dinucleotide swa_rna_gagu_08_append_dinucleotide swa_rna_gagu_09_sample_virtual_ribose swa_rna_gagu_10_prepend_and_ccd_close swa_rna_gagu_11_append_and_ccd_close swa_rna_gagu_12_helix_addition swa_rna_gagu_13_chunk_combination_and_closure swa_rna_gagu_15_combine_long_loop_sampling swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide swa_rna_gagu_18_rebuild_bulge swa_rna_gagu_19_prepend_floating_base_by_jump swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump swa_rna_gagu_22_prepend_and_kic_close swa_rna_gagu_23_append_and_kic_close swm_beta_peptide_loop swm_build_full_model 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 swm_protein_preminimize threefold_symm_peptide_design tna_base_pairs validate_database vancomycin
Test: linux.clang.performance

Failed sub-tests (click for more details):
core_scoring_Score_100x_envsmooth