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Revisions №61314

branch: master 「№61314」
Commited by: Labonte
GitHub commit link: 「330e8d96378d24ae」 「№4148」
Difference from previous tested commit:  code diff
Commit date: 2020-06-13 00:44:31
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.valgrind integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.antibody_grafting.debug scientific.antibody_grafting scientific.antibody_h3_modeling.debug scientific.antibody_h3_modeling scientific.antibody_snugdock.debug scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.dock_glycans.debug scientific.dock_glycans scientific.docking.debug scientific.docking scientific.enzyme_design.debug scientific.enzyme_design scientific.ligand_docking.debug scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_kic_12res.debug scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.loop_modeling_ngk_12res.debug scientific.make_fragments.debug scientific.make_fragments scientific.mhc_epitope_energy.debug scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_decoy_discrimination scientific.mp_f19_energy_landscape.debug scientific.mp_f19_energy_landscape scientific.mp_f19_sequence_recovery.debug scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.full scientific.relax_cartesian.debug scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast_5iter.debug scientific.relax_fast_5iter scientific.relax_fast scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.simple_cycpep_predict.debug scientific.simple_cycpep_predict scientific.stepwise_rna_favorites.debug 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 unit.valgrind gcc-9.gcc.unit util.apps

Merge pull request #4148 from RosettaCommons/JWLabonte/PDB_IO/HETATM_records PDB IO: Correcting how HETATM records are decided This merge corrects how Rosetta decides between writing a PDB ATOM record and writing a HETATM record. Historically, Rosetta saved LIGAND ResidueTypes with HETATM and POLYMER ResidueTypes with ATM. This was in conflict with how the records are defined by the PDB, which is that only canonical AAs and NAs get ATOM records; all other types of residues should receive HETATM. See issue #3509 for further details/discussion. All unit tests pass. 98 integration tests give expected changes with a multiplicity of .pdb output lines changing from ATOM to HETATM.

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Test: mac.clang.python27.build.xcode

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Test: linux.gcc.mpi.serialization.integration.mpi

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database_md5
Test: linux.clang.integration.release_debug_no_symbols

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CCD_loop_closure DNA_methylation Enzrevert_xml FlipChirality MutateResidue_selector PeptideCyclizeMover UBQ_Gp_LYX-Cterm UnsatSelector backbonegridsampler backbonegridsampler_multiresidue binselector binselector_probins c-term_conjugation carbohydrates cart_min_glycans coenzymes crosslinkermover_octahedral_s2_symm crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tma crosslinkermover_tma_symm custom_basetype_packer_palette cyclization cycpep_design_pipeline d_workflow database_md5 design_glycans design_w_custom_palette-NCAAs disulfidize_beta_cys dock_glycans doug_dock_design_min_mod2_cal_cal explicit_membrane farnesyl features fit_helixparams_a3b fit_helixparams_rms genkic_dihedral_copying genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_tree_relax glycomutagenesis glycosylation interaction_graph_summary_metric ld_converter mirror_symm mmtfIO_score_test ncaa_fixbb ncbb_packer_palette oligourea_predict phiselector phosphonate phosphorylation pna pna_base_pairs polyaramid_test_trivial posttranslationalmod_io rama_mutation_selector read_polymeric_components real_virt_mover restype_converter rings rosetta_scripts_include rosetta_scripts_jd3 seed_ensemble_JD2_JI simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_bondangle_bondlength 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_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_glycosylation simple_metrics_per_residue swm_protein_preminimize threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs vancomycin
Test: linux.clang.tensorflow.integration.tensorflow

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database_md5
Test: linux.clang.integration.tutorials

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

Failed sub-tests (click for more details):
CCD_loop_closure DNA_methylation Enzrevert_xml FlipChirality MutateResidue_selector PeptideCyclizeMover UBQ_Gp_LYX-Cterm UnsatSelector backbonegridsampler backbonegridsampler_multiresidue binselector binselector_probins c-term_conjugation carbohydrates cart_min_glycans coenzymes crosslinkermover_octahedral_s2_symm crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tma crosslinkermover_tma_symm custom_basetype_packer_palette cyclization cycpep_design_pipeline d_workflow database_md5 design_glycans design_w_custom_palette-NCAAs disulfidize_beta_cys dock_glycans doug_dock_design_min_mod2_cal_cal explicit_membrane farnesyl features fit_helixparams_a3b fit_helixparams_rms genkic_dihedral_copying genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_tree_relax glycomutagenesis glycosylation interaction_graph_summary_metric ld_converter mirror_symm mmtfIO_score_test ncaa_fixbb ncbb_packer_palette oligourea_predict phiselector phosphonate phosphorylation pna pna_base_pairs polyaramid_test_trivial posttranslationalmod_io rama_mutation_selector read_polymeric_components real_virt_mover restype_converter rings rosetta_scripts_include rosetta_scripts_jd3 seed_ensemble_JD2_JI simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_bondangle_bondlength 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_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_glycosylation simple_metrics_per_residue swm_protein_preminimize threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs vancomycin
Test: linux.clang.performance

Failed sub-tests (click for more details):
core_pack_denseig_current_default_sfxn
Test: mac.clang.python36.release.PyRosetta4.Debug

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Test: linux.clang.scientific.antibody_h3_modeling

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Test: linux.clang.scientific.dock_glycans.debug

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Test: linux.clang.scientific.dock_glycans

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Test: linux.clang.scientific.docking.debug

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Test: linux.clang.scientific.ligand_scoring_ranking

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Test: linux.clang.scientific.mp_symdock.debug

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Test: linux.clang.scientific.mp_symdock

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Test: linux.gcc.unit.release

Failed sub-tests (click for more details):
core:EPRSpinLabelTest:test_histograms