branch: master 「№61848」
Commited by: Vikram K. Mulligan
GitHub commit link: 「7da5b15aed68fa1c」 「№5573」
Difference from previous tested commit:  code diff
Commit date: 2022-03-07 16:53:22
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 m1.clang.python38.PyRosetta4.unit m1.clang.python39.PyRosetta4.unit mac.clang.python36.PyRosetta4.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size 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.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.source scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.peptide_pnear_vs_ic50.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 mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5573 from RosettaCommons/vmullig/citation_info_in_docs Ensure that the CitationManager exports citation information in the auto-generated documentation @jadolfbr suggested this a while back, and I think it's a good idea. UPDATE: The act of doing this revealed a number of bugs and issues with local movers setting global state. Many of these are corrected in this PR -- see notes at the bottom. Tasks: - [x] Ensure that this happens for movers. - [x] Ensure that this happens for filters. - [x] Ensure that this happens for residue selectors. - [x] Ensure that this happens for task operations. - [x] Ensure that this happens for residue level task operations. - [x] Ensure that this happens for packer palettes. - [x] Ensure that this happens for simple metrics. - [x] Ensure that this happens for constraint generators. - [x] Switch author info to put e-mail addresses in square brackets instead of pointy brackets, since the XSD doesn't like additional pointy brackets. - [x] Update the auto-generated documentation. - [x] Add an integration test for the `-output_schema` flag of the `rosetta_scripts` application. - Add integration test to find movers, filters, etc. that (a) do not call `xsd_type_definition_w_attributes` or `xsd_type_definition_w_attributes_and_repeatable_subelements` and (b) do not manually include their own citation info. (Do this by checking the xsd of each mover/filter/taskop, etc. for the citation string.) --> At some point in the future. TODO: - [x] In `BackboneTorsionSampler` mover, move scorefunction initialization to parse_my_tag/apply time so that we don't get unnecessary scorefunction loading during instantiation. - [x] Same with `BackboneTorsionPerturbation` mover. - [x] Figure out why some header information in PDB files is no longer printing and restore it. - [x] Fix cppcheck error while I'm at it. - [x] Fix failing integration tests --> remaining failure seems to be in `HybridizeProtocol`. - [x] Check that the failure-to-run cases were fixed. - [x] Check changes. - [x] Fix unit test failure. - [x] Pull request #5581 should be merged before this one. - [x] Fix scripts that are failing validation. This addresses issue #5557. **Update**: So it turns out that a bunch of movers and filters cannot be instantiated with default options, which prevents their `CitationManager` information from being accessed. In hindsight, I'm kind of wishing I had made the `provide_citation_info()` function static, though that would have prevented configuration-specific citation information from being written out (e.g. if mover X only uses filter Y, and cites it, if option Z is set by the user in a RosettaScripts script). I've had to clean up the following movers and filters: - `ErraserMinimizerMover` (Wanted to create a scorefunction that doesn't exist on initialization. I don't know whether there's some specialized protocol that provides this scorefunction, so I've put this in a try/catch block. The mover now loads the scorefunction with the nearest name on failure, and prints a big red warning.) - `DumpSingleResidueRotamers` (Failed on initialization if the user didn't provide configuration with a custom flag. I'm moving the failure to apply-time. Yes, it would be better for this mover not to expect a commandline flag for configuration.) - `BackboneTorsionSampler` and `BackboneTorsionPerturbation` (Both wanted to create talaris2013 as their scorefunction, and crashed when instantiated if the restore talaris behaviour flag wasn't passed. I've put this in a catch/throw block, and now I print a big red warning and then get the default scorefunction if talaris initialization fails.) - `GALigandDock` (If the right scorefunction flags aren't passed, on initialization the GALigandDock mover tries to create an object that is unable to read from database on initialization. I'm moving this to an apply-time failure, and cleaning up some inefficient apply-time object copying in the process.) - `GlycanDockProtocol` (On instantiation, this mover reads from the global options and fails if not set properly. Not only does this prevent setup from RosettaScripts, it also prevents -info from working. I'm moving the checks of correct configuration to apply time. Yes, it would be better for this mover not to expect a commandline flag for configuration.) - `AsyncMPITemperingBase` and `ParallelTempering` (Throws on instantiation in non-MPI builds. I'm moving this to a throw on first use.) - `LoopHashDiversifier` (Tried to load its loop hash library on initialization, based on paths set on the commandline. If no path is set, this would fail. I'm moving this to an apply-time loading.) - `CaIrmsdFilter`, `IrmsdFilter`, `LrmsdFilter`, `FnonnatFilter`, and `FnatFilter` (Tried to set native pose on initialization, and would fail if no -in:file:native commandline flag was supplied. I've switched this to an apply-time check.) - `ParallelBetaPairingPreferenceFilter` (Tries to initialize itself from a file that doesn't exist. I can't fix that, but I can at least make it happen at apply time instead of on instantiation.) - `BCLFragmentBaseMover` and `BCLFragmentMutateMover` were checking for the `extras=bcl` build in their constructors. They now check in their `apply()` and `parse_my_tag()` functions. - Certain movers, namely the `Tomponents` framework (or anything using the `StructureDataFactory`), `ligand_docking`, and the `Matcher`, required `-preserve_header` to be set to `true`. They were silently switching this internally, altering everything that happened downstream by changing the global state if they were ever instantiated. This is a big no-no. I've switched this to a parse- or apply-time failure with an informative error message saying that the flag is required in cases in which there wasn't an easy way to get around the requirement, and in one case, to a scheme that uses a _local_ options setting instead of changing the _global_ options setting. Many integration tests will change, since initialization order is different. I've checked that there's no substantial change to output that isn't expected, though.

...
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_stub_constraints hts_io hybridization interaction_graph_summary_metric iphold job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design output_schema pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bridge_chains bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_stub_constraints hts_io hybridization interaction_graph_summary_metric inverse_rotamer_remodel iphold job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_relax_w_ligand mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design output_schema pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.scientific.loop_modeling_kic_fragments_12res.debug

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Test: linux.clang.scientific.loop_modeling_kic_fragments_12res

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branch: master 「№61847」
Commited by: Sergey Lyskov
GitHub commit link: 「604c2b98ad0cdb35」
Difference from previous tested commit:  code diff
Commit date: 2022-03-07 14:12:07
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 m1.clang.python38.PyRosetta4.unit m1.clang.python39.PyRosetta4.unit mac.clang.python36.PyRosetta4.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.mp_f19_sequence_recovery 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 mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

updating ROSIE scripts Skip ligands when considering fasta sequences

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

Failed sub-tests (click for more details):
helical_bundle_predict_psipred
Test: linux.clang.integration.release_debug_no_symbols

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


branch: master 「№61846」
Commited by: Davide Sala
GitHub commit link: 「f8ed4c5de9e18bcd」 「№5882」
Difference from previous tested commit:  code diff
Commit date: 2022-03-05 04:20:52
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 m1.clang.python38.PyRosetta4.unit m1.clang.python39.PyRosetta4.unit mac.clang.python36.PyRosetta4.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size 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.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.loop_modeling_kic_fragments_12res.debug scientific.peptide_pnear_vs_ic50.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 mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5882 from RosettaCommons/revert-5880-revert-5869-davidesala/CCM_release Re-merge "documentation improved" (i.e. revert the reversion)

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

Failed sub-tests (click for more details):
helical_bundle_predict_psipred
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking


branch: master 「№61845」
Commited by: Vikram K. Mulligan
GitHub commit link: 「433f0fcb5cc4b453」 「№5880」
Difference from previous tested commit:  code diff
Commit date: 2022-03-03 23:35:16
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 m1.clang.python38.PyRosetta4.unit m1.clang.python39.PyRosetta4.unit mac.clang.python36.PyRosetta4.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size 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.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python37.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python36.release.PyRosetta.MinSizeRel mac.clang.python37.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python37.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.make_fragments.debug scientific.sb_franklin2019_mpddg 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 mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5880 from RosettaCommons/revert-5869-davidesala/CCM_release Revert "documentation improved" Reverts #5869 This broke most unit and integration tests, since the XSD no longer generates properly. @davidesala, after this reversion is merged, please create a PR to revert this reversion (you can do that through the Github web interface), pull that branch, fix the problem in the branch, and run full tests before re-merging.

...
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rnp_ddg_finalize rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bridge_chains bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric inverse_rotamer_remodel job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_relax_w_ligand mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.scientific.make_fragments.debug

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branch: master 「№61844」
Commited by: Sergey Lyskov
GitHub commit link: 「e1d355aa77cc648d」
Difference from previous tested commit:  code diff
Commit date: 2022-03-03 14:30:41
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 m1.clang.python38.PyRosetta4.unit m1.clang.python39.PyRosetta4.unit mac.clang.python36.PyRosetta4.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size 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 release.PyRosetta.Debug m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python36.release.PyRosetta.Release release.PyRosetta.conda.Release release.source 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 mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

ROSIE script update: Fix bug with 'keep' option of mutation cluster

...
Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation make_and_perturb_bundle_multirepeat make_symmdef_file metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric job_definition_script_vars kinemage_grid_output ligand_database_io ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation make_and_perturb_bundle_multirepeat make_symmdef_file metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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_H3_same splice_out_H3_shorter 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 startfrom_file stored_residue_subset swm_add_rosettascripts symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.gcc.integration.valgrind

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy