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Rosetta
2021.07
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Namespaces | |
monte_carlo | |
polar_hydrogens | |
protein | |
rna | |
StringOptionKey const basic::options::OptionKeys::stepwise::align_pdb |
Referenced by add_rosetta_options_13(), main(), and rebuild_test().
ResidueChainVectorOptionKey const basic::options::OptionKeys::stepwise::alignment_anchor_res |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::atr_rep_screen |
Referenced by add_rosetta_options_13(), main(), and rebuild_test().
BooleanOptionKey const basic::options::OptionKeys::stepwise::atr_rep_screen_for_docking |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::backbone_only1 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::backbone_only2 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::boltzmann_choice_post_enumerated_minimize |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::choose_random |
Referenced by add_rosetta_options_13(), main(), and rna_sample_virtual_sugar().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::definitely_virtualize |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::dump |
Referenced by add_rosetta_options_13(), initialize_native_pose(), post_rebuild_bulge_assembly(), and swa_rna_cluster().
BooleanOptionKey const basic::options::OptionKeys::stepwise::enumerate |
Referenced by pyrosetta.distributed.cluster.base::_get_packed_pose_kwargs_pairs_list(), add_rosetta_options_13(), pyrosetta.distributed.viewer.modules.setDisulfides::apply(), auto-DRRAFTER_setup::auto_setup_helices(), pyrosetta.bindings.pose::display_secstruct(), pyrosetta.distributed.cluster.core.PyRosettaCluster::distribute(), erraser_wrapper::erraser_single_res(), erraser_single_res_analysis::extract_info(), auto-DRRAFTER_setup_next_round::figure_out_next_round(), DRRAFTER_util::get_helix_stems(), util::get_surrounding_res(), auto-DRRAFTER_setup_next_round::get_top_ten_models_from_silent_files(), DRRAFTER_util::graph_from_ss(), pyrosetta.protocols.structure_search.alignment::length_blocks(), get_lowest_scoring_relaxed_models::main(), sidechain_cst_3::main(), options::main(), main(), erraser_util::phenix_rna_validate(), pyrosetta.tests.distributed.test_viewer.TestViewer::setUp(), DRRAFTER::setup_job(), drrafter_rna::setup_next_round(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_pose_io(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_rep_search(), options_class::wrapCStrig(), and arls_impl::write_setup_script().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::fixed_res |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::force_moving_res_for_erraser |
Referenced by add_rosetta_options_14().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::input_res1 |
Referenced by add_rosetta_options_13().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::input_res2 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::lores |
Referenced by add_rosetta_options_14(), get_stepwise_score_function(), and StepWiseJobQueen::StepWiseJobQueen().
IntegerOptionKey const basic::options::OptionKeys::stepwise::max_tries_multiplier_for_ccd |
Referenced by add_rosetta_options_13().
RealOptionKey const basic::options::OptionKeys::stepwise::min_tolerance |
Referenced by add_rosetta_options_14().
StringOptionKey const basic::options::OptionKeys::stepwise::min_type |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::minimize_waters |
Referenced by add_rosetta_options_13().
StringOptionKey const basic::options::OptionKeys::stepwise::minimizer_mode |
Referenced by add_rosetta_options_13().
StringVectorOptionKey const basic::options::OptionKeys::stepwise::move |
Referenced by add_rosetta_options_14(), binder::bind_member_functions_for_call_back(), StepWiseJobQueen::complete_larval_job_maturation(), erraser_wrapper::erraser_minimize(), main(), utility::thread::MutableCache< K, V >::operator=(), stepwise_monte_carlo_legacy(), and StepWiseJobQueen::StepWiseJobQueen().
StringOptionKey const basic::options::OptionKeys::stepwise::new_align_pdb |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::new_move_selector |
Referenced by add_rosetta_options_13(), and main().
IntegerOptionKey const basic::options::OptionKeys::stepwise::num_pose_minimize |
Referenced by add_rosetta_options_13(), and main().
IntegerOptionKey const basic::options::OptionKeys::stepwise::num_random_samples |
Referenced by add_rosetta_options_13(), and main().
BooleanOptionKey const basic::options::OptionKeys::stepwise::output_cluster_size |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::output_minimized_pose_list |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::pack_protein_side_chains |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::preminimize |
Referenced by add_rosetta_options_13(), and main().
RealOptionKey const basic::options::OptionKeys::stepwise::rmsd_screen |
Referenced by add_rosetta_options_13(), main(), and rna_fullatom_minimize_test().
StringVectorOptionKey const basic::options::OptionKeys::stepwise::s1 |
StringVectorOptionKey const basic::options::OptionKeys::stepwise::s2 |
StringOptionKey const basic::options::OptionKeys::stepwise::sampler_silent_file |
Referenced by add_rosetta_options_14().
StringVectorOptionKey const basic::options::OptionKeys::stepwise::silent1 |
Referenced by add_rosetta_options_13().
StringVectorOptionKey const basic::options::OptionKeys::stepwise::silent2 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::skip_minimize |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::skip_preminimize |
Referenced by add_rosetta_options_13().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::slice_res1 |
Referenced by add_rosetta_options_13().
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::slice_res2 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::stepwise |
BooleanOptionKey const basic::options::OptionKeys::stepwise::superimpose_over_all |
StringVectorOptionKey const basic::options::OptionKeys::stepwise::tags1 |
Referenced by add_rosetta_options_13().
StringVectorOptionKey const basic::options::OptionKeys::stepwise::tags2 |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::test_all_moves |
Referenced by add_rosetta_options_13().
BooleanOptionKey const basic::options::OptionKeys::stepwise::test_encapsulation |
Referenced by add_rosetta_options_13(), rebuild_test(), and swa_rna_sample().
BooleanOptionKey const basic::options::OptionKeys::stepwise::use_green_packer |
Referenced by add_rosetta_options_13(), and main().
BooleanOptionKey const basic::options::OptionKeys::stepwise::VERBOSE |
Referenced by add_rosetta_options_13(), main(), and swa_rna_cluster().
BooleanOptionKey const basic::options::OptionKeys::stepwise::verbose_sampler |
Referenced by add_rosetta_options_14().
BooleanOptionKey const basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native |
Referenced by add_rosetta_options_14(), BuildFullModel::BuildFullModel(), main(), and my_main().
BooleanOptionKey const basic::options::OptionKeys::stepwise::virtualize_packable_moieties_in_screening_pose |
Referenced by add_rosetta_options_13().