Variables
basic::options::StringOptionKey	ss ("challenge:ss")

basic::options::BooleanOptionKey	aligned ("challenge:aligned")

basic::options::IntegerVectorOptionKey	chunk_mapping ("challenge:chunk_mapping")

basic::options::FileVectorOptionKey	template_structure ("challenge:template_structure")

basic::options::BooleanOptionKey	close_loops ("challenge:close_loops")

basic::options::IntegerOptionKey	max_registry_shift ("challenge:max_registry_shift")

basic::options::BooleanOptionKey	virtual_loops ("challenge:virtual_loops")

basic::options::BooleanOptionKey	revert_real_loops ("challenge:revert_real_loops")

Variable Documentation

◆ aligned

basic::options::BooleanOptionKey challenge::aligned("challenge:aligned") ( "challenge:aligned" )

Referenced by do_tmalign(), main(), and apps::pilot::MultiTemplateAlignChunkMover::MultiTemplateAlignChunkMover().

◆ chunk_mapping

basic::options::IntegerVectorOptionKey challenge::chunk_mapping("challenge:chunk_mapping") ( "challenge:chunk_mapping" )

Referenced by apps::pilot::MultiTemplateAlignChunkMover::get_alignment_from_chunk_mapping(), main(), and apps::pilot::MultiTemplateAlignChunkMover::MultiTemplateAlignChunkMover().

◆ close_loops

basic::options::BooleanOptionKey challenge::close_loops("challenge:close_loops") ( "challenge:close_loops" )

Referenced by ChallengeMover::apply(), main(), and my_main().

◆ max_registry_shift

basic::options::IntegerOptionKey challenge::max_registry_shift("challenge:max_registry_shift") ( "challenge:max_registry_shift" )

Referenced by apps::pilot::SampleSecondaryStructureAlignmentMover::apply(), main(), and ChallengeMover::realign().

◆ revert_real_loops

basic::options::BooleanOptionKey challenge::revert_real_loops("challenge:revert_real_loops") ( "challenge:revert_real_loops" )

Referenced by apps::pilot::SampleSecondaryStructureAlignmentMover::apply(), and main().

◆ ss

basic::options::StringOptionKey challenge::ss("challenge:ss") ( "challenge:ss" )

Referenced by ObjexxFCL::internal::ObserverMediator::acyclic(), add_protocols(), RMSByResStatistics::apply(), ConstraintMinimizer::apply(), Sasa::apply(), apps::pilot::CustomStarTreeMover::apply(), MetalSiteFinderMover::apply(), SwapElementsMover1::apply(), SwapElementsMover2::apply(), BUNS_Output::apply(), zinc1_homodimer_design::apply(), ObjexxFCL::format::Bite< T >::assign(), byres_analysis(), calc_rama_scores(), check_silent_error(), myspace::collect_silent(), convert(), define_cut_points(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), dock(), dump_insert_pdb_and_remodel_blueprint(), energy_cluster(), extract_ss_chunks_from_seq(), utility::from_string(), get_res_data_ss(), get_ss(), get_surface_points(), get_vallfrags(), get_working_directory(), graft_pdb(), ObjexxFCL::index(), ObjexxFCL::last_index(), protocols::jumping::LibraryJumpSetup::LibraryJumpSetup(), load_loops_from_file(), myspace::Scheduler::loophash_search(), main(), apps::pilot::momeara::HBondConformation::make_conformation(), make_frag_set(), VallReader::make_fragment_lines(), make_fragments(), make_mutation_tag(), VallReader::make_nmer_profile(), make_rand_ss(), numeric::interpolation::make_spline(), map_secstruct(), minimize_with_constraints(), molten_get_vallfrags(), MSA_design(), my_main(), myspace::Scheduler::NM_linesearch(), GetURLHandler::OnOpen(), ConstraintConfig::parse_config_file(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), parse_position(), ConstraintConfig::pick_sequence(), pose_to_string(), Prepare(), print_matrix_to_file(), RBSegmentRelax_test(), read_B_vals(), read_complex_type(), read_ERMS(), read_in_cl_data(), read_library_simple(), read_library_w_simpose(), read_occupancy_data(), read_silent_input_as_library(), report_and_dump(), rescore_pose(), restore_hack(), retag(), reverse_convert(), rna_design_test(), RotamerAnalysis(), DomainAssemblerNDocker::run(), TryScoreFilter::run(), myspace::Scheduler::run_combine(), myspace::Scheduler::run_LH(), myspace::Scheduler::run_NM(), run_parallel_docking(), run_pep_prep(), run_sandbox(), save_cluster_tree_lite(), save_per_residue_scores(), scan_neutral(), score12_plot_test(), SecondaryStructureChunk::set_ss(), apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree(), ConstraintConfig::show_cst_grids(), ConstraintConfig::show_sequence(), numeric::interpolation::spline_from_file(), numeric::interpolation::spline_from_stream(), utility::split_whitespace(), ConstraintConfig::ssstr(), utility::string2float(), utility::string2int(), utility::string2Real(), utility::string2Size(), utility::string2uint(), utility::string_split(), string_to_pose(), utility::to_string(), utility::tag::Tag::to_string(), and myspace::write_silent().

◆ template_structure

basic::options::FileVectorOptionKey challenge::template_structure("challenge:template_structure") ( "challenge:template_structure" )

Referenced by main(), my_main(), and read_template_structures().

◆ virtual_loops

basic::options::BooleanOptionKey challenge::virtual_loops("challenge:virtual_loops") ( "challenge:virtual_loops" )

Referenced by main(), and apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree().

Variables