basic::options::OptionKeys::in::file Namespace Reference

Variables
BooleanOptionKey const	file
FileVectorOptionKey const	s
FileVectorOptionKey const	t
FileVectorOptionKey const	l
FileOptionKey const	job_definition_file
FileVectorOptionKey const	list
FileVectorOptionKey const	screening_list
FileOptionKey const	screening_job_file
BooleanOptionKey const	shuffle_screening_jobs
FileOptionKey const	native
FileOptionKey const	torsion_bin_probs
FileOptionKey const	PCS_frag_cst
FileOptionKey const	talos_phi_psi
FileOptionKey const	talos_cs
FileOptionKey const	ambig_talos_cs_A
FileOptionKey const	ambig_talos_cs_B
IntegerVectorOptionKey const	native_exclude_res
StringVectorOptionKey const	tags
StringVectorOptionKey const	user_tags
FileOptionKey const	tagfile
FileVectorOptionKey const	frag_files
StringVectorOptionKey const	remap_pdb_atom_names_for
FileVectorOptionKey const	extra_res
FileVectorOptionKey const	extra_res_fa
FileVectorOptionKey const	extra_res_mol
FileVectorOptionKey const	extra_res_mmCIF
BooleanOptionKey const	load_PDB_components
StringOptionKey const	PDB_components_file
StringOptionKey const	extra_res_database
StringOptionKey const	extra_res_pq_schema
StringOptionKey const	extra_res_database_mode
FileOptionKey const	extra_res_database_resname_list
FileVectorOptionKey const	extra_res_cen
PathVectorOptionKey const	extra_res_path
PathVectorOptionKey const	extra_rot_lib_path
PathVectorOptionKey const	override_rot_lib_path
PathVectorOptionKey const	extra_res_batch_path
FileVectorOptionKey const	extra_patch_fa
FileVectorOptionKey const	extra_patch_cen
StringOptionKey const	frag3
StringOptionKey const	frag9
StringOptionKey const	fragA
StringOptionKey const	fragB
StringOptionKey const	surface_vectors
StringOptionKey const	xyz
BooleanOptionKey const	keep_input_scores
BooleanOptionKey const	lazy_silent
FileVectorOptionKey const	silent
BooleanOptionKey const	force_silent_bitflip_on_read
FileVectorOptionKey const	atom_tree_diff
StringOptionKey const	zip
FileVectorOptionKey const	boinc_wu_zip
BooleanOptionKey const	fullatom
BooleanOptionKey const	centroid_input
BooleanOptionKey const	centroid
BooleanOptionKey const	assign_gasteiger_atom_types
StringOptionKey const	treat_residues_in_these_chains_as_separate_chemical_entities
StringOptionKey const	residue_type_set
FileOptionKey const	pca
RealOptionKey const	silent_energy_cut
FileVectorOptionKey const	silent_list
BooleanOptionKey const	silent_renumber
StringOptionKey const	silent_struct_type
BooleanOptionKey const	silent_read_through_errors
StringOptionKey const	silent_score_prefix
IntegerOptionKey const	silent_select_random
IntegerOptionKey const	silent_select_range_start
IntegerOptionKey const	silent_select_range_mul
IntegerOptionKey const	silent_select_range_len
BooleanOptionKey const	skip_failed_simulations
StringVectorOptionKey const	silent_scores_wanted
FileVectorOptionKey const	fasta
FileVectorOptionKey const	pssm
StringVectorOptionKey const	seq
FileOptionKey const	checkpoint
FileOptionKey const	binary_chk
FileVectorOptionKey const	alignment
FileVectorOptionKey const	alignment2
FileOptionKey const	rama2b_map
FileOptionKey const	psipred_ss2
FileOptionKey const	dssp
BooleanOptionKey const	fail_on_bad_hbond
FileOptionKey const	movemap
BooleanOptionKey const	repair_sidechains
BooleanOptionKey const	no_binary_dunlib
IntegerOptionKey const	extended_pose
FileVectorOptionKey const	template_pdb
FileOptionKey const	template_silent
FileVectorOptionKey const	rdc
FileVectorOptionKey const	csa
FileVectorOptionKey const	dc
FileVectorOptionKey const	burial
FileVectorOptionKey const	vall
BooleanOptionKey const	rescore
StringOptionKey const	spanfile
StringOptionKey const	lipofile
StringOptionKey const	HDX
RealOptionKey const	d2h_sa_reweight
FileOptionKey const	sucker_params
FileOptionKey const	fold_tree
BooleanOptionKey const	obey_ENDMDL
BooleanOptionKey const	new_chain_order
FileOptionKey const	ddg_predictions_file
ResidueChainVectorOptionKey const	input_res
IntegerVectorOptionKey const	minimize_res
StringOptionKey const	md_schfile
FileOptionKey const	native_contacts

Variable Documentation

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment

Referenced by add_rosetta_options_0(), and main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::assign_gasteiger_atom_types

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff

Referenced by add_rosetta_options_0(), and main().

FileOptionKey const basic::options::OptionKeys::in::file::binary_chk

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip

Referenced by add_rosetta_options_0(), and main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::burial

Referenced by add_rosetta_options_0(), calculate_burial(), and main().

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid

Referenced by add_rosetta_options_0(), main(), rebuild_test(), and numeric::geometry::vector_normal_to_ring_plane_of_best_fit().

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::checkpoint

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::csa

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::in::file::d2h_sa_reweight

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::dc

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::dssp

Referenced by add_rosetta_options_0(), AnchorFinderMover::apply(), ExposedStrandMover::apply(), HDdesignMover::calc_bb_E(), make_fragments(), and run().

IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_cen

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_fa

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_batch_path

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database_mode

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::extra_res_database_resname_list

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa

Referenced by add_rosetta_options_0(), and main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mmCIF

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_pq_schema

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_rot_lib_path

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta

Referenced by add_rosetta_options_0(), main(), and run().

BooleanOptionKey const basic::options::OptionKeys::in::file::file

Referenced by add_rosetta_options_0(), BuildBindings::buildModule_All(), BuildBindings::buildModule_One(), BuildBindings::buildModule_UsingCppParser(), BuildBindings::BuildRosettaOnWindows(), ca_to_allatom_main(), BuildBindings::calculate_source_modification_date(), BuildPackagedBindings.ModuleBuilder::compileBindings(), BuildBindings.ModuleBuilder::compileBindings(), utility::file::create_temp_filename(), fmt::File::fdopen(), tools.CppParser::generate_monolith_main(), BuildBindings.ModuleBuilder::generate_monolith_main(), BuildPackagedBindings.ModuleBuilder::generateBindings(), BuildBindings.ModuleBuilder::generateBindings(), BuildBindings::get_all_rosetta_objs(), utility::io::get_lines_from_file_data(), BuildBindings::getAllRosettaSourceFiles(), exclude::isFileInScons(), BuildBindings.ModuleBuilder::link_monolith_main(), BuildPackagedBindings.ModuleBuilder::linkBindings(), BuildBindings.ModuleBuilder::linkBindings(), mp_ddG::main(), predict_ddG::main(), BuildBindings::main(), TestBindings::main(), main(), make_templates::makeFile(), BuildBindings::prepareMiniLibs(), mp_ddG::print_ddG_breakdown(), predict_ddG::print_ddG_breakdown(), mp_ddG::print_score_labels_to_file(), predict_ddG::print_score_labels_to_file(), TestBindings::run_test(), BuildBindings::split_obj_file_in_to_chunks(), basic::options::start_files(), stepwise_monte_carlo(), BuildBindings::windows_buildOneNamespace(), and options_class::writeToFile().

FileOptionKey const basic::options::OptionKeys::in::file::fold_tree

Referenced by add_rosetta_options_0(), main(), and DockFragmentsMover::run().

BooleanOptionKey const basic::options::OptionKeys::in::file::force_silent_bitflip_on_read

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::frag3

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::frag9

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragA

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragB

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom

Referenced by add_rosetta_options_0(), and main().

StringOptionKey const basic::options::OptionKeys::in::file::HDX

Referenced by add_rosetta_options_0().

ResidueChainVectorOptionKey const basic::options::OptionKeys::in::file::input_res

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::job_definition_file

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores

Referenced by add_rosetta_options_0(), and main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::l

Referenced by add_rosetta_options_0(), ObjexxFCL::format::Bite< T >::assign(), utility::BitVector< B >::BitVector(), utility::signals::SignalHub< ReturnType, Signal >::current_links(), ObjexxFCL::format::F(), utility::file::file_size(), ObjexxFCL::format::G(), numeric::fourier::SO3coeffs::genWigner_ds(), binder::indent(), numeric::interpolation::periodic_range::full::interpolated(), numeric::interpolation::periodic_range::half::interpolated(), Kernel::Kernel(), main(), numeric::model_quality::maxsub(), ObjexxFCL::mod(), ObjexxFCL::operator>>(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), register_options(), numeric::RemainderSelector< T, true >::remainder(), ObjexxFCL::RemainderSelector< T, true >::remainder(), run(), utility::options::OptionCollection::show_all_hier(), utility::options::OptionCollection::show_table_text(), sigmoid_train(), numeric::fourier::SHT::so3CombineCoef(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), basic::options::start_files(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_load_model(), svm_predict_values(), svm_save_model(), svm_train(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::utility_vector_binder(), utility::options::OptionCollection::wrapped(), and basic::Emitter::write_raw().

BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::lipofile

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::list

Referenced by add_rosetta_options_0(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::add_row(), BuildBindings::BuildRosettaOnWindows(), exclude::finalize(), build::generate_rosetta_external_cmake_files(), tools.CppParser::generateIncludes(), app.pyrosetta_toolkit.modules.tools.input::get_pdb_list_from_dir(), app.pyrosetta_toolkit.modules.tools.input::get_residuetypeset_from_path_array(), exclude::getIncludes(), utility::graph::RingDetection< Graph >::GetRings(), graft_pdb(), map_wrapper< Key, Val >::items(), map_wrapper< Key, Val >::keys(), main(), make_1mer_frags(), make_frags(), MakeRelativePathsInFlagsAbsolute(), tools.CppParser.GccXML::parse(), utility::graph::RingDetection< Graph >::Remove(), yaml.representer.BaseRepresenter::represent_data(), yaml.representer.Representer::represent_instance(), yaml.representer.Representer::represent_object(), run(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::scoreOption(), basic::options::start_files(), map_wrapper< Key, Val >::values(), and utility::tag::XMLSchemaRestriction::write_definition().

BooleanOptionKey const basic::options::OptionKeys::in::file::load_PDB_components

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::md_schfile

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::minimize_res

Referenced by add_rosetta_options_0(), main(), and rna_fullatom_minimize_test().

FileOptionKey const basic::options::OptionKeys::in::file::movemap

Referenced by add_rosetta_options_0(), LigandRepackMinimizeProtocol::apply(), Minimize::apply(), main(), SmallMoverBenchmark::setUp(), ShearMoverBenchmark::setUp(), SmallMoverBenchmark::tearDown(), and ShearMoverBenchmark::tearDown().

FileOptionKey const basic::options::OptionKeys::in::file::native

Referenced by add_rosetta_options_0(), supercharge::apply(), CaToAllAtom::CaToAllAtom(), basic::resource_manager::fallback_configuration::NativeFallbackConfiguration::fallback_specified(), basic::resource_manager::fallback_configuration::NativeFallbackConfiguration::get_native_filename_from_options(), main(), register_options(), rna_fullatom_minimize_test(), and run().

FileOptionKey const basic::options::OptionKeys::in::file::native_contacts

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib

Referenced by add_rosetta_options_0(), and validate_dunbrack_binaries().

BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::override_rot_lib_path

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::pca

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::PDB_components_file

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::remap_pdb_atom_names_for

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::rescore

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set

Referenced by add_rosetta_options_0(), PeptoidDesignMover::apply(), create_theozyme_pdb(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), UBQ_GTPaseMover::init_on_new_input(), UBQ_E2Mover::init_on_new_input(), load_loops_from_file(), main(), match_main(), mg_modeler_test(), mutate_to_ala(), run(), and DockFragmentsMover::run().

FileVectorOptionKey const basic::options::OptionKeys::in::file::s

Referenced by ObjexxFCL::format::A(), add_rosetta_options_0(), align_pdbs(), ObjexxFCL::format::Bite< T >::assign(), basic::Tracer::calculate_tracer_level(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::can_hold_another(), ObjexxFCL::center(), ObjexxFCL::centered(), numeric::kinematic_closure::chainXYZ(), numeric::kinematic_closure::radians::chainXYZ(), ObjexxFCL::char_of(), binder::Context::create_all_nested_namespaces(), create_theozyme_pdb(), ObjexxFCL::date(), supercharge::design_supercharge(), ObjexxFCL::double_of(), utility::down_cast(), ObjexxFCL::equali(), basic::Emitter::escape_string(), binder::expresion_to_string(), fill_optional_options(), ObjexxFCL::float_of(), utility::fmt_real(), fmt::internal::PrintfFormatter< Char >::format(), fmt::BasicFormatter< Char >::format(), numeric::xyzTransform< numeric::Real >::from_quaternion(), binder::Context::generate(), ObjexxFCL::get(), utility::sql_database::DatabaseSessionManager::get_session_mysql(), utility::sql_database::DatabaseSessionManager::get_session_postgres(), utility::sql_database::DatabaseSessionManager::get_session_sqlite3(), ObjexxFCL::head(), ObjexxFCL::IACHAR(), ObjexxFCL::ICHAR(), basic::Tracer::in(), PhProtocol::init_options(), ObjexxFCL::int_of(), ObjexxFCL::ints_of(), ObjexxFCL::is_bool(), ObjexxFCL::is_char(), ObjexxFCL::is_double(), ObjexxFCL::is_float(), ObjexxFCL::is_int(), ObjexxFCL::is_long(), ObjexxFCL::is_longdouble(), binder::Config::is_namespace_binding_requested(), binder::Config::is_namespace_skipping_requested(), ObjexxFCL::is_short(), ObjexxFCL::is_type< char >(), ObjexxFCL::is_uint(), ObjexxFCL::is_ulong(), ObjexxFCL::is_ushort(), numeric::jacobi_rotation(), ObjexxFCL::left_justified(), ObjexxFCL::left_justify(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::legal_string(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::legal_string(), ObjexxFCL::long_of(), ObjexxFCL::longdouble_of(), ObjexxFCL::lowercase(), ObjexxFCL::lpad(), ObjexxFCL::lpadded(), ObjexxFCL::lstrip(), ObjexxFCL::lstrip_whitespace(), ObjexxFCL::lstripped(), ObjexxFCL::lstripped_whitespace(), main(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_has_insertion_operator(), minimize_with_constraints(), nucleobase_probe_score_test(), numeric::kinematic_closure::numchanges(), numeric::kinematic_closure::numroots(), utility::options::operator+(), utility::operator+(), utility::operator-(), basic::Report::operator<<(), fmt::BasicWriter< Char >::operator<<(), ObjexxFCL::operator==(), ObjexxFCL::operator>>(), utility::operator|(), ObjexxFCL::overlay(), ObjexxFCL::pad(), utility::pad_left(), utility::pad_right(), ObjexxFCL::padded(), fmt::BasicFormatter< Char >::parse_arg_name(), fmt::internal::PrintfFormatter< Char >::parse_flags(), fmt::internal::PrintfFormatter< Char >::parse_header(), pdb_to_silent_file(), utility::options::OptionCollection::prefix(), basic::Tracer::prepend_channel_name(), basic::database::schema_generator::Index::print(), numeric::BodyPosition< typename >::q_refresh(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), read_pose(), reduce_fa_rep(), register_options(), numeric::remainder_conversion(), ObjexxFCL::remainder_conversion(), remark_vector_repr(), ObjexxFCL::right_justified(), ObjexxFCL::right_justify(), rna_build_helix_test(), rna_fullatom_minimize_test(), rna_score_test(), ObjexxFCL::rpad(), ObjexxFCL::rpadded(), ObjexxFCL::rstrip(), ObjexxFCL::rstrip_whitespace(), ObjexxFCL::rstripped(), ObjexxFCL::rstripped_whitespace(), utility::signals::SignalHub< ReturnType, Signal >::send(), sequence_tolerance_main(), basic::Emitter::set_indent(), LigandDockBenchmark::setUp(), LigandDockScriptBenchmark::setUp(), ObjexxFCL::short_of(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::shortd(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::shortd(), ObjexxFCL::size(), ObjexxFCL::sized(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), utility::keys::ClassKeyVector< K, T, C >::sort(), utility::options::OptionCollection::space_prefixed(), spanfile_from_pdb(), numeric::fourier::SHT::sph_standardize(), basic::options::start_files(), std_vector_str(), store_energies(), ObjexxFCL::strip(), ObjexxFCL::strip_whitespace(), ObjexxFCL::stripped(), ObjexxFCL::stripped_whitespace(), utility::options::OptionCollection::suffix(), basic::svd::SVD_Solver::svbksb(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), ObjexxFCL::format::SW(), basic::ComparingTracer::t_flush(), basic::TracerToFile::t_flush(), basic::Tracer::TracerProxy::t_flush(), utility::options::OptionCollection::tab_prefixed(), binder::template_argument_to_string(), numeric::kinematic_closure::torsion(), numeric::kinematic_closure::radians::torsion(), ObjexxFCL::trim(), utility::options::OptionCollection::trim(), ObjexxFCL::trim_whitespace(), ObjexxFCL::trimmed(), utility::options::OptionCollection::trimmed(), ObjexxFCL::trimmed_whitespace(), ObjexxFCL::type_of< char >(), ObjexxFCL::type_of< std::string >(), ObjexxFCL::uint_of(), ObjexxFCL::ulong_of(), ObjexxFCL::unique(), ObjexxFCL::uppercase(), ObjexxFCL::ushort_of(), vector1_str(), utility::options::OptionCollection::wrapped(), and write_base_pair_step_to_silent_struct().

FileOptionKey const basic::options::OptionKeys::in::file::screening_job_file

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::screening_list

Referenced by add_rosetta_options_0(), and basic::options::start_files().

StringVectorOptionKey const basic::options::OptionKeys::in::file::seq

Referenced by add_rosetta_options_0(), composite_sequences_from_cmd_line(), main(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_sequence_of_subelement_sets(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_required_ordered(), rna_build_helix_test(), and rna_thread_test().

BooleanOptionKey const basic::options::OptionKeys::in::file::shuffle_screening_jobs

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent

Referenced by add_rosetta_options_0(), align_pdbs(), calc_rms_test(), calculate_pairwise_RMSD(), extract_pdbs_test(), fill_optional_options(), main(), mutate_residues_wrapper(), nucleobase_probe_score_test(), pdb_to_silent_file(), post_rebuild_bulge_assembly(), rebuild_test(), register_options(), rna_build_helix_test(), rna_fullatom_minimize_test(), rna_score_test(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and write_base_pair_step_to_silent_struct().

RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber

Referenced by add_rosetta_options_0(), and main().

StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_len

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_mul

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_start

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type

Referenced by add_rosetta_options_0(), and main().

BooleanOptionKey const basic::options::OptionKeys::in::file::skip_failed_simulations

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::spanfile

Referenced by add_rosetta_options_0(), and spanfile_from_pdb().

FileOptionKey const basic::options::OptionKeys::in::file::sucker_params

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::surface_vectors

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::t

Referenced by numeric::add(), binder::add_relevant_includes(), add_rosetta_options_0(), ObjexxFCL::FArray< T >::attach(), binder::base_default_default_constructor_available(), binder::ClassBinder::bind(), binder::ClassBinder::bind_with(), ObjexxFCL::format::bite(), ObjexxFCL::CArray< typename >::CArray(), ObjexxFCL::CArrayP< typename >::CArrayP(), utility::options::OptionCollection::cleaned(), ObjexxFCL::FArray1D< double >::dimension(), ObjexxFCL::KeyFArray1D< typename >::dimension(), ObjexxFCL::FArray2D< double >::dimension(), ObjexxFCL::KeyFArray2D< typename >::dimension(), ObjexxFCL::FArray3D< typename >::dimension(), ObjexxFCL::KeyFArray3D< typename >::dimension(), ObjexxFCL::FArray4D< typename >::dimension(), ObjexxFCL::KeyFArray4D< typename >::dimension(), ObjexxFCL::FArray5D< typename >::dimension(), ObjexxFCL::KeyFArray5D< typename >::dimension(), ObjexxFCL::FArray6D< typename >::dimension(), ObjexxFCL::KeyFArray6D< typename >::dimension(), numeric::crick_equations::dz_ddz1(), ObjexxFCL::format::E(), ObjexxFCL::equali(), numeric::model_quality::erfcc(), numeric::statistics::erfcx_y100(), basic::sampling::orientations::Quaternion::euler(), PerformanceBenchmark::execute(), ObjexxFCL::format::F(), ObjexxFCL::FArray1D< double >::FArray1D(), ObjexxFCL::FArray2D< double >::FArray2D(), ObjexxFCL::FArray3D< typename >::FArray3D(), ObjexxFCL::FArray4D< typename >::FArray4D(), ObjexxFCL::FArray5D< typename >::FArray5D(), ObjexxFCL::FArray6D< typename >::FArray6D(), ObjexxFCL::fixed_Fstring_of(), ObjexxFCL::fixed_string_of(), utility::from_string(), ObjexxFCL::Fstring_of(), ObjexxFCL::Fstring_of< std::string >(), ObjexxFCL::general_Fstring_of(), ObjexxFCL::general_string_of(), binder::get_type_dependencies(), numeric::hsv_to_rgb(), ObjexxFCL::format::I(), ObjexxFCL::FArray1D< double >::initializer(), ObjexxFCL::KeyFArray1D< typename >::initializer(), ObjexxFCL::FArray2D< double >::initializer(), ObjexxFCL::KeyFArray2D< typename >::initializer(), ObjexxFCL::FArray3D< typename >::initializer(), ObjexxFCL::KeyFArray3D< typename >::initializer(), ObjexxFCL::FArray4D< typename >::initializer(), ObjexxFCL::KeyFArray4D< typename >::initializer(), ObjexxFCL::FArray5D< typename >::initializer(), ObjexxFCL::KeyFArray5D< typename >::initializer(), ObjexxFCL::FArray6D< typename >::initializer(), ObjexxFCL::KeyFArray6D< typename >::initializer(), instantiate_numeric_functions(), binder::is_bindable(), binder::is_binding_requested(), binder::is_skipping_requested(), ObjexxFCL::Fstring::is_type(), ObjexxFCL::is_type(), ObjexxFCL::FArray< T >::is_uniform(), map_wrapper< Key, Val >::items(), numeric::jacobi_rotation(), ObjexxFCL::KeyFArray1D< typename >::KeyFArray1D(), ObjexxFCL::KeyFArray2D< typename >::KeyFArray2D(), ObjexxFCL::KeyFArray3D< typename >::KeyFArray3D(), ObjexxFCL::KeyFArray4D< typename >::KeyFArray4D(), ObjexxFCL::KeyFArray5D< typename >::KeyFArray5D(), ObjexxFCL::KeyFArray6D< typename >::KeyFArray6D(), map_wrapper< Key, Val >::keys(), numeric::fourier::kf_bfly2(), numeric::fourier::kf_bfly_generic(), ObjexxFCL::lead_zero_Fstring_of(), ObjexxFCL::lead_zero_string_of(), ObjexxFCL::left_Fstring_of(), ObjexxFCL::left_string_of(), ObjexxFCL::format::LJ(), ObjexxFCL::lowercased(), main(), numeric::model_quality::maxsub(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_has_equal_operator(), utility::options::OptionCollection::merged(), multiclass_probability(), numeric::multiply(), basic::sampling::orientations::Quaternion::Normalize(), ObjexxFCL::operator!=(), utility::json_spirit::Value_impl< Config >::Variant_converter_visitor::operator()(), ObjexxFCL::operator*(), numeric::sphericalVector< typename >::operator*=(), numeric::xyzTriple< typename >::operator*=(), numeric::xyzVector< core::Real >::operator*=(), ObjexxFCL::CArray< typename >::operator*=(), ObjexxFCL::FArray< T >::operator*=(), ObjexxFCL::CArrayP< typename >::operator*=(), numeric::xyzMatrix< T >::operator*=(), ObjexxFCL::operator+(), numeric::sphericalVector< typename >::operator+=(), numeric::xyzTriple< typename >::operator+=(), numeric::xyzVector< core::Real >::operator+=(), ObjexxFCL::CArray< typename >::operator+=(), ObjexxFCL::FArray< T >::operator+=(), ObjexxFCL::CArrayP< typename >::operator+=(), numeric::xyzMatrix< T >::operator+=(), ObjexxFCL::operator-(), numeric::sphericalVector< typename >::operator-=(), numeric::xyzTriple< typename >::operator-=(), numeric::xyzVector< core::Real >::operator-=(), ObjexxFCL::CArray< typename >::operator-=(), ObjexxFCL::FArray< T >::operator-=(), ObjexxFCL::CArrayP< typename >::operator-=(), numeric::xyzMatrix< T >::operator-=(), ObjexxFCL::operator/(), ObjexxFCL::CArray< typename >::operator/=(), ObjexxFCL::FArray< T >::operator/=(), ObjexxFCL::CArrayP< typename >::operator/=(), numeric::operator<<(), utility::io::ocstream::operator<<(), utility::io::orstream::operator<<(), utility::io::ozstream::operator<<(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), ObjexxFCL::CArray< typename >::operator=(), numeric::sphericalVector< typename >::operator=(), numeric::xyzTriple< typename >::operator=(), numeric::xyzVector< core::Real >::operator=(), ObjexxFCL::CArrayP< typename >::operator=(), numeric::xyzMatrix< T >::operator=(), ObjexxFCL::operator>(), ObjexxFCL::operator>=(), numeric::operator>>(), utility::io::icstream::operator>>(), utility::io::irstream::operator>>(), utility::io::izstream::operator>>(), powi(), basic::prof_show(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), basic::YamlEmitter::quote_string(), basic::JsonEmitter::quote_string(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::read_row(), ObjexxFCL::FArray1D< double >::redimension(), ObjexxFCL::KeyFArray1D< typename >::redimension(), ObjexxFCL::FArray2D< double >::redimension(), ObjexxFCL::KeyFArray2D< typename >::redimension(), ObjexxFCL::FArray3D< typename >::redimension(), ObjexxFCL::KeyFArray3D< typename >::redimension(), ObjexxFCL::FArray4D< typename >::redimension(), ObjexxFCL::KeyFArray4D< typename >::redimension(), ObjexxFCL::FArray5D< typename >::redimension(), ObjexxFCL::KeyFArray5D< typename >::redimension(), ObjexxFCL::FArray6D< typename >::redimension(), ObjexxFCL::KeyFArray6D< typename >::redimension(), ObjexxFCL::right_Fstring_of(), ObjexxFCL::right_string_of(), ObjexxFCL::format::RJ(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), ObjexxFCL::rvalue_cast(), ObjexxFCL::scientific_Fstring_of(), ObjexxFCL::scientific_string_of(), Solver::select_working_set(), Solver_NU::select_working_set(), sequence_tolerance_main(), src.utility::Set(), pyrosetta::Set(), src::Set(), sigmoid_train(), numeric::xyzTriple< typename >::square(), numeric::xyzVector< core::Real >::square(), ObjexxFCL::format::SS(), ObjexxFCL::string_of(), utility::string_split(), numeric::subtract(), ObjexxFCL::format::SW(), swap(), numeric::Quaternion< T >::swap(), basic::T(), binder::template_specialization(), numeric::kinematic_closure::test_point_value2(), basic::gpu::Timer::Timer(), utility::to_string(), numeric::geometry::BoundingBox< Vector >::translate(), ObjexxFCL::Fstring::type_of(), ObjexxFCL::type_of(), ObjexxFCL::uppercased(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::utility_vector_binder(), map_wrapper< Key, Val >::values(), src.utility::Vector1(), pyrosetta::Vector1(), src::Vector1(), and numeric::statistics::w_im_y100().

FileOptionKey const basic::options::OptionKeys::in::file::tagfile

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::tags

Referenced by add_rosetta_options_0(), utility::get_resnum_and_chain(), utility::get_resnum_and_segid(), main(), and rna_fullatom_minimize_test().

FileOptionKey const basic::options::OptionKeys::in::file::talos_cs

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb

Referenced by add_rosetta_options_0(), and main().

FileOptionKey const basic::options::OptionKeys::in::file::template_silent

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::vall

Referenced by add_rosetta_options_0(), and fill_optional_options().

StringOptionKey const basic::options::OptionKeys::in::file::xyz

Referenced by add_rosetta_options_0(), app.surface_docking.append_data::append_constraints(), HDmakerMover::bb_score(), ExposedStrandMover::bb_score(), demo.D090_Ala_scan::calc_binding_energy(), app.surface_docking.surf_param::centerG_P(), app.surface_docking.surf_param::centerG_S(), numeric::comma_seperated_string_to_xyz(), pyrosetta.toolbox.mutants::compare_hbonds(), toolbox.mutants::compare_hbonds(), app.pyrosetta_toolkit.modules.tools.general_tools::getDist(), demo.D060_Folding::guess_disulfides(), main(), toolbox::restrict_non_nbrs_from_repacking(), pyrosetta.toolbox::restrict_non_nbrs_from_repacking(), and numeric::spherical_to_xyz().

StringOptionKey const basic::options::OptionKeys::in::file::zip

Referenced by app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_get_formatted_html_string(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_get_simple_html_string(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_set_field_names(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_stringify_row(), add_rosetta_options_0(), and main().