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
BooleanOptionKey const	srlz
BooleanOptionKey const	srlz_override
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
BooleanOptionKey const	no_detect_pseudobonds
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_directory
StringVectorOptionKey const	PDB_components_overrides
BooleanOptionKey const	check_all_PDB_components
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
FileOptionKey const	hrf_ms_labeling
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(), register_options(), 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().

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

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(), HBondReporter::apply(), HDdesignMover::calc_bb_E(), calc_rama_scores(), harvest_motifs(), 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(), collect_residue_types(), and register_options().

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(), collect_residue_types(), main(), and register_options().

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

Referenced by add_rosetta_options_0(), load_as_fullatom(), and register_options().

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

Referenced by add_rosetta_options_0(), load_as_fullatom(), and register_options().

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(), MPDomainAssembly::init_from_cmd(), main(), read_fasta(), MPDomainAssembly::register_options(), rna_fullatom_minimize_test(), and run().

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

Referenced by add_rosetta_options_0(), ca_to_allatom_main(), utility::file::create_temp_filename(), fmt::File::fdopen(), utility::io::get_lines_from_file_data(), handle_assert_failure(), mp_ddG::main(), main(), make_templates::makeFile(), mp_ddG::print_ddG_breakdown(), mp_ddG::print_score_labels_to_file(), numeric::read_tensor_from_file(), utility::save_crash_report(), basic::options::start_files(), stepwise_monte_carlo_legacy(), 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(), MPDomainAssembly::init_from_cmd(), and MPDomainAssembly::register_options().

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

Referenced by add_rosetta_options_0(), MPDomainAssembly::init_from_cmd(), and MPDomainAssembly::register_options().

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(), load_as_fullatom(), and main().

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

Referenced by add_rosetta_options_0().

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

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(), convert(), and reverse_convert().

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(), rosetta_binders::list_add_on_binder(), rosetta_binders::list_add_on_binder_maybe_has_equal_operator(), 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 pyrosetta.bindings.pose.PoseResidueLabelAccessor::__str__(), pyrosetta.distributed.docs.MoverDocs::_component_names(), pyrosetta.distributed.docs.FilterDocs::_component_names(), pyrosetta.distributed.viewer.modules::_pose_to_residue_chain_tuples(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::_repr_pretty_(), add_rosetta_options_0(), pyrosetta.bindings.pose.PoseScoreAccessor::all(), pyrosetta.bindings.rt::as_array(), pyrosetta.bindings.homogeneous_transform::as_array(), utility::graph::ArrayPool< T >::clear(), pyrosetta.toolbox.atom_pair_energy::dump_atom_pair_energy_table(), pyrosetta.toolbox.atom_pair_energy::dump_residue_pair_energies(), pyrosetta.bindings.pose.PoseScoreAccessor::extra(), mutant_modeler::figure_out_WT_seq(), erraser_util::find_error_res(), mutant_modeler::find_pairs(), DRRAFTER_util::find_pairs(), DRRAFTER::find_pairs(), build::generate_bindings(), pyrosetta.toolbox.generate_resfile::generate_resfile_from_pose(), build::generate_rosetta_external_cmake_files(), mutant_modeler.MutantModeler::get_med_res_command_lines(), pyrosetta.io.silent_file_map.SilentFilePoseAccessor::keys(), pyrosetta.io.silent_file_map.SilentFileEnergyAccessor::keys(), pyrosetta.protocols.structure_search.alignment::length_grouped_broadcast_metric(), pyrosetta.protocols.structure_search.alignment::length_grouped_pairwise_metric(), main(), make_1mer_frags(), make_bindings_via_cmake::make_all_includes(), make_frags(), utility::graph::ArrayPool< T >::mine(), pyrosetta.mpi::MPIJobDistributor(), pyrosetta.toolbox.py_jobdistributor::output_scorefile(), pyrosetta.protocols.structure_search.StructureSearchManager::pair_query(), util::parse_tag(), DRRAFTER_util::parse_tag(), erraser_util::pdb2rosetta(), pyrosetta.toolbox.extract_coords_pose::pose_coords_as_cols(), pyrosetta.toolbox.extract_coords_pose::pose_coords_as_rows(), pyrosetta.bindings.energies::residue_pair_energies_array(), run(), demo.D090_Ala_scan::scanning(), drrafter_rna::setup_next_round(), pyrosetta.protocols.structure_search.StructureSearchManager::single_query(), basic::options::start_files(), pyrosetta.io.silent_file_map.SilentFileMap::tags(), pyrosetta.tests.distributed.test_concurrency.TestConcurrentScripts::test_concurrent_multi_task(), pyrosetta.tests.distributed.test_concurrency.TestConcurrentScripts::test_concurrent_on_task(), pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor::test_labels(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_pose_io(), pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent::test_poses_to_silent(), pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor::test_residues(), and pyrosetta.utility.array::to_structured_array().

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(), Minimize::apply(), LigandRepackMinimizeProtocol::apply(), compute_folding_energies(), and main().

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

Referenced by add_rosetta_options_0(), MPDomainAssembly::apply(), supercharge::apply(), CaToAllAtom::CaToAllAtom(), MPDomainAssembly::init_from_cmd(), main(), register_options(), MPDomainAssembly::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::no_detect_pseudobonds

Referenced by add_rosetta_options_0().

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_directory

Referenced by add_rosetta_options_0().

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

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(), MPDomainAssembly::create_residue_from_olc(), MPDomainAssembly::create_residue_from_resn(), create_theozyme_pdb(), UBQ_GTPase_disulfide_Mover::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(), binder::add_relevant_includes(), add_rosetta_options_0(), align_pdbs(), analyze_base_pair_test(), ObjexxFCL::format::Bite< T >::assign(), binder::ClassBinder::bind(), binder::binding_public_data_members(), binder::binding_public_member_functions(), basic::TracerImpl::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(), fmt::internal::check_sign(), 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::BasicFormatter< CharType, ArgFormatter >::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::TracerImpl::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(), rosetta_binders::list_add_on_binder_maybe_has_insertion_operator(), ObjexxFCL::long_of(), ObjexxFCL::longdouble_of(), utility::lower(), 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_default_constructible(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_has_insertion_operator(), measure_sequence_recovery(), 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|(), RNA_DeNovoJobQueen::output_to_silent_file(), ObjexxFCL::overlay(), ObjexxFCL::pad(), utility::pad_left(), utility::pad_right(), ObjexxFCL::padded(), fmt::BasicFormatter< CharType, ArgFormatter >::parse_arg_name(), pdb_to_silent_file(), utility::options::OptionCollection::prefix(), 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(), ObjexxFCL::right_justified(), ObjexxFCL::right_justify(), rna_build_helix_test(), rna_fullatom_minimize_test(), rna_motif_test(), ObjexxFCL::rpad(), ObjexxFCL::rpadded(), ObjexxFCL::rstrip(), ObjexxFCL::rstrip_whitespace(), ObjexxFCL::rstripped(), ObjexxFCL::rstripped_whitespace(), utility::signals::SignalHub< ReturnType, Signal >::send(), sequence_tolerance_main(), rosetta_binders::set_add_on_binder(), rosetta_binders::set_add_on_binder_maybe_has_insertion_operator(), 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(), store_energies(), rosetta_binders::stringstream_add_on_binder(), 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::TracerImpl::TracerProxyImpl::t_flush(), utility::options::OptionCollection::tab_prefixed(), binder::template_argument_to_string(), utility::timestamp_millis(), utility::timestamp_millis_short(), 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(), utility::upper(), ObjexxFCL::uppercase(), ObjexxFCL::ushort_of(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::utility_vector_binder(), 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(), helix_from_sequence(), main(), my_main(), Prepare(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_sequence_of_subelement_sets(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_required_ordered(), print_seq_map(), 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(), analyze_base_pair_test(), RNA_ScoreMover::apply(), calc_rms_test(), calculate_pairwise_RMSD(), extract_pdbs_test(), fill_optional_options(), main(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), RNA_DeNovoJobQueen::output_silent_struct(), RNA_DeNovoJobQueen::output_to_silent_file(), pdb_to_silent_file(), post_rebuild_bulge_assembly(), rebuild_test(), register_options(), resample_full_model_test(), rna_build_helix_test(), rna_fullatom_minimize_test(), rna_motif_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().

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

Referenced by add_rosetta_options_0().

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

Referenced by add_rosetta_options_0().

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(), utility::get_current_date(), binder::get_type_dependencies(), binder::Context::global_insertion_operator(), 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(), binder::is_binding_requested(), binder::is_skipping_requested(), binder::is_std_function_bindable(), ObjexxFCL::Fstring::is_type(), ObjexxFCL::is_type(), ObjexxFCL::FArray< T >::is_uniform(), 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(), 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(), 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()(), numeric::interpolation::TempStruct< T, N >::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::rms_fit(), 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(), pyrosetta::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(), binder::template_specialization(), numeric::kinematic_closure::test_point_value2(), basic::gpu::Timer::Timer(), utility::timestamp_millis(), utility::timestamp_millis_short(), utility::to_string(), utility::to_string< char >(), 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(), pyrosetta::Vector1(), numeric::statistics::w_im_y100(), and rosetta_binders::xyzVector_add_on_binder().

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(), calc_rmsf_and_avrg(), utility::xsd_util::generate_human_readable_recursive(), utility::xsd_util::generate_human_readable_summary(), utility::get_resnum_and_chain_and_segid(), utility::get_resnum_and_segid(), main(), basic::resource_manager::ResourceManager::read_resources_from_xml(), rna_fullatom_minimize_test(), and rna_motif_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(), and main().

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(), pyrosetta.distributed.viewer.modules.setHydrogenBonds::apply(), pyrosetta.distributed.viewer.modules.setHydrogens::apply(), HDmakerMover::bb_score(), ExposedStrandMover::bb_score(), demo.D090_Ala_scan::calc_binding_energy(), check_silent_error(), numeric::comma_seperated_string_to_xyz(), get_sphere_xyz(), demo.D060_Folding::guess_disulfides(), numeric::geometry::hashing::MinimalClashHash::init(), main(), measure_sequence_recovery(), relax_with_restraints_on_constres(), pyrosetta.toolbox.mutants::restrict_non_nbrs_from_repacking(), SphereGrinder(), and numeric::spherical_to_xyz().

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

Referenced by pyrosetta.toolbox.atom_pair_energy::_atom_pair_energy_table(), pyrosetta.distributed.viewer.modules::_pose_to_residue_chain_tuples(), add_rosetta_options_0(), pyrosetta.distributed.utility.log.ProgressLogger::enumerate(), pyrosetta.distributed.viewer.core::init(), main(), util::parse_tag(), DRRAFTER_util::parse_tag(), pyrosetta.utility.array::rolling_window(), and pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_pair_search().