- t -

• t : basic::options::OptionKeys::in::file
• T : test::T007_TracerIO
• table : app::pyrosetta_toolkit::modules::SQLPDB , utility::options::OptionKeys::options::table
• taboo_in_fa : basic::options::OptionKeys::loops
• taboo_sampling : basic::options::OptionKeys::loops
• tag : basic::options::OptionKeys::matdes , basic::options::OptionKeys::resample , basic::options::OptionKeys::rna::farna , basic::options::OptionKeys::rot_anl
• tag2string : basic
• tagfile : basic::options::OptionKeys::in::file
• taglist : basic::options::OptionKeys::willmatch
• tags : basic::options::OptionKeys::in::file
• tags1 : basic::options::OptionKeys::stepwise
• tags2 : basic::options::OptionKeys::stepwise
• tail_mode : basic::options::OptionKeys::krassk
• tail_mode_name : basic::options::OptionKeys::krassk
• tail_output_file_name : basic::options::OptionKeys::krassk
• TailSegment : basic::options::OptionKeys::TailSegment
• talos_cs : basic::options::OptionKeys::in::file
• talos_phi_psi : basic::options::OptionKeys::in::file
• target : basic::options::OptionKeys::hotspot
• target_aa : basic::options::OptionKeys::motifs
• target_dist : basic::options::OptionKeys::hotspot
• target_dna_defs : basic::options::OptionKeys::motifs
• target_net_charge : local
• target_net_charge_active : local
• target_pdb : basic::options::OptionKeys::AnchoredPDBCreator
• target_res : basic::options::OptionKeys::hotspot
• target_residues : basic::options::OptionKeys::in
• targetdir : basic::options::OptionKeys::evolution
• task : app::delta_score_per_mutation , test::G200_Module_Region
• task_design : test::T500_Packing , test::Workshop6test
• task_operations : basic::options::OptionKeys::task_operations
• task_pack : loops , loops_kic , test::T500_Packing , test::T650_LoopsKIC , test::Workshop6test
• tasks : make_templates
• temp_final : basic::options::OptionKeys::MonteCarlo
• temp_initial : basic::options::OptionKeys::MonteCarlo
• temp_pose : app::delta_score_per_mutation
• temperature : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::ddg , basic::options::OptionKeys::docking , basic::options::OptionKeys::loops::ccd , basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::remodel::RemodelLoopMover , basic::options::OptionKeys::rigid , basic::options::OptionKeys::rna::farna , basic::options::OptionKeys::smhybrid , basic::options::OptionKeys::stepwise::monte_carlo
• template_pdb : basic::options::OptionKeys::in::file
• template_scores : basic::options::OptionKeys::cluster
• template_silent : basic::options::OptionKeys::in::file
• templates : basic::options::OptionKeys::templates
• tensor_weight : basic::options::OptionKeys::rdc
• terminal_res : basic::options::OptionKeys::full_model::rna
• termini : basic::options::OptionKeys::mp
• test : app::pyrosetta_toolkit::window_modules::options_system::OptionSystemManager , test::Workshop5test
• test2 : test::Workshop5test
• test_all_moves : basic::options::OptionKeys::stepwise
• test_cycles : basic::options::OptionKeys::run
• test_encapsulation : basic::options::OptionKeys::stepwise
• test_pose : test::T220_AtomAtomPairEnergies , test::Workshop9test
• test_suite : app::pyrosetta_toolkit::modules::prettytable::setup
• testing : basic::options::OptionKeys::AnchoredDesign::testing , basic::options::OptionKeys::testing
• tether_jump : basic::options::OptionKeys::stepwise::rna
• tether_ligand : basic::options::OptionKeys::docking::ligand
• tether_to_closest_res : basic::options::OptionKeys::magnesium
• text : utility::options::OptionKeys::options::table
• tf : test::G200_Module_Region , test::T500_Packing
• tgt_amino : basic::options::OptionKeys::pose_metrics::shobuns
• tgt_atom : basic::options::OptionKeys::pose_metrics::shobuns
• tgt_res : basic::options::OptionKeys::pose_metrics::shobuns
• thickness : basic::options::OptionKeys::membrane , basic::options::OptionKeys::mp , basic::options::OptionKeys::mp::viewer , basic::options::OptionKeys::mp::visualize
• thinout_factor : basic::options::OptionKeys::cluster
• thorough : basic::options::OptionKeys::relax
• thread_unaligned : basic::options::OptionKeys::james
• threads : basic::options::OptionKeys::gpu , basic::options::OptionKeys::packstat
• threadsc : basic::options::OptionKeys::threadsc
• three_fold_symmetry_90_210_330 : basic::options::OptionKeys::make_rot_lib
• threshold : basic::options::OptionKeys::hotspot , revert_app
• threshold_for_boost_closure : basic::options::OptionKeys::remodel::RemodelLoopMover
• tilt : basic::options::OptionKeys::docking
• tilt1_center : basic::options::OptionKeys::docking
• tilt2_center : basic::options::OptionKeys::docking
• tilt_angle : basic::options::OptionKeys::mp::benchmark::tilt_angle
• time_diff : app::surface_docking::surface_docking
• time_end : app::surface_docking::surface_docking
• time_start : app::surface_docking::surface_docking
• timer : basic::options::OptionKeys::loops , basic::options::OptionKeys::run
• TMprojection : basic::options::OptionKeys::mp
• to_centroid : docking , loops , loops_kic , test::T600_Docking , test::T650_LoopsKIC
• to_fullatom : docking , loops , loops_kic , test::T650_LoopsKIC
• tol : loops_kic , test::T650_LoopsKIC
• tolerance : basic::options::OptionKeys::loops::ccd
• top : test::G204_Module_ScoreAnalysis
• top_designs : basic::options::OptionKeys::antibody::design
• topN : basic::options::OptionKeys::templates::cst , basic::options::OptionKeys::templates::fragsteal
• topology_file : basic::options::OptionKeys::jumps
• topology_rank_cutoff : basic::options::OptionKeys::templates
• tops : test::G204_Module_ScoreAnalysis
• torsion_bin_probs : basic::options::OptionKeys::in::file
• torsion_thresholds : basic::options::OptionKeys::james
• torsionsMCM : basic::options::OptionKeys::flexPepDocking
• total_clock : basic
• total_weight : basic::options::OptionKeys::rdc
• TR : basic::resource_manager::locator , basic::resource_manager
• trajectory : basic::options::OptionKeys::backrub
• trajectory_gz : basic::options::OptionKeys::backrub
• trajectory_stride : basic::options::OptionKeys::backrub
• trans_mag_smooth : basic::options::OptionKeys::fold_and_dock
• trans_magnitude : basic::options::OptionKeys::enzdes
• transform : basic::options::OptionKeys::mp::transform
• transform_into_membrane : basic::options::OptionKeys::mp::setup
• transition_threshold : basic::options::OptionKeys::canonical_sampling::sampling
• translation : basic::options::OptionKeys::rigid , demo::D100_Docking
• treat_residues_in_these_chains_as_separate_chemical_entities : basic::options::OptionKeys::in::file
• trg_anchor : basic::options::OptionKeys::threadsc
• trg_chain : basic::options::OptionKeys::threadsc
• trg_first_resid : basic::options::OptionKeys::threadsc
• trial : demo::D060_Folding
• trial_mover : test::Workshop5test
• trial_output : demo::D090_Ala_scan
• trialmover : test::T400_Refinement , test::Workshop5test
• trials : demo::D090_Ala_scan
• trim_proportion : basic::options::OptionKeys::wum
• turn_off_rna_chem_map_during_optimize : basic::options::OptionKeys::stepwise::rna
• tweak_sxfn : basic::options::OptionKeys::docking::ligand
• two : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• two_body : basic::options::OptionKeys::rotamerdump
• two_chain_tree : basic::options::OptionKeys::remodel
• two_fold_symmetry_0_180 : basic::options::OptionKeys::make_rot_lib
• two_fold_symmetry_135_315 : basic::options::OptionKeys::make_rot_lib
• two_ubiquitins : basic::options::OptionKeys::chemically_conjugated_docking
• type : basic::options::OptionKeys::frags::contacts
• type_ : tools::CppParser