- t -

• t : basic::options::OptionKeys::in::file , gpu_set_args , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , predPRE
• T : pyrosetta.distributed.cluster.exceptions , pyrosetta.distributed.cluster.serialization , test.T007_TracerIO
• t : test.T009_Exceptions
• t0 : test.T900_distributed
• t1 : test.T900_distributed
• table : utility::options::OptionKeys::options::table
• taboo_in_fa : basic::options::OptionKeys::loops
• taboo_sampling : basic::options::OptionKeys::loops
• taboo_threshold : metapatch
• tag : basic::options::OptionKeys::matdes , basic::options::OptionKeys::resample , basic::options::OptionKeys::rna::denovo , basic::options::OptionKeys::rot_anl , byres_data , chrisk , extract_by_sidechain_sasa_score , hbscan , test.T009_Exceptions
• tag2string : basic
• tagfile : basic::options::OptionKeys::in::file
• taglist : basic::options::OptionKeys::willmatch
• tags : basic::options::OptionKeys::in::file , extract_by_sidechain_sasa_score
• 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
• TAR_BLOCK_SIZE : utility::io
• target : basic::options::OptionKeys::hotspot
• target_aa : basic::options::OptionKeys::motifs
• target_chain : basic::options::OptionKeys::constel
• target_clash_pdb : basic::options::OptionKeys::score
• target_cnl : basic::options::OptionKeys::constel
• 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
• target_residues_contact : basic::options::OptionKeys::motifs
• target_residues_sf : basic::options::OptionKeys::motifs
• target_xyz : basic::options::OptionKeys::rna::denovo::out
• targetdir : basic::options::OptionKeys::evolution
• task : test.G200_Module_Region , vancomycin
• task2 : vancomycin
• 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
• tauc : PREcst , predPRE
• TBMB_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• TBMB_positions : basic::options::OptionKeys::cyclic_peptide
• TBMB_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• tcr_template_db_path : basic::options::OptionKeys::tcrmodel
• tcrmodel : basic::options::OptionKeys::tcrmodel
• temp : erraser_analysis
• temp_file : rna_rosetta_ready_set
• temp_final : basic::options::OptionKeys::MonteCarlo
• temp_initial : basic::options::OptionKeys::MonteCarlo
• 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::mp::lipids , basic::options::OptionKeys::remodel::RemodelLoopMover , basic::options::OptionKeys::rigid , basic::options::OptionKeys::rna::denovo , basic::options::OptionKeys::smhybrid , basic::options::OptionKeys::stepwise::monte_carlo , local
• template_identity_cutoff : basic::options::OptionKeys::tcrmodel
• template_pdb : basic::options::OptionKeys::in::file
• template_scores : basic::options::OptionKeys::cluster
• template_silent : basic::options::OptionKeys::in::file
• template_structure : challenge
• templates : basic::options::OptionKeys::templates
• templates_path : conf
• TEMPORARY_VISITED : utility::graph
• temps : basic::options::OptionKeys::recces
• tensor_weight : basic::options::OptionKeys::rdc
• term_tol : chrisk
• terminal_pdb : enumerate_junctions
• terminal_res : basic::options::OptionKeys::full_model::rna
• termini : basic::options::OptionKeys::mp
• test : 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 : create_a3b_hbs , test.T220_AtomAtomPairEnergies , test.Workshop9test
• test_score : pna
• test_suite : pyrosetta.tests.distributed.test_dask
• testing : basic::options::OptionKeys::AnchoredDesign::testing , basic::options::OptionKeys::testing
• tests : test.T900_distributed
• tether_jump : basic::options::OptionKeys::stepwise::rna
• tether_ligand : basic::options::OptionKeys::docking::ligand
• tether_to_closest_res : basic::options::OptionKeys::magnesium
• tetrahedral_metal_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• tetrahedral_metal_positions : basic::options::OptionKeys::cyclic_peptide
• tetrahedral_metal_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• texinfo_documents : conf
• text : utility::options::OptionKeys::options::table
• tf : test.G200_Module_Region , test.T500_Packing
• tfm : evaluate_beta_mutants
• tfm_rt : evaluate_beta_mutants
• tfmb : evaluate_beta_mutants
• tfmb_rt : evaluate_beta_mutants
• tgt_amino : basic::options::OptionKeys::pose_metrics::shobuns
• tgt_atom : basic::options::OptionKeys::pose_metrics::shobuns
• tgt_res : basic::options::OptionKeys::pose_metrics::shobuns
• thermal_sampling : basic::options::OptionKeys::recces::thermal_sampling
• theta_constraint_prob_cutoff : basic::options::OptionKeys::trRosetta
• theta_constraint_weight : basic::options::OptionKeys::trRosetta
• 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
• third_pivot : closure_error
• this_project_include : make_bindings_via_cmake
• this_project_namespace_to_bind : make_bindings_via_cmake
• this_project_source : make_bindings_via_cmake
• thorough : basic::options::OptionKeys::relax
• thread_unaligned : basic::options::OptionKeys::james
• threads : basic::options::OptionKeys::gpu , basic::options::OptionKeys::packstat
• threads_per_worker : basic::options::OptionKeys::cyclic_peptide
• 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
• ticks : 3d_histogram
• 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
• timer : basic::options::OptionKeys::loops , basic::options::OptionKeys::run
• title : correlation_time
• tm_alpha : basic::options::OptionKeys::mp::lipid_acc
• TM_pose_number : basic::options::OptionKeys::mp::assembly
• TMA_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• TMA_positions : basic::options::OptionKeys::cyclic_peptide
• TMA_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• tmp_data : enumerate_junctions
• TMprojection : basic::options::OptionKeys::mp
• tn : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• to_centroid : docking , loops , loops_kic , test.T600_Docking , test.T650_LoopsKIC
• to_fullatom : docking , loops , loops_kic , test.T650_LoopsKIC
• todo_include_todos : conf
• tol : loops_kic , test.T650_LoopsKIC
• tolerance : basic::options::OptionKeys::loops::ccd , basic::options::OptionKeys::pb_potential
• top : test.G204_Module_ScoreAnalysis
• top_designs : basic::options::OptionKeys::antibody::design
• top_label_locations : subloop_histogram
• top_labels : subloop_histogram
• top_n : metapatch
• 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
• tori : test_terpenes
• torsion_bin_probs : basic::options::OptionKeys::in::file
• torsion_distr_params_file : basic::options::OptionKeys::score
• torsion_error : make_comparison
• torsion_thresholds : basic::options::OptionKeys::james
• torsions : autocorrelation , internal_coordinates , torsion_vs_time
• torsionsMCM : basic::options::OptionKeys::flexPepDocking
• torval : test_terpenes
• total_clock : basic
• total_energy_cutoff : basic::options::OptionKeys::cyclic_peptide
• total_fractions : BundlePairRmsdCalculator
• total_res : rna_decompose
• total_threads : basic::options::OptionKeys::multithreading
• total_time : rna_rosetta_ready_set , rna_rosetta_to_pdb
• total_weight : basic::options::OptionKeys::rdc
• tr : apps::pilot::momeara
• TR : basic::database::schema_generator , basic::database
• tr : basic::datacache
• TR : basic::datacache , basic::mpi , basic::options , basic::resource_manager::locator , basic::resource_manager , basic
• tr : protocols::abinitio
• TR : protocols::loops::loop_mover::perturb , protocols::loops::loop_mover::refine , test.G000_Main_GUI
• TR_Error : basic
• TR_hh : basic::datacache
• TR_Warning : basic
• trajectories : correlation_time
• trajectory : basic::options::OptionKeys::backrub , basic::options::OptionKeys::coupled_moves , gaussian-sampling
• trajectory_file : basic::options::OptionKeys::coupled_moves
• trajectory_gz : basic::options::OptionKeys::backrub , basic::options::OptionKeys::coupled_moves
• trajectory_path : correlation_time
• trajectory_stride : basic::options::OptionKeys::backrub , basic::options::OptionKeys::coupled_moves
• trans2 : vancomycin
• trans_mag_smooth : basic::options::OptionKeys::fold_and_dock
• trans_magnitude : basic::options::OptionKeys::enzdes
• trans_mover : pna
• transform : basic::options::OptionKeys::mp::transform
• transform_into_membrane : basic::options::OptionKeys::mp::setup
• transition_threshold : basic::options::OptionKeys::canonical_sampling::sampling
• translate : beta_nonlocal , vancomycin
• translation : basic::options::OptionKeys::rigid , demo.D100_Docking
• translation_mag : basic::options::OptionKeys::recces::base_pair
• translocation_sampling : basic::options::OptionKeys
• treat_residues_in_these_chains_as_separate_chemical_entities : basic::options::OptionKeys::in::file
• tree_based_min_pack : basic::options::OptionKeys::carbohydrates::glycan_sampler
• tree_type : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• trg_anchor : basic::options::OptionKeys::threadsc
• trg_chain : basic::options::OptionKeys::threadsc
• trg_first_resid : basic::options::OptionKeys::threadsc
• trial : demo.D060_Folding , gaussian-sampling
• trial_mover : test.Workshop5test
• trial_output : demo.D090_Ala_scan
• trialmover : test.T400_Refinement , test.Workshop5test
• trials : demo.D090_Ala_scan
• triazolamer_design_first : tddm
• trigonal_planar_metal_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• trigonal_planar_metal_positions : basic::options::OptionKeys::cyclic_peptide
• trigonal_planar_metal_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• trigonal_pyramidal_metal_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• trigonal_pyramidal_metal_positions : basic::options::OptionKeys::cyclic_peptide
• trigonal_pyramidal_metal_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• trim : basic::options::OptionKeys::sc
• trim_proportion : basic::options::OptionKeys::wum
• trim_tol : chrisk
• triple_all_res : basic::options::OptionKeys::constel
• triple_target_resnum : basic::options::OptionKeys::constel
• trp : evaluate_beta_mutants
• trp_min : evaluate_beta_mutants
• trp_mm : evaluate_beta_mutants
• trp_pos : evaluate_beta_mutants
• trRosetta : basic::options::OptionKeys::trRosetta
• True : auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , drrafter_rna , enumerate_junctions
• tryptamine : basic::options::OptionKeys::constel
• tt : basic
• tuning_param : basic::options::OptionKeys::in
• turn_off_rna_chem_map_during_optimize : basic::options::OptionKeys::stepwise::rna
• tweak_sxfn : basic::options::OptionKeys::docking::ligand
• twin : subloop_histogram
• 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
• twoprime : basic::options::OptionKeys::full_model
• type : 3d_histogram , app_runner , auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , autocorrelation , basic::options::OptionKeys::frags::contacts , closure_error , combine_pdbs , correlation_time , DRRAFTER , drrafter_rna , dummy-distribution , enumerate_junctions , execute , explosion_error , finalize_models , find_lowest_scoring_relaxed_struct , gaussian-sampling , general_RNP_setup_script , get_final_ddG_scores , get_lowest_scoring_relaxed_models , histogram , kic_runner , make_comparison , percent_subangstrom , pivot_selection , pyrosetta.tests.distributed.cluster.print_discovered_test_cases , pyrosetta.tests.distributed.test_dask , relax_starting_structure , run_backbone , run_sidechain , score_vs_rmsd , setup_for_complex_scoring_general , submit_jobs