- t -

• T() : core::pack::interaction_graph , core::pack::task
• t() : core::scoring::hbonds
• T() : core::scoring
• tag_from_line() : core::chemical
• tag_from_pdb_fname() : core::scoring::motif
• tag_from_pose() : core::pose
• tag_into_pose() : core::pose
• take_Base_pointer() : protocols::toolbox::py_inheritance_test
• take_Base_reference() : protocols::toolbox::py_inheritance_test
• take_Base_SP() : protocols::toolbox::py_inheritance_test
• take_O_1A_pointer() : protocols::toolbox::py_inheritance_test
• take_O_1A_reference() : protocols::toolbox::py_inheritance_test
• take_O_1A_SP() : protocols::toolbox::py_inheritance_test
• take_O_2A_pointer() : protocols::toolbox::py_inheritance_test
• take_O_2A_reference() : protocols::toolbox::py_inheritance_test
• take_O_2A_SP() : protocols::toolbox::py_inheritance_test
• take_pose_op() : protocols::toolbox
• TALARIS_2013() : core::scoring
• TALARIS_2013_CART() : core::scoring
• TALARIS_2014() : core::scoring
• target_constel() : protocols::constel
• TASK_FACTORY_TAG() : core::pack::task
• task_from_bool_mask() : core::pack::task::residue_selector
• task_from_resnums() : core::pack::task::residue_selector
• task_op_schema_empty() : core::pack::task::operation
• task_op_schema_w_attributes() : core::pack::task::operation
• TASK_OPERATIONS_TAG() : core::pack::task
• tautomerize_anomer() : core::pose::carbohydrates
• tear_down_constraints() : protocols::star
• templates_from_cmd_line() : protocols::comparative_modeling
• test_merge_and_slice_with_two_helix_test_case() : protocols::stepwise::modeler
• test_res_res_aln() : protocols::protein_interface_design::movers
• tether_ligand_tracer() : protocols::ligand_docking
• theta_torsion_beta_aa() : core::id
• theta_torsion_meta_aramid() : core::id
• theta_torsion_oligourea() : core::id
• theta_torsion_ortho_aramid() : core::id
• theta_torsion_para_aramid() : core::id
• theta_torsion_post_methylene_meta_aramid() : core::id
• theta_torsion_post_methylene_ortho_aramid() : core::id
• theta_torsion_post_methylene_para_aramid() : core::id
• theta_torsion_pre_methylene_meta_aramid() : core::id
• theta_torsion_pre_methylene_ortho_aramid() : core::id
• theta_torsion_pre_methylene_para_aramid() : core::id
• theta_torsion_pre_methylene_post_methylene_meta_aramid() : core::id
• theta_torsion_pre_methylene_post_methylene_ortho_aramid() : core::id
• theta_torsion_pre_methylene_post_methylene_para_aramid() : core::id
• thread_sequence_on_pose() : protocols::evolution::AlignmentCleanerTools
• three_body_approximate_buried_unsat_calculation() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• throw_sm_override_error() : core::simple_metrics
• TMalign_poses() : protocols::hybridization
• to_centroid() : protocols::medal , protocols::star
• to_json() : protocols::indexed_structure_store::search , protocols::indexed_structure_store , protocols::pdbinfo_manipulations
• to_left() : core::membrane
• to_str() : protocols::indexed_structure_store
• to_string() : core::id , core::pose::full_model_info , core::scoring::rna , protocols::moves , protocols::stepwise::modeler::rna::phosphate , protocols::stepwise::monte_carlo::mover
• toFloat() : protocols::cluster::calibur
• toInt() : protocols::cluster::calibur
• tokenize() : core::pose::rna
• Tokenize() : protocols::rbsegment_relax
• tokenize() : protocols::stepwise::modeler::rna
• Tokenize() : protocols
• tokenize_line() : core::pack::task
• TOL_H_DIRECT() : protocols::noesy_assign
• TOL_H_INDIRECT() : protocols::noesy_assign
• TOL_LABEL() : protocols::noesy_assign
• tors_deriv_to_cartesian() : core::optimization
• torsion2big_bin() : protocols::frags
• torsion2big_bin_id() : protocols::frag_picker::quota
• torsion_constraints_from_chi_rotamers() : protocols::ligand_docking
• torsion_constraints_from_mean_sd() : protocols::ligand_docking
• torsion_constraints_from_rotamers() : protocols::ligand_docking
• torsion_dev_score() : protocols::frags
• torsional_derivative_from_cartesian_derivatives() : core::optimization
• total_energy_from_pose() : core::pose
• ToUpper() : core::scoring::packstat
• TR() : core::chemical::gasteiger
• tr() : core::chemical::gasteiger
• TR() : core::chemical::mainchain_potential , core::chemical::mmCIF , core::chemical::orbitals , core::chemical::rna , core::chemical::rotamers , core::chemical::sdf
• tr() : core::chemical::sdf
• TR() : core::chemical
• tr() : core::chemical
• TR() : core::conformation::parametric , core::conformation::symmetry , core::conformation , core::energy_methods , core::fragment::picking_old::vall::eval , core::fragment::picking_old::vall , core::fragment::rna
• tr() : core::fragment , core::id
• TR() : core::id
• tr() : core::import_pose::libraries , core::import_pose::pose_stream , core::import_pose
• TR() : core::import_pose , core::init , core::io::mmcif , core::io::nmr , core::io::pdb , core::io::pose_from_sfr , core::io::pose_to_sfr , core::io::raw_data , core::io::rcsb , core::io::rna , core::io::sequence_comparation
• tr() : core::io::silent
• TR() : core::io
• tr() : core::kinematics
• TR() : core::kinematics , core::kinematics::tree , core::optimization::symmetry , core::optimization , core::pack::annealer , core::pack::dunbrack::cenrot , core::pack::dunbrack , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty , core::pack::guidance_scoreterms::buried_unsat_penalty , core::pack::guidance_scoreterms::hbnet_energy , core::pack::guidance_scoreterms::voids_penalty_energy , core::pack::hbonds , core::pack::interaction_graph , core::pack::palette , core::pack::rotamer_set , core::pack::rotamers , core::pack::scmin , core::pack::task::operation , core::pack::task::residue_selector
• tr() : core::pack::task
• TR() : core::pack::task , core::pack , core::pose::reference_pose , core::pose::symmetry , core::pose , core::scoring::aa_composition_energy , core::scoring::aa_repeat_energy , core::scoring::bin_transitions
• tr() : core::scoring::constraints
• TR() : core::scoring::constraints , core::scoring::cryst
• tr() : core::scoring::custom_pair_distance
• TR() : core::scoring::disulfides , core::scoring::dna
• tr() : core::scoring::dssp
• TR() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::epr_deer , core::scoring::etable , core::scoring::fiber_diffraction
• tr() : core::scoring::func , core::scoring::geometric_solvation , core::scoring::hbonds
• TR() : core::scoring::hbonds , core::scoring::interface_ , core::scoring::lkball , core::scoring::methods::dfire , core::scoring::methods
• tr() : core::scoring::methods
• TR() : core::scoring::methods
• tr() : core::scoring::methods
• TR() : core::scoring::methods , core::scoring::mhc_epitope_energy , core::scoring::mm , core::scoring::motif , core::scoring::netcharge_energy , core::scoring::nmr::pcs , core::scoring::nmr::pre , core::scoring::nmr::rdc , core::scoring::nmr , core::scoring::nv , core::scoring::orbitals , core::scoring::packing , core::scoring::saxs , core::scoring
• tr() : core::scoring
• TR() : core::scoring , core::scoring::util_methods , core::scoring::vdwaals , core::select::jump_selector , core::select::residue_selector
• tr() : core::sequence
• TR() : core::util , protocols::abinitio , protocols::antibody::clusters , protocols::antibody
• tr() : protocols::boinc
• TR() : protocols::calc_taskop_filters , protocols::calc_taskop_movers , protocols::canonical_sampling::mc_convergence_checks
• tr() : protocols::canonical_sampling
• TR() : protocols::cartesian , protocols::checkpoint
• tr() : protocols::cluster
• TR() : protocols::comparative_modeling
• tr() : protocols::comparative_modeling
• TR() : protocols::constel , protocols::constraint_filters , protocols::constraint_generator , protocols::constraints_additional , protocols::contact_map , protocols::cryst , protocols::cutoutdomain , protocols::cyclic_peptide , protocols::ddg::CartesianddG , protocols::design_opt , protocols::dna , protocols::docking , protocols::electron_density
• tr() : protocols::environment , protocols::enzdes::enzutil
• TR() : protocols::enzdes
• tr() : protocols::enzdes , protocols::evaluation
• TR() : protocols::evolution::AlignmentCleanerTools , protocols::evolution , protocols::features::strand_assembly , protocols::features
• tr() : protocols::features
• TR() : protocols::fibril , protocols::filters , protocols::fldsgn::potentials , protocols::fldsgn , protocols::flexpack::annealer , protocols::flexpack::interaction_graph , protocols::flexpack::rotamer_set
• tr() : protocols::flexpack
• TR() : protocols::fold_from_loops::filters , protocols::fold_from_loops::movers , protocols::fold_from_loops , protocols::fold_from_loops::utils , protocols::forge::build , protocols::forge::components , protocols::forge::methods , protocols::forge::remodel , protocols::frag_picker::nonlocal
• tr() : protocols::frag_picker::scores
• TR() : protocols::frag_picker
• tr() : protocols::frag_picker
• TR() : protocols::frags , protocols::generalized_kinematic_closure::filter , protocols::generalized_kinematic_closure::perturber , protocols::generalized_kinematic_closure::selector , protocols::generalized_kinematic_closure , protocols::genetic_algorithm , protocols::hbnet , protocols::helical_bundle::parameters , protocols::helical_bundle , protocols::helix_capper , protocols::hotspot_hashing::movers , protocols::hotspot_hashing
• tr() : protocols::hotspot_hashing
• TR() : protocols::hybridization , protocols::idealize , protocols::indel , protocols::indexed_structure_store::filters , protocols::indexed_structure_store , protocols::jd2
• tr() : protocols::jd2
• TR() : protocols::jd3::chunk_library_inputters , protocols::jd3::full_model_inputters , protocols::jd3::job_distributors , protocols::jd3::pose_inputters , protocols::jd3::pose_outputters , protocols::jd3::standard , protocols::jd3 , protocols::jobdist
• tr() : protocols::jobdist , protocols::jumping
• TR() : protocols::legacy_sewing::sampling::requirements
• tr() : protocols::legacy_sewing::sampling::requirements
• TR() : protocols::legacy_sewing::scoring , protocols::legacy_sewing , protocols::ligand_docking::ga_ligand_dock
• tr() : protocols::ligand_docking::rdf
• TR() : protocols::ligand_docking , protocols::loop_build , protocols::loop_grower , protocols::loop_modeler , protocols::loop_modeling , protocols::loophash , protocols::loops::loop_closure::ccd
• tr() : protocols::loops::loop_closure::ccd
• TR() : protocols::loops::loop_closure::kinematic_closure , protocols::loops::loop_mover::perturb , protocols::loops::loop_mover::refine
• tr() : protocols::loops::loop_mover
• TR() : protocols::loops::loops_definers
• tr() : protocols::loops::loops_definers
• TR() : protocols::loops
• tr() : protocols::loops
• TR() : protocols::make_rot_lib , protocols::match::downstream , protocols::match::output , protocols::match
• tr() : protocols::match
• TR() : protocols::match::upstream , protocols::matdes , protocols::md , protocols::mean_field , protocols::medal , protocols::minimization_packing , protocols::motif_grafting::movers , protocols::motifs , protocols::moves
• tr() : protocols::moves
• TR() : protocols::mpi_refinement , protocols::multistate_design , protocols::neighbor , protocols::nmr::pcs , protocols::nmr::pre , protocols::nmr::rdc , protocols::nmr
• tr() : protocols::noesy_assign
• TR() : protocols::nonlocal , protocols::optimize_weights , protocols::pack_daemon
• tr() : protocols::pack_interface
• TR() : protocols::parser , protocols::pb_potential , protocols::pmut_scan , protocols::pockets , protocols::pose_creation , protocols::pose_metric_calculators , protocols::protein_interface_design::filters
• tr() : protocols::protein_interface_design::filters
• TR() : protocols::protein_interface_design::filters , protocols::protein_interface_design::movers
• tr() : protocols::protein_interface_design::movers
• TR() : protocols::protein_interface_design::movers , protocols::protein_interface_design , protocols::qsar::scoring_grid , protocols::qsar , protocols::rbsegment_relax
• tr() : protocols::rbsegment_relax
• TR() : protocols::rbsegment_relax , protocols::recon_design , protocols::relax , protocols::residue_selectors
• tr() : protocols::rigid
• TR() : protocols::rigid , protocols::rna::denovo , protocols::rna::movers , protocols::rosetta_scripts , protocols::rotamer_recovery
• tr() : protocols::rotamer_recovery
• TR() : protocols::rotamer_recovery , protocols::rpc , protocols::score_filters , protocols::scoring::methods , protocols::seeded_abinitio , protocols::sewing::requirements , protocols::sewing::scoring , protocols::sic_dock::scores , protocols::sic_dock , protocols::simple_ddg , protocols::simple_filters
• tr() : protocols::simple_filters
• TR() : protocols::simple_filters
• tr() : protocols::simple_filters
• TR() : protocols::simple_moves::asym_fold_and_dock , protocols::simple_moves::bin_transitions , protocols::simple_moves::rational_mc , protocols::simple_moves::sidechain_moves
• tr() : protocols::simple_moves
• TR() : protocols::simple_moves
• tr() : protocols::simple_moves
• TR() : protocols::simple_moves
• tr() : protocols::simple_moves , protocols::sparta
• TR() : protocols::splice
• tr() : protocols::ss_prediction
• TR() : protocols::star , protocols::stepwise::sampler::rna , protocols::struct_fragment , protocols::switches , protocols::symmetric_docking , protocols::symmetry , protocols::task_operations , protocols::testing
• tr() : protocols::toolbox::match_enzdes_util
• TR() : protocols::toolbox::match_enzdes_util
• tr() : protocols::toolbox::match_enzdes_util
• TR() : protocols::toolbox::match_enzdes_util , protocols::toolbox::pose_manipulation
• tr() : protocols::toolbox::rotamer_set_operations , protocols::toolbox
• TR() : protocols::topology_broker , protocols , protocols::trajectory , protocols::vip , protocols::wum
• TR2() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• TR_BGEDGE() : core::pack::interaction_graph
• TR_BGNODE() : core::pack::interaction_graph
• TR_call_order() : protocols::rosetta_scripts
• TR_ccd() : protocols::seeded_abinitio , protocols::splice
• TR_constraints() : protocols::splice
• TR_cst() : protocols::protein_interface_design::movers
• TR_database() : protocols::protein_interface_design::filters
• TR_debug() : protocols::seeded_abinitio
• TR_DI() : protocols::toolbox::pose_manipulation
• TR_EDGE() : core::pack::interaction_graph
• TR_HIG() : core::pack::interaction_graph
• TR_it() : core::scoring
• TR_min() : protocols::splice
• TR_NODE() : core::pack::interaction_graph
• TR_PatchOperations() : core::chemical
• TR_pcs_d() : protocols::scoring::methods::pcs
• TR_PCS_d_i() : protocols::scoring::methods::pcs
• TR_PCS_d_i_Ts1() : protocols::scoring::methods::pcsTs1
• TR_PCS_d_i_Ts2() : protocols::scoring::methods::pcsTs2
• TR_PCS_d_i_Ts3() : protocols::scoring::methods::pcsTs3
• TR_PCS_d_i_Ts4() : protocols::scoring::methods::pcsTs4
• TR_pcs_d_p_l() : protocols::scoring::methods::pcs
• TR_pcs_d_p_l_Ts1() : protocols::scoring::methods::pcsTs1
• TR_pcs_d_p_l_Ts2() : protocols::scoring::methods::pcsTs2
• TR_pcs_d_p_l_Ts3() : protocols::scoring::methods::pcsTs3
• TR_pcs_d_p_l_Ts4() : protocols::scoring::methods::pcsTs4
• TR_pcs_d_Ts1() : protocols::scoring::methods::pcsTs1
• TR_pcs_d_Ts2() : protocols::scoring::methods::pcsTs2
• TR_pcs_d_Ts3() : protocols::scoring::methods::pcsTs3
• TR_pcs_d_Ts4() : protocols::scoring::methods::pcsTs4
• TR_PCS_Energy() : protocols::scoring::methods::pcs
• TR_PCS_Energy_Ts1() : protocols::scoring::methods::pcsTs1
• TR_PCS_Energy_Ts2() : protocols::scoring::methods::pcsTs2
• TR_PCS_Energy_Ts3() : protocols::scoring::methods::pcsTs3
• TR_PCS_Energy_Ts4() : protocols::scoring::methods::pcsTs4
• TR_PcsDataCenter() : protocols::scoring::methods::pcs2
• TR_PcsDataCenterManager() : protocols::scoring::methods::pcs2
• TR_PcsDataCenterManagerSingleton() : protocols::scoring::methods::pcs2
• TR_PcsDataLanthanide() : protocols::scoring::methods::pcs2
• TR_PcsEnergy() : protocols::scoring::methods::pcs2
• TR_PcsEnergyParameter() : protocols::scoring::methods::pcs2
• TR_PcsEnergyParameterManager() : protocols::scoring::methods::pcs2
• TR_PcsInputCenter() : protocols::scoring::methods::pcs2
• TR_PcsInputCenterManager() : protocols::scoring::methods::pcs2
• TR_PcsInputFile() : protocols::scoring::methods::pcs2
• TR_PcsInputLine() : protocols::scoring::methods::pcs2
• TR_pssm() : protocols::splice
• TR_pymol() : protocols::protein_interface_design::filters
• TR_report() : protocols::protein_interface_design::movers , protocols::rosetta_scripts
• TR_residue_scan() : protocols::protein_interface_design::filters
• TR_Results() : protocols::helical_bundle
• TR_rms_error_with_noise() : core::import_pose::atom_tree_diffs
• tr_score() : protocols::jd2
• TR_seg() : protocols::rbsegment_relax
• TR_spec() : protocols::dna
• TR_STATS() : core::pack::interaction_graph
• TR_tail() : protocols::splice
• TR_TensorsOptimizer() : protocols::scoring::methods::pcs2
• TR_TensorsOptimizerFix() : protocols::scoring::methods::pcs2
• TR_TensorsOptimizerSvd() : protocols::scoring::methods::pcs2
• TR_tsr_opt() : protocols::scoring::methods::pcs
• TR_tsr_opt_Ts1() : protocols::scoring::methods::pcsTs1
• TR_tsr_opt_Ts2() : protocols::scoring::methods::pcsTs2
• TR_tsr_opt_Ts3() : protocols::scoring::methods::pcsTs3
• TR_tsr_opt_Ts4() : protocols::scoring::methods::pcsTs4
• TR_VERBOSE() : protocols::optimize_weights
• trABEGO_SS_Config() : protocols::frag_picker::quota
• trABEGO_SS_Pool() : protocols::frag_picker::quota
• trABEGO_SS_Score() : protocols::frag_picker::scores
• tracer() : protocols::frag_picker
• TRACER() : protocols::loop_grower
• tracer() : protocols::peptide_deriver
• trAdaptiveScoreHistogram() : protocols::frag_picker::scores
• trAmbigCSScore() : protocols::frag_picker::scores
• trans_omega() : protocols::forge::methods
• trans_pose() : protocols::matdes , protocols::sic_dock
• transfer_jumps() : core::pose
• transfer_phi_psi() : core::pose
• transform_moving_partition_to_origin() : protocols::toolbox::rigid_body
• transform_res_to_subunit() : protocols::loop_grower
• transform_sequence_to_mutation_set() : protocols::antibody::design
• transform_to_closest_symmunit() : protocols::loop_grower
• transform_tracer() : protocols::ligand_docking
• transitive_map() : core::sequence
• translate() : protocols::toolbox::rigid_body
• translate_and_rotate_residue_to_origin() : protocols::toolbox::rigid_body
• translate_tracer() : protocols::ligand_docking
• translate_virtual_anchor_to_first_rigid_body() : protocols::rna::denovo
• trAtomBasedConstraintsScore() : protocols::frag_picker::scores
• trAtomPairConstraintsScore() : protocols::frag_picker::scores
• trBestTotalScoreSelector() : protocols::frag_picker
• TRBM() : protocols::rigid , protocols::topology_broker
• TRcs() : core::scoring::packstat
• trCSScore() : protocols::frag_picker::scores
• trCustomScoreSelector() : protocols::frag_picker
• trDihedralConstraintsScore() : protocols::frag_picker::scores
• trDiversifyCrmsdByClustering() : protocols::frag_picker
• trDiversifyCrmsdSelector() : protocols::frag_picker
• trDiversifyDihedralsSelector() : protocols::frag_picker
• trDMEScore() : protocols::frag_picker::scores
• tree_distance() : protocols::backrub
• trFormFactor() : core::scoring::saxs
• trFormFactorManager() : core::scoring::saxs
• trFragmentCandidate() : protocols::frag_picker
• trGunnCost() : protocols::frag_picker::scores , protocols::simple_moves
• trGunnScore() : protocols::frag_picker::scores
• trie_vs_path() : core::scoring::trie
• trie_vs_trie() : core::scoring::trie
• trim_back_sequence_mapping() : protocols::loops
• trim_neighbors_by_distance() : core::select
• trInterbondAngleScore() : protocols::frag_picker::scores
• triple_constel_set() : protocols::constel
• triple_constel_set_idx3() : protocols::constel
• trJCoupling() : protocols::frag_picker::scores
• trJCouplingIO() : protocols::frag_picker
• trKillHairpinsIO() : core::scoring
• trMinMultiHarmonicFunc() : core::scoring::func
• trPartialSecondarySimilarity() : protocols::frag_picker::scores
• trPdbFilter() : protocols::frag_picker
• trPDDFEnergy() : protocols::scoring::methods::saxs
• trPhiPsiRmsd() : protocols::frag_picker::scores
• trProfScore() : protocols::frag_picker::scores
• trProfScoreBlosum62() : protocols::frag_picker::scores
• trProfScoreDistWeight() : protocols::frag_picker::scores
• trProfScoreL1() : protocols::frag_picker::scores
• trProfScoreSubMatrix() : protocols::frag_picker::scores
• trQuotaCollector() : protocols::frag_picker::quota
• trQuotaConfig() : protocols::frag_picker::quota
• trQuotaSelector() : protocols::frag_picker::quota
• trRDCScore() : protocols::frag_picker::scores
• TRReport() : protocols::helical_bundle
• trRmsScore() : protocols::frag_picker::scores
• trSAXSEnergy() : core::scoring::saxs
• trSecondarySimilarity() : protocols::frag_picker::scores
• trSecondaryStructurePool() : protocols::frag_picker::quota
• trTalosSSSimilarity() : protocols::frag_picker::scores
• trTmScore() : protocols::frag_picker::scores
• truncate_abego() : protocols::denovo_design::components
• TS() : core::scoring::cryst , core::util , protocols::ligand_docking::ga_ligand_dock , protocols::rbsegment_relax
• TSG() : protocols::cryst
• TSW() : protocols::cryst
• tt() : core::pack::rotamer_set::symmetry , core::pack::rotamer_set , core::pack , protocols::loops
• type2name() : protocols::frag_picker
• type_map_add() : core::scoring::packstat
• type_set_mode_from_string() : core::chemical
• TZ() : protocols::hybridization , protocols::symmetry