- t -

• t() : core::scoring::hbonds
• T() : core::pack::interaction_graph , core::pack::task , core::scoring , core::pack::interaction_graph
• tag_from_line() : core::chemical
• tag_from_pose() : core::pose
• tag_into_pose() : core::pose
• tccd() : protocols::loops::loop_closure::ccd
• tear_down_constraints() : protocols::star
• templates_from_cmd_line() : protocols::comparative_modeling
• test_res_res_aln() : protocols::protein_interface_design::movers
• tether_ligand_tracer() : protocols::ligand_docking
• TMalign_poses() : protocols::hybridization
• to_centroid() : protocols::medal , protocols::star
• Tokenize() : protocols , protocols::rbsegment_relax , protocols::swa::rna
• 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_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
• torsional_derivative_from_cartesian_derivatives() : core::optimization
• total_energy_from_pose() : core::pose
• ToUpper() : core::scoring::packstat
• tr() : core::io::silent , protocols::jd2
• TR() : core::scoring::mm , protocols::rosetta_scripts , protocols::rotamer_recovery , core::scoring::mm , protocols::rotamer_recovery
• tr() : protocols::jobdist
• TR() : core::scoring::mm , protocols::rotamer_recovery , core::scoring::nv , protocols::rotamer_recovery
• tr() : core::io::silent , protocols::jumping
• TR() : core::scoring::orbitals , protocols::rotamer_recovery , core::scoring::packing , protocols::rotamer_recovery
• tr() : protocols::jumping
• TR() : core::scoring::packing , protocols::rotamer_recovery , core::scoring::saxs , protocols::rotamer_recovery , protocols::seeded_abinitio
• tr() : core::io::silent , protocols::jumping
• TR() : core::scoring::symmetry , protocols::seeded_abinitio , core::util , protocols::seeded_abinitio
• tr() : protocols::jumping
• TR() : core::util , protocols::sic_dock , protocols::simple_filters , protocols::abinitio , protocols::simple_filters
• tr() : core::io::silent , protocols::jumping
• TR() : protocols::canonical_sampling::mc_convergence_checks , protocols::simple_filters , protocols::cartesian , protocols::simple_filters
• tr() : protocols::loops
• TR() : protocols::checkpoint , protocols::simple_filters , protocols::coarse_rna , protocols::simple_filters
• tr() : core::io::silent , protocols::loops::loop_closure::ccd
• TR() : protocols::constraints_additional , protocols::simple_filters , protocols::constraints_additional , protocols::simple_filters
• tr() : protocols::loops::loop_closure::ccd
• TR() : protocols::contact_map , protocols::simple_filters , protocols::design_opt , protocols::simple_filters
• tr() : core::io::silent , protocols::loops::loop_closure::ccd
• TR() : protocols::design_opt , protocols::simple_filters , protocols::design_opt , protocols::simple_filters , protocols::simple_moves::asym_fold_and_dock
• tr() : protocols::loops::loop_closure::ccd
• TR() : protocols::dna , protocols::simple_moves::asym_fold_and_dock , protocols::simple_moves , protocols::dna , protocols::simple_moves
• tr() : core::io::silent , protocols::loops
• TR() : protocols::dna , protocols::simple_moves , protocols::dna , protocols::simple_moves
• tr() : protocols::loops
• TR() : protocols::wum2 , protocols::wum , protocols::vip , protocols::toolbox::pose_metric_calculators , protocols::toolbox::pose_manipulation , protocols::toolbox::match_enzdes_util , protocols::symmetric_docking , protocols::star , protocols::simple_moves::symmetry , protocols::simple_moves , protocols::simple_moves::sidechain_moves , protocols::simple_moves , protocols::dna , protocols::simple_moves , protocols::simple_moves::rational_mc , protocols::simple_moves , protocols::dna , protocols::simple_moves
• tr() : core::kinematics , protocols::loops::loops_definers
• TR() : protocols::dna , protocols::simple_moves , protocols::dna
• tr() : protocols::loops
• TR() : protocols::dna , protocols::electron_density
• tr() : core::chemical , core::kinematics , protocols::match
• TR() : protocols::electron_density , protocols::simple_moves , protocols::enzdes
• tr() : protocols::match
• TR() : protocols::enzdes , protocols::features
• tr() : core::pack::task , protocols::moves
• TR() : protocols::features
• tr() : protocols::protein_interface_design::filters
• TR() : protocols::features
• tr() : core::chemical , core::pose , protocols::protein_interface_design::movers
• TR() : protocols::features
• tr() : protocols::rbsegment_relax
• TR() : protocols::features
• tr() : core::scoring::constraints , protocols::rna
• TR() : protocols::features
• tr() : protocols::rna
• TR() : protocols::features
• tr() : core::chemical , core::scoring::constraints , protocols::rna
• TR() : protocols::features
• tr() : protocols::rotamer_recovery
• TR() : protocols::features
• tr() : core::scoring::constraints , protocols::simple_filters
• TR() : protocols::features
• tr() : protocols::simple_moves
• TR() : protocols::rosetta_scripts , protocols::rna , protocols::rigid , protocols::relax , protocols::rbsegment_relax , protocols::qsar::scoring_grid , protocols::qsar , protocols::protein_interface_design::movers , protocols::features , protocols::protein_interface_design::movers , protocols::features
• tr() : core::chemical
• TR() : protocols::protein_interface_design::movers , protocols::protein_interface_design::filters
• tr() : core::scoring::custom_pair_distance
• TR() : protocols::protein_interface_design::filters , protocols::pockets
• tr() : protocols::simple_moves
• TR() : protocols::features , protocols::pb_potential , protocols::pack_daemon , protocols::outputter , protocols::optimize_weights , protocols::nonlocal , protocols::fibril , protocols::nonlocal , protocols::multistate_design , protocols::moves , protocols::motifs , protocols::medal , protocols::match::upstream , protocols::match::output
• tr() : protocols::sparta
• TR() : protocols::fibril , protocols::match , protocols::match::downstream , protocols::match , protocols::loops , protocols::loops::loops_definers , protocols , protocols::filters , protocols::loops::loop_mover::refine , protocols::loops::loop_mover::perturb , protocols::loops::loop_closure::kinematic_closure , protocols::loops , protocols::loophash
• tr() : core::scoring::dssp , protocols::sparta
• TR() : protocols::filters , protocols::loophash , protocols::loop_build , protocols::ligand_docking , protocols::jobdist , protocols::jd2 , protocols::filters , protocols::jd2::parser , protocols::jd2 , protocols::inputter , protocols::idealize , protocols::hybridization
• tr() : protocols::toolbox
• TR() : protocols::filters , protocols::hotspot_hashing , protocols::hotspot_hashing::movers , protocols::hotspot_hashing , protocols::genetic_algorithm , protocols::frag_picker , protocols::frag_picker::nonlocal , protocols::forge::remodel , protocols::filters , protocols::forge::remodel , protocols::forge::methods , protocols::forge::components , protocols::forge::build , protocols::flexpack::rotamer_set , protocols::flexpack::interaction_graph , protocols::flexpack::annealer , protocols::fldsgn::potentials
• tr() : core::chemical , core::scoring::geometric_solvation , protocols::toolbox
• TR() : protocols::fldsgn
• tr() : protocols::toolbox
• TR() : protocols::fldsgn::potentials
• tr() : core::scoring::hbonds , protocols::toolbox::match_enzdes_util , core::chemical , core::scoring::hbonds , protocols::toolbox::match_enzdes_util , core::scoring::hbonds , protocols::toolbox::match_enzdes_util , protocols::toolbox::rotamer_set_operations , core::chemical , core::scoring::hbonds , protocols::toolbox::rotamer_set_operations
• TR() : protocols::forge::remodel
• tr() : protocols::toolbox , core::scoring::methods
• TR() : core::chemical::orbitals , core::chemical
• tr() : core::chemical , core::scoring::methods
• TR() : core::coarse , core::conformation
• tr() : core::scoring::methods
• TR() : core::conformation::symmetry
• tr() : core::chemical , core::scoring
• TR() : core::conformation::symmetry , protocols::hotspot_hashing , protocols::hybridization , core::conformation::symmetry
• tr() : core::scoring
• TR() : core::fragment::picking_old::vall::eval
• tr() : core::chemical , core::sequence
• TR() : core::fragment::picking_old::vall::eval , core::fragment::picking_old::vall
• tr() : core::sequence
• TR() : core::import_pose , core
• tr() : core::chemical , core::sequence
• TR() : core::io::pdb , protocols::jd2::parser , core::io::pdb
• tr() : core::sequence
• TR() : core::io::pdb , core::io::raw_data
• tr() : core::chemical::rna , core::sequence
• TR() : core::io::sequence_comparation , core::kinematics
• tr() : core::sequence
• TR() : core::kinematics::tree , core::kinematics
• tr() : core::fragment , core::sequence
• TR() : core::optimization , protocols::loophash , core::scoring::mm , core::scoring::methods , protocols::protein_interface_design::movers , core::scoring::methods::dfire , core::scoring::methods , core::scoring , core::scoring::interface , core::scoring::electron_density_atomwise , protocols::protein_interface_design::movers , core::scoring::electron_density , core::scoring::dna , core::scoring::disulfides , protocols::protein_interface_design::filters , core::scoring::disulfides , core::scoring::constraints , protocols::loophash , core::scoring::constraints , core::scoring , core::pose , core::pose::symmetry , core::pose , core::pack::task , protocols::nonlocal , core::pack::task::operation , core::pack , protocols::match::output , core::pack , core::pack::interaction_graph , core::pack::dunbrack , protocols::loops::loop_mover::refine , core::pack::annealer , core::optimization::symmetry , core::optimization , protocols::loophash
• tr() : core::sequence
• TR() : core::optimization
• tr() : core::fragment , protocols::canonical_sampling , protocols::cluster , core::fragment , protocols::comparative_modeling
• TR() : core::pack::annealer
• tr() : protocols::comparative_modeling , core::fragment , protocols::comparative_modeling , core::fragment , protocols::enzdes
• TR() : core::pack::rotamer_set , protocols::match::output
• tr() : protocols::enzdes::enzutil , core::fragment , protocols::enzdes , core::fragment , protocols::enzdes
• TR() : core::pack::task::operation
• tr() : protocols::enzdes , core::fragment , protocols::enzdes , core::fragment , protocols::evaluation
• TR() : core::scoring::constraints , protocols::pmut_scan
• tr() : protocols::evaluation , core::fragment , protocols::features , core::fragment , protocols::flexpack
• TR() : core::scoring::disulfides
• tr() : protocols::frag_picker , core::id , protocols::frag_picker , core::import_pose , protocols::frag_picker
• TR() : core::scoring::electron_density , protocols::protein_interface_design::movers
• tr() : protocols::frag_picker::scores , core::import_pose , protocols::frag_picker::scores , core::import_pose::pose_stream , protocols::hotspot_hashing
• TR() : core::scoring::methods
• tr() : protocols::jd2 , core::import_pose::pose_stream , protocols::jd2
• TR_BGEDGE() : core::pack::interaction_graph
• TR_BGNODE() : core::pack::interaction_graph
• TR_call_order() : protocols::rosetta_scripts
• TR_ccd() : protocols::seeded_abinitio , protocols::protein_interface_design::movers
• 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_dump_pdb_dummy() : core::io::pdb
• TR_EDGE() : core::pack::interaction_graph
• TR_hh() : protocols::moves
• TR_HIG() : core::pack::interaction_graph
• 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_p_l() : protocols::scoring::methods::pcs
• TR_PCS_Energy() : protocols::scoring::methods::pcs
• 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_REMODEL() : protocols::forge::remodel
• TR_report() : protocols::rosetta_scripts , protocols::protein_interface_design::movers
• TR_residue_scan() : protocols::protein_interface_design::filters
• TR_seg() : protocols::rbsegment_relax
• TR_spec() : protocols::dna
• TR_STATS() : core::pack::interaction_graph
• 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_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
• traced_dump_pdb() : core::io::pdb
• tracer() : protocols::frag_picker
• TRACER() : core::scoring::constraints
• trAdaptiveScoreHistogram() : protocols::frag_picker::scores
• trAmbigCSScore() : protocols::frag_picker::scores
• trans_omega() : protocols::forge::methods
• transfer_jumps() : core::pose
• transfer_phi_psi() : core::pose
• transform_pose() : protocols::protein_interface_design
• transform_tracer() : protocols::ligand_docking
• transitive_map() : core::sequence
• translate() : protocols::swa
• translate_and_rotate_residue_to_origin() : protocols::swa
• translate_then_rotate_pose() : protocols::swa::rna
• translate_tracer() : protocols::ligand_docking
• translate_virtual_anchor_to_first_rigid_body() : protocols::rna
• trAtomBasedConstraintsScore() : protocols::frag_picker::scores
• trAtomPairConstraintsScore() : protocols::frag_picker::scores
• trBestTotalScoreSelector() : protocols::frag_picker
• TRBM() : protocols::rigid
• 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
• trg_RG() : protocols::enzdes
• trGunnCost() : protocols::frag_picker::scores , protocols::simple_moves
• trGunnScore() : protocols::frag_picker::scores
• tricubic_interpolation() : core::pack::dunbrack
• trie_vs_path() : core::scoring::trie
• trie_vs_trie() : core::scoring::trie
• trim_back_sequence_mapping() : protocols::loops
• TRIMETHYLATION() : core::chemical
• trInterbondAngleScore() : protocols::frag_picker::scores
• trJCoupling() : protocols::frag_picker::scores
• trJCouplingIO() : protocols::frag_picker
• trKillHairpinsIO() : core::scoring
• trMinMultiHarmonicFunc() : core::scoring::constraints
• 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
• trRmsScore() : protocols::frag_picker::scores
• trSAXSEnergy() : core::scoring::saxs
• trSecondarySimilarity() : protocols::frag_picker::scores
• trSecondaryStructurePool() : protocols::frag_picker::quota
• trTalosSSSimilarity() : protocols::frag_picker::scores
• trTorsionBinPool() : protocols::frag_picker::quota
• TS() : protocols::rbsegment_relax
• tt() : core::pack::rotamer_set , protocols::loops , core::pack::rotamer_set , core::pack::rotamer_set::symmetry , core::pack , core::pack::rotamer_set
• tw() : core::chemical
• type2name() : protocols::frag_picker
• type_map_add() : core::scoring::packstat
• TZ() : protocols::hybridization , protocols::simple_moves::symmetry