Rosetta Protocols
2015.09
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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
TMalign_poses() :
protocols::hybridization
to_centroid() :
protocols::medal
,
protocols::star
to_string() :
protocols::moves
,
protocols::stepwise::modeler::rna::phosphate
,
protocols::stepwise::monte_carlo
Tokenize() :
protocols::rbsegment_relax
tokenize() :
protocols::stepwise::modeler::rna
Tokenize() :
protocols
TOL_H_DIRECT() :
protocols::noesy_assign
TOL_H_INDIRECT() :
protocols::noesy_assign
TOL_LABEL() :
protocols::noesy_assign
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
TR() :
protocols::abinitio
,
protocols::antibody::clusters
,
protocols::antibody
tr() :
protocols::boinc
TR() :
protocols::canonical_sampling::mc_convergence_checks
tr() :
protocols::canonical_sampling
TR() :
protocols::cartesian
,
protocols::checkpoint
tr() :
protocols::cluster
TR() :
protocols::coarse_rna
tr() :
protocols::comparative_modeling
TR() :
protocols::constraints_additional
,
protocols::contact_map
,
protocols::cryst
,
protocols::design_opt
,
protocols::dna
,
protocols::electron_density
tr() :
protocols::environment
,
protocols::enzdes::enzutil
TR() :
protocols::enzdes
tr() :
protocols::enzdes
,
protocols::evaluation
TR() :
protocols::farna
tr() :
protocols::farna
TR() :
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::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::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::indexed_structure_store::filters
,
protocols::inputter
,
protocols::jd2::parser
,
protocols::jd2
tr() :
protocols::jd2
TR() :
protocols::jd2
tr() :
protocols::jd2
TR() :
protocols::jd2
tr() :
protocols::jd2
TR() :
protocols::jobdist
tr() :
protocols::jobdist
,
protocols::jumping
,
protocols::ligand_docking::rdf
TR() :
protocols::ligand_docking
,
protocols::loop_build
,
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::medal
,
protocols::motif_grafting::movers
,
protocols::motifs
,
protocols::moves
tr() :
protocols::moves
TR() :
protocols::multistate_design
,
protocols::neighbor
tr() :
protocols::noesy_assign
TR() :
protocols::nonlocal
,
protocols::optimize_weights
,
protocols::outputter
,
protocols::pack_daemon
,
protocols::pb_potential
,
protocols::pmut_scan
,
protocols::pockets
,
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::qsar::scoring_grid
,
protocols::qsar
,
protocols::rbsegment_relax
tr() :
protocols::rbsegment_relax
TR() :
protocols::rbsegment_relax
,
protocols::relax
,
protocols::rigid
tr() :
protocols::rigid
TR() :
protocols::rigid
,
protocols::rosetta_scripts
tr() :
protocols::rotamer_recovery
TR() :
protocols::rpc
,
protocols::scoring::methods
,
protocols::seeded_abinitio
,
protocols::sic_dock::scores
,
protocols::sic_dock
,
protocols::simple_filters
tr() :
protocols::simple_filters
TR() :
protocols::simple_filters
,
protocols::simple_moves::asym_fold_and_dock
,
protocols::simple_moves::bin_transitions
,
protocols::simple_moves::rational_mc
,
protocols::simple_moves::sidechain_moves
,
protocols::simple_moves::symmetry
,
protocols::simple_moves
tr() :
protocols::simple_moves
TR() :
protocols::simple_moves
tr() :
protocols::simple_moves
TR() :
protocols::simple_moves
tr() :
protocols::sparta
,
protocols::ss_prediction
TR() :
protocols::star
,
protocols::stepwise::sampler::rna
,
protocols::symmetric_docking
,
protocols::toolbox::match_enzdes_util
tr() :
protocols::toolbox::match_enzdes_util
TR() :
protocols::toolbox::match_enzdes_util
,
protocols::toolbox::pose_manipulation
,
protocols::toolbox::pose_metric_calculators
tr() :
protocols::toolbox::rotamer_set_operations
TR() :
protocols::toolbox::task_operations
tr() :
protocols::toolbox
TR() :
protocols::topology_broker
,
protocols
,
protocols::trajectory
,
protocols::vip
,
protocols::wum2
,
protocols::wum
TR_call_order() :
protocols::rosetta_scripts
TR_ccd() :
protocols::seeded_abinitio
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_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_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_seg() :
protocols::rbsegment_relax
TR_spec() :
protocols::dna
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::analysis
,
protocols::frag_picker
trAdaptiveScoreHistogram() :
protocols::frag_picker::scores
trAmbigCSScore() :
protocols::frag_picker::scores
trans_omega() :
protocols::forge::methods
trans_pose() :
protocols::matdes
,
protocols::sic_dock
transform_moving_partition_to_origin() :
protocols::toolbox::rigid_body
transform_tracer() :
protocols::ligand_docking
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::farna
trAtomBasedConstraintsScore() :
protocols::frag_picker::scores
trAtomPairConstraintsScore() :
protocols::frag_picker::scores
trBestTotalScoreSelector() :
protocols::frag_picker
TRBM() :
protocols::rigid
,
protocols::topology_broker
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
trFragmentCandidate() :
protocols::frag_picker
trGunnCost() :
protocols::frag_picker::scores
,
protocols::simple_moves
trGunnScore() :
protocols::frag_picker::scores
trim_back_sequence_mapping() :
protocols::loops
trInterbondAngleScore() :
protocols::frag_picker::scores
trJCoupling() :
protocols::frag_picker::scores
trJCouplingIO() :
protocols::frag_picker
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
trSecondarySimilarity() :
protocols::frag_picker::scores
trSecondaryStructurePool() :
protocols::frag_picker::quota
trTalosSSSimilarity() :
protocols::frag_picker::scores
trTmScore() :
protocols::frag_picker::scores
TS() :
protocols::rbsegment_relax
tt() :
protocols::loops
type2name() :
protocols::frag_picker
TZ() :
protocols::hybridization
,
protocols::simple_moves::symmetry
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