Here is a list of all class members with links to the classes they belong to:

- u -

• u : protocols::hybridization::TMalign
• U_ANGLES : protocols::sparta::Sparta::SpartaLib
• U_CO_HB : protocols::sparta::Sparta::SpartaLib
• U_HA_HB : protocols::sparta::Sparta::SpartaLib
• U_HN_HB : protocols::sparta::Sparta::SpartaLib
• U_NAME : protocols::sparta::Sparta::SpartaLib
• U_RING_SHIFTS : protocols::sparta::Sparta::SpartaLib
• ubi_e2c_modeler() : protocols::ub_e2c::ubi_e2c_modeler
• ubr_ : protocols::toolbox::task_operations::JointSequenceOperation
• UDPSocketClient() : protocols::moves::UDPSocketClient
• uem_iter : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• unaligned() : protocols::star::Extender
• unaligned_ : protocols::star::Extender
• UNAMBIG_MED_PROB : protocols::noesy_assign::CrossPeak
• unassigned() : protocols::loops::ResidueIndexDescription
• unassigned_ : protocols::loops::ResidueIndexDescription
• unbind() : protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_moves::ddG
• unbound() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• unbound_ : protocols::optimize_weights::DGBindOptEData , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• unbound_energies_ : protocols::simple_moves::ddG
• unbound_mode_ : protocols::anchored_design::AnchorMoversData
• unbound_per_residue_energies_ : protocols::simple_moves::ddG
• unbound_score() : protocols::dna::DnaInterfacePacker
• unbound_struct() : protocols::optimize_weights::DGBindOptEData
• unbound_total_energy_ : protocols::simple_moves::ddG
• unboundrot_ : protocols::ligand_docking::LigandBaseProtocol , protocols::toolbox::task_operations::ImportUnboundRotamersOperation
• UnconstrainedTorsionsMover() : protocols::ligand_docking::UnconstrainedTorsionsMover
• undefined_coef1_ : protocols::branch_angle::BranchAngleOptimizer
• undefined_coef2_ : protocols::branch_angle::BranchAngleOptimizer
• undefined_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• undercount_sugar_rotamers_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• unfinished_batches() : protocols::jd2::archive::ArchiveManager
• unfinished_blocks_ : protocols::jd2::SingleFileBuffer
• UNFOLDED_ : protocols::noesy_assign::CrossPeak
• unfolded_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• unfolded_energy_emap_vector() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• unfolded_energy_emap_vector_ : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• UnfoldedStateEnergyCalculatorJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor
• UnfoldedStateEnergyCalculatorMover() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• unfreeze() : protocols::rigid::RigidBodyMover
• uniform_backrub_ : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• uniform_modeler() : protocols::stepwise::sampler::MC_StepWiseSampler
• uniform_modeler_ : protocols::stepwise::sampler::MC_StepWiseSampler
• uniform_trans_ : protocols::docking::DockingInitialPerturbation
• uniform_translate_ligand() : protocols::ligand_docking::Translate
• UniformPolicy() : protocols::nonlocal::UniformPolicy
• UniformRigidBodyCM() : protocols::rigid::UniformRigidBodyCM
• UniformRigidBodyMover() : protocols::rigid::UniformRigidBodyMover
• UniformRotationMover() : protocols::simple_moves::UniformRotationMover
• UniformSphereTransMover() : protocols::rigid::UniformSphereTransMover
• UniformTranslationMover() : protocols::simple_moves::UniformTranslationMover
• union_of_intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
• UnionEdge() : protocols::pockets::UnionEdge
• unique_basepairs_ : protocols::dna::DNAParameters
• unique_basestep_starts_ : protocols::dna::DNAParameters
• unique_id() : protocols::motifs::IRCollection
• unique_id_ : protocols::motifs::IRCollection
• unique_match_names_ : protocols::match::output::CloudPDBWriter
• unit_length_ : protocols::forge::remodel::RemodelLoopMover
• unixtime_creation_ : protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase::WU_Header
• unixtime_start_ : protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase::WU_Header
• unixtime_stop_ : protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase::WU_Header
• unknown_pool_name_ : protocols::frag_picker::FragmentCandidate
• unknown_tag() : protocols::topology_broker::TopologyClaimer
• unlock_file() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• unlock_semaphore() : protocols::boinc::Boinc
• unlocks_ : protocols::environment::ProtectedConformation
• unpack() : protocols::rpc::JSON_RPC
• unparsed_identities_ : protocols::toolbox::task_operations::RestrictIdentitiesOperation
• unparsed_residue_ : protocols::seeded_abinitio::CoordinateCst
• unparsed_residues_ : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• unperturbed_angles_ : protocols::kinematic_closure::ClosureProblem
• unperturbed_lengths_ : protocols::kinematic_closure::ClosureProblem
• unperturbed_torsions_ : protocols::kinematic_closure::ClosureProblem
• unperturbed_xyzs_ : protocols::kinematic_closure::ClosureProblem
• UnrecognizedAtomFeatures() : protocols::features::UnrecognizedAtomFeatures
• UnrecognizedAtomFeaturesCreator() : protocols::features::UnrecognizedAtomFeaturesCreator
• unselectable_ : protocols::match::Bool3DGridKinemageWriter
• unweighted_ : protocols::simple_filters::ScoreCutoffFilter
• unweighted_energies_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• unweighted_energies_map_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• up_coll_filt() : protocols::match::output::MatchProcessor
• up_coll_filt_ : protocols::match::output::MatchProcessor
• up_down_filt() : protocols::match::output::MatchProcessor
• up_down_filt_ : protocols::match::output::MatchProcessor
• up_jump_atom_ : protocols::simple_filters::JumpEvaluator
• up_stub_ : protocols::simple_filters::JumpEvaluator
• update() : protocols::canonical_sampling::BiasEnergy , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::MC_StepWiseSampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::trajectory::DbTrajectoryWriter , protocols::viewer::triangle
• update_ : protocols::md::Rattle
• update_a_ik() : protocols::cluster::APCluster
• update_after_boltzmann() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::simple_moves::DOFHistogramRecorder
• update_allow_insert() : protocols::farna::RNA_ChunkLibrary
• update_allow_insert_with_extra_minimize_res() : protocols::farna::RNA_Minimizer
• update_allow_sc_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• update_assignment_list() : protocols::noesy_assign::CrossPeakList
• update_bank() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• update_base_bin_map() : protocols::stepwise::screener::BaseBinMapUpdater
• update_base_stub_list() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• update_base_stub_list_and_check_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• update_base_stub_list_and_check_that_terminal_res_are_unstacked() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• update_boinc_ : protocols::moves::MonteCarlo
• update_bond_connections() : protocols::noesy_assign::ResonanceList
• update_calc_rms_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• update_center() : protocols::pockets::SmallMol
• update_center_after_move_ : protocols::rigid::RigidBodyRandomizeMover
• update_chemshiftscore() : protocols::noesy_assign::CrossPeakList
• update_chemshiftscore_from_peak() : protocols::noesy_assign::PeakAssignment
• update_chunks() : protocols::rigid::RigidBodyMotionMover
• update_com() : protocols::environment::CoMTrackerCM
• update_comm() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• update_counting_last_PDR() : protocols::simple_moves::BBGaussianMover
• update_decoy_compatibility_score() : protocols::noesy_assign::CrossPeakList
• update_denovo_scorefxn_weights() : protocols::farna::RNA_DeNovoProtocol
• update_domain_rot_trans_mag() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• update_energy() : protocols::moves::PyMolMover
• update_energy_ : protocols::moves::PyMolMover
• update_entity_history() : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• update_fcalc_ : protocols::cryst::UpdateSolventMover
• update_fold_tree_at_virtual_sugars() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• update_frag_size() : protocols::farna::RNA_DeNovoProtocol
• update_fragment_library_pointers() : protocols::hybridization::CartesianSampler
• update_full_model_info_and_switch_focus_to_new_pose() : protocols::stepwise::monte_carlo::mover::FromScratchMover
• update_grids() : protocols::qsar::scoring_grid::GridManager
• update_hydrogens() : protocols::simple_moves::oop::OopMover
• update_hydrogens_() : protocols::simple_moves::oop::OopMover
• update_indices() : protocols::fldsgn::topology::BB_Pos
• update_inertia_tensor() : protocols::normalmode::NormalMode
• update_insert_map() : protocols::farna::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• update_internal_energy_sums() : protocols::flexpack::interaction_graph::FlexbbNode
• update_internal_energy_totals() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• update_internal_vectors() : protocols::flexpack::interaction_graph::FlexbbNode
• update_interval() : protocols::moves::PyMolMover
• update_interval_ : protocols::moves::PyMolMover
• update_library_NSGAII() : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::MultiObjective
• update_mask_ : protocols::cryst::UpdateSolventMover
• update_matrix_A() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• update_matrix_A_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• update_matrix_A_all_for_cstyle() : protocols::scoring::methods::pcs2::PcsDataCenter
• update_matrix_A_all_for_svd() : protocols::scoring::methods::pcs2::PcsDataCenter
• update_matrix_A_cstyle() : protocols::scoring::methods::pcs2::PcsDataCenter
• update_max_seq_sep() : protocols::abinitio::abscript::AbscriptStageMover
• update_membrane_ : protocols::moves::PyMolMover
• update_movemap() : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• update_movemap_ : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• update_movemap_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• update_moves() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• update_my_A_matrix() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• update_my_A_matrix_for_cstyle() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• update_my_A_matrix_for_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• update_noesy_filter_files() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• update_offset_data() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• update_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• update_original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• update_packer_task() : protocols::simple_moves::MSDMover
• update_pct_complete() : protocols::boinc::Boinc
• update_pdb_numbering() : protocols::cyclic_peptide::PeptideStubMover
• update_pdb_numbering_ : protocols::cyclic_peptide::PeptideStubMover
• update_pdb_remarks() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• update_pdb_remarks_for_backbone_params() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• update_pdblist_file() : protocols::docking::DockingEnsemble
• update_peak_volumina() : protocols::noesy_assign::CrossPeakList
• update_pose_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• update_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• update_r_ik() : protocols::cluster::APCluster
• update_range() : protocols::optimize_weights::OptEPositionData
• update_ranks() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• update_reference_pose_local() : protocols::stepwise::modeler::align::StepWisePoseAligner
• update_residue_map() : protocols::noesy_assign::ResonanceList
• update_resonances_from_peak() : protocols::noesy_assign::PeakAssignment
• update_restraint() : protocols::md::CartesianMD
• update_rhos_() : protocols::pockets::PlaidFingerprint
• update_rot_trans_mag() : protocols::farna::MultipleDomainMover
• update_rotamer_ids() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• update_rounds_ : protocols::antibody::CDRsMinPackMin
• update_sampler_weights() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• update_segments() : protocols::backrub::BackrubSidechainMover
• update_sequence() : protocols::antibody_legacy::Antibody , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• update_spin_axis_ : protocols::rigid::RigidBodySpinMover
• update_superimpose_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• update_symmetry_score() : protocols::noesy_assign::CrossPeakList
• update_task_and_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
• update_time : protocols::boinc::BoincSharedMemory
• update_tracking_residue() : protocols::environment::CoMTrackerCM
• update_type() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• update_upperdistance_score() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignment
• update_value_from_list() : protocols::optimize_weights::OptEVariableExpression
• update_VDW_screen_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• update_weighted_total() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• update_weights() : protocols::moves::RampingMover
• update_working_moving_suite() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• update_working_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• update_X_Y_Z_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• updateChains() : protocols::flexpep_docking::FlexPepDockingFlags
• updateChainsAndAnchors_fromParamsFile() : protocols::flexpep_docking::FlexPepDockingFlags
• UpdateEnzdesHeaderMover() : protocols::enzdes::UpdateEnzdesHeaderMover
• UpdateSolventMover() : protocols::cryst::UpdateSolventMover
• updateWithDsspAssignment() : protocols::forge::remodel::RemodelData
• upper() : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
• upper_ : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
• upper_anchor_connID_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• upper_angle_ : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• upper_bound : protocols::qsar::ColorGradient
• upper_bound_ : protocols::simple_filters::RangeFilter
• upper_chain() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• upper_chains_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• upper_threshold() : protocols::matdes::InterfacePackingFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter
• upper_threshold_ : protocols::enzdes::LigDSasaFilter , protocols::matdes::InterfacePackingFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• upper_trim_ : protocols::filters::ReplicateFilter
• upper_value() : protocols::helical_bundle::PerturbBundleOptions
• upper_value_ : protocols::helical_bundle::PerturbBundleOptions
• uppers1_ : protocols::sic_dock::LinkerScore
• uppers2_ : protocols::sic_dock::LinkerScore
• upstream_builder() : protocols::match::Matcher
• upstream_builders_ : protocols::match::Matcher
• upstream_chains_ : protocols::analysis::InterfaceAnalyzerMover
• upstream_conf_id() : protocols::match::Hit , protocols::match::upstream_hit
• upstream_conformation_for_hit() : protocols::match::output::UpstreamHitCacher
• upstream_confs_ : protocols::match::output::UpstreamHitCacher
• upstream_downstream_atom_collision_tolerance() : protocols::match::MatcherTask
• upstream_downstream_atom_collision_tolerance_ : protocols::match::MatcherTask
• upstream_downstream_residue_collision_score_cutoff() : protocols::match::MatcherTask
• upstream_downstream_residue_collision_score_cutoff_ : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_atr() : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_atr_ : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_rep() : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_rep_ : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_sol() : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_sol_ : protocols::match::MatcherTask
• upstream_hit() : protocols::match::upstream_hit
• upstream_hits : protocols::match::match_dspos1
• upstream_kin_writer_ : protocols::match::output::WriteKinemageOutputter
• upstream_only() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage
• upstream_only_geom_cst() : protocols::match::MatcherTask
• upstream_only_geom_cst_ : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• upstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• upstream_pose_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::Matcher , protocols::match::MatcherTask
• upstream_pose_build_resids_for_geometric_constraint() : protocols::match::MatcherTask
• upstream_pose_name() : protocols::match::MatcherTask
• upstream_pose_name_ : protocols::match::MatcherTask
• upstream_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• upstream_resids_and_radii_defining_active_site() : protocols::match::MatcherTask
• upstream_resids_and_radii_defining_active_site_ : protocols::match::Matcher , protocols::match::MatcherTask
• upstream_residue_collision_score_cutoff() : protocols::match::MatcherTask
• upstream_residue_collision_score_cutoff_ : protocols::match::MatcherTask
• upstream_residue_collision_tolerance() : protocols::match::MatcherTask
• upstream_residue_collision_tolerance_ : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_atr() : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_atr_ : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_rep() : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_rep_ : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_sol() : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_sol_ : protocols::match::MatcherTask
• upstream_restype_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• upstream_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• upstream_restypes_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• UpstreamCollisionFilter() : protocols::match::output::UpstreamCollisionFilter
• UpstreamDownstreamCollisionFilter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• UpstreamHitCacher() : protocols::match::output::UpstreamHitCacher
• UpstreamHitSets : protocols::match::output::CloudPDBWriter
• UpstreamResTypeGeometry() : protocols::match::upstream::UpstreamResTypeGeometry
• us_ds_chemical_bond_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• us_hitset_end_its_ : protocols::match::output::CloudPDBWriter
• us_hitset_its_ : protocols::match::output::CloudPDBWriter
• use_ : protocols::md::Rattle
• use_abego_ : protocols::fldsgn::filters::SecondaryStructureFilter , protocols::jd2::parser::FragmentReader
• use_abego_bias() : protocols::fldsgn::BluePrintBDR
• use_abego_bias_ : protocols::fldsgn::BluePrintBDR
• use_all_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_all_pivot_res_ : protocols::simple_moves::BBGaussianMover
• use_backbone_only_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_bp_seq_ : protocols::forge::remodel::RemodelMover::instruction_flags
• use_cartesian() : protocols::loop_modeling::refiners::MinimizationRefiner
• use_cartesian_ : protocols::loop_modeling::refiners::MinimizationRefiner
• use_ccd_refine_ : protocols::forge::remodel::RemodelMover::instruction_flags
• use_ccd_trim_ : protocols::forge::remodel::RemodelMover::instruction_flags
• use_cen_score : protocols::flexpep_docking::FlexPepDockingFlags
• use_centroid_ : protocols::analysis::InterfaceAnalyzerMover
• use_chain_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_chem_shift_data_ : protocols::farna::RNA_DeNovoProtocol
• use_cluster_constraints_ : protocols::antibody::design::AntibodySeqDesignMover
• use_coarse_vdw() : protocols::relax::ClassicRelax
• use_constraints_ : protocols::docking::DockingLowResFilter
• use_coordinate_constraints() : protocols::farna::RNA_Minimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• use_coordinate_constraints_ : protocols::farna::RNA_Minimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• use_cstid_list_ : protocols::enzdes::DetectProteinLigandInterface
• use_cstids_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RepackWithoutLigandFilter
• use_csts_ : protocols::antibody::AntibodyModelerProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• use_current_ : protocols::simple_moves::FavorSequenceProfile
• use_current_pose() : protocols::toolbox::task_operations::JointSequenceOperation
• use_current_pose_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_custom_task() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• use_custom_task_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• use_cutpoints() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• use_cutpoints_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• use_debug_pause_ : protocols::viewer::ConformationViewer
• use_default_extend_loops : protocols::LoopRebuild
• use_default_master_ : protocols::match::output::WriteUpstreamHitKinemage
• use_default_mc_ : protocols::relax::ClassicRelax
• use_default_movemap() : protocols::grafting::AnchoredGraftMover
• use_default_movemap_ : protocols::grafting::AnchoredGraftMover
• use_default_pack_full_repack_ : protocols::relax::ClassicRelax
• use_default_pack_rottrial_ : protocols::relax::ClassicRelax
• use_defaults() : protocols::helical_bundle::PerturbBundleOptions
• use_defaults_ : protocols::helical_bundle::PerturbBundleOptions
• use_deterministic_algorithm_ : protocols::antibody::design::AntibodyGraftDesignMover
• use_different_build_points_for_each_geometric_constraint() : protocols::match::MatcherTask
• use_distance_cst() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• use_distance_cst_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• use_disulf_fa_score_ : protocols::forge::remodel::RemodelMover
• use_dynamic_weights_for_sampling_ : protocols::abinitio::IterativeBase
• use_ellipsoidal_randomization_ : protocols::docking::DockingInitialPerturbation
• use_epitope_constraints_ : protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• use_fast_relax_ : protocols::flxbb::FlxbbDesign
• use_fasta_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_file_name_ : protocols::ligand_docking::StartFrom
• use_filter_omega_ : protocols::anchored_design::AnchoredDesignMover
• use_filter_SASA_ : protocols::anchored_design::AnchoredDesignMover
• use_filter_score_ : protocols::anchored_design::AnchoredDesignMover
• use_fold_tree_from_claimer_ : protocols::topology_broker::TopologyBroker
• use_fragments() : protocols::loop_modeling::LoopBuilder
• use_frags_ : protocols::seeded_abinitio::SegmentHybridizer
• use_fullmer() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild
• use_fullmer_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover::instruction_flags
• use_green_packer() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• use_green_packer_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• use_hash_ : protocols::simple_moves::CopyDofMover
• use_hhpot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_hierarchical_clustering() : protocols::canonical_sampling::CanonicalSamplingMover
• use_hierarchical_clustering_ : protocols::canonical_sampling::CanonicalSamplingMover
• use_hspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_icoor_geometry_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• use_increased_vdw_radii_ : protocols::relax::CentroidRelax
• use_input_ : protocols::jd2::AtomTreeDiffJobOutputter
• use_input_for_ref() : protocols::jd2::AtomTreeDiffJobOutputter
• use_input_partners_ : protocols::scoring::Interface
• use_input_sc() : protocols::match::MatcherTask
• use_input_sc_ : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::upstream::ProteinUpstreamBuilder
• use_interface() : protocols::dna::DnaInterfaceMinMover
• use_job_pose() : protocols::topology_broker::TopologyBroker
• use_jobname_ : protocols::analysis::InterfaceAnalyzerMover
• use_jumps_ : protocols::seeded_abinitio::CoordinateCst
• use_late_scoring_for_zeros() : protocols::frag_picker::scores::FragmentScoreManager
• use_legacy_protocol_ : protocols::docking::DockingProtocol
• use_light_chain_type_ : protocols::antibody::design::AntibodyGraftDesignMover
• use_local_distviol_ : protocols::noesy_assign::PeakAssignmentParameters
• use_loops_from_observer_cache() : protocols::loops::loop_mover::LoopMover
• use_loops_from_threading_job() : protocols::topology_broker::RigidChunkClaimer
• use_loose_rep_cutoff_ : protocols::stepwise::screener::PartitionContactScreener
• use_lowest_ : protocols::frag_picker::scores::FragmentScoringMethod
• use_match_rt_ : protocols::forge::remodel::RemodelMover
• use_mean() : protocols::ddg::ddGMover
• use_min() : protocols::ddg::ddGMover
• use_mover_status() : protocols::moves::SequenceMover
• use_mover_status_ : protocols::moves::SequenceMover
• use_MPI_bcast() : protocols::canonical_sampling::CanonicalSamplingMover
• use_MPI_sync_pools() : protocols::canonical_sampling::CanonicalSamplingMover
• use_natro() : protocols::toolbox::task_operations::JointSequenceOperation
• use_natro_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_nobias() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_nobias_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• use_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• use_omega_ : protocols::normalmode::NormalModeMultifunc
• use_only_calpha() : protocols::fldsgn::NcontactsCalculator
• use_only_calpha_ : protocols::fldsgn::NcontactsCalculator
• use_original_ : protocols::flxbb::LayerDesignOperation
• use_original_seq() : protocols::flxbb::LayerDesignOperation
• use_original_seq_ : protocols::flxbb::DesignTask_Layer
• use_original_weights() : protocols::toolbox::pose_metric_calculators::EnergiesData
• use_original_weights_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• use_origseq_for_not_dsgned_layer() : protocols::flxbb::FlxbbDesign
• use_origseq_for_not_dsgned_layer_ : protocols::flxbb::FlxbbDesign
• use_packer_instead_of_rotamer_trials() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• use_packer_instead_of_rotamer_trials_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker
• use_phenix_geo() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_phenix_geo_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_phi_ : protocols::normalmode::NormalMode
• use_poly_val_ : protocols::fldsgn::BluePrintBDR
• use_pose_sequence_as_native() : protocols::antibody::design::ConservativeDesignOperation
• use_precomputed_library() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_precomputed_library_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• use_prefiltering() : protocols::loophash::LoopHashSampler
• use_preset_task() : protocols::simple_moves::DesignRepackMover
• use_preset_task_ : protocols::simple_moves::DesignRepackMover
• use_psi_ : protocols::normalmode::NormalMode
• use_rama_2B() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• use_rama_2b_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• use_random_conformer() : protocols::docking::ConformerSwitchMover
• use_rattle() : protocols::md::CartesianMD
• use_rattle_ : protocols::md::CartesianMD
• use_relative_bfactors_ : protocols::match::BfactorMPM
• use_relevant_residues_as_loop_length_ : protocols::features::LoopAnchorFeatures
• use_resE_ : protocols::simple_filters::ResidueIEFilter
• use_resfile_ : protocols::analysis::InterfaceAnalyzerMover
• use_rt() : protocols::forge::build::ConnectRight
• use_rt_ : protocols::forge::build::ConnectRight
• use_seq_ : protocols::seeded_abinitio::SegmentHybridizer
• use_seqprof_constraints_ : protocols::simple_moves::ConsensusDesignMover
• use_sequence_bias() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• use_sequence_bias_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• use_sidechain_neighbors() : protocols::toolbox::SelectResiduesByLayer
• use_sidechain_neighbors_ : protocols::toolbox::SelectResiduesByLayer
• use_single_residue_to_define_anchor_transfrom_ : protocols::features::LoopAnchorFeatures
• use_soft_rep_ : protocols::ligand_docking::LigandBaseProtocol , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• use_ss_length_screen() : protocols::simple_moves::SmoothFragmentMover
• use_sspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_stored_best_energy : protocols::vip::VIP_Mover
• use_transactions_ : protocols::features::ReportToDB
• use_triangle_inequality_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• use_unbound_for_sequence_profile_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• use_uniform_k_ : protocols::normalmode::NormalMode
• use_value_from_other_helix_ : protocols::helical_bundle::PerturbBundleOptions
• use_variance_archive_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• use_VDW_rep_pose_for_screening_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• used_for_calibration_ : protocols::noesy_assign::DistanceScoreMover
• used_for_searching_ : protocols::frag_picker::CSTalosIO
• used_tags_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• user_csts_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• user_defined_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::docking::DockingProtocol
• user_defined_calc_rms_res_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• user_defined_cycles_ : protocols::farna::RNA_DeNovoProtocol
• user_defined_move_map_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• user_defined_mover_name_ : protocols::simple_moves::GenericMonteCarloMover
• user_defined_name_ : protocols::filters::Filter , protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_filters::DomainInterfaceFilter
• user_input_VDW_bin_checker_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseConnectionSampler
• user_inputted_VDW_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• user_inputted_VDW_screen_pose_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• user_options() : protocols::jd2::archive::Batch
• user_pos_ : protocols::hybridization::CartesianSampler
• user_provided_movers_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• user_provided_movers_apply_cycle() : protocols::forge::remodel::RemodelLoopMover
• user_provided_movers_apply_cycle_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• using_parser() : protocols::jd2::JobDistributor
• using_predefined_moving_rsd_list_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• using_stub_ : protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::VDW_BinScreener
• using_unfolded_energy_term_ : protocols::optimize_weights::IterativeOptEDriver
• utility::SingletonBase< CovalentCompliance > : protocols::noesy_assign::CovalentCompliance
• utility::SingletonBase< EntityElementFactory > : protocols::genetic_algorithm::EntityElementFactory
• utility::SingletonBase< EvaluatorFactory > : protocols::evaluation::EvaluatorFactory
• utility::SingletonBase< GridFactory > : protocols::qsar::scoring_grid::GridFactory
• utility::SingletonBase< InterchainPotential > : protocols::scoring::InterchainPotential
• utility::SingletonBase< JobInputterFactory > : protocols::jd2::JobInputterFactory
• utility::SingletonBase< JobOutputterFactory > : protocols::jd2::JobOutputterFactory
• utility::SingletonBase< LoopMoverFactory > : protocols::loops::LoopMoverFactory
• utility::SingletonBase< LoopRefineInnerCycleFactory > : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• utility::SingletonBase< LoopsDefinerFactory > : protocols::loops::loops_definers::LoopsDefinerFactory
• utility::SingletonBase< MethylNameLibrary > : protocols::noesy_assign::MethylNameLibrary
• utility::SingletonBase< PCS_data_input_manager > : protocols::scoring::methods::pcs::PCS_data_input_manager
• utility::SingletonBase< PcsEnergyParameterManager > : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• utility::SingletonBase< PcsGridSearchParameterManager > : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• utility::SingletonBase< PoseSelectorFactory > : protocols::rosetta_scripts::PoseSelectorFactory
• utility::SingletonBase< RotamerRecoveryFactory > : protocols::rotamer_recovery::RotamerRecoveryFactory
• utility::SingletonBase< StandardDisulfPairingLibrary > : protocols::jumping::StandardDisulfPairingLibrary
• utility::SingletonBase< StandardPairingLibrary > : protocols::jumping::StandardPairingLibrary
• utility::SingletonBase< SymDofMoverSampler > : protocols::matdes::SymDofMoverSampler
• uuid_ : protocols::moves::UDPSocketClient