- 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_opt : protocols::hybridization::TMalign
• U_RING_SHIFTS : protocols::sparta::Sparta::SpartaLib
• ub_ : core::kinematics::TreeVizBuilder , core::scoring::constraints::BoundFunc
• ubr_ : protocols::toolbox::task_operations::JointSequenceOperation
• unaligned_ : protocols::star::Extender
• unassigned_ : protocols::loops::ResidueIndexDescription
• unbound_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::optimize_weights::DGBindOptEData , protocols::protein_interface_design::filters::FilterScanFilter
• unbound_energies_ : protocols::simple_moves::ddG
• unbound_mode_ : protocols::anchored_design::AnchorMoversData
• unbound_per_residue_energies_ : protocols::simple_moves::ddG
• unbound_total_energy_ : protocols::simple_moves::ddG
• unboundrot_ : protocols::ligand_docking::LigandBaseProtocol
• undefined_coef1_ : protocols::branch_angle::BranchAngleOptimizer
• undefined_coef2_ : protocols::branch_angle::BranchAngleOptimizer
• undercount_ribose_rotamers_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• unf_state_ : core::scoring::ScoringManager
• unf_state_potential_ : core::scoring::methods::UnfoldedStateEnergy
• unfinished_blocks_ : protocols::jd2::SingleFileBuffer
• unfolded_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• UNFOLDED_ : protocols::noesy_assign::CrossPeak
• unfolded_energies_type_ : core::scoring::methods::EnergyMethodOptions
• unfolded_energy_ : core::scoring::UnfoldedStatePotential
• unfolded_energy_emap_vector_ : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• unfolded_potential_file_weights_ : core::scoring::UnfoldedStatePotential
• uniform_trans_ : protocols::docking::DockingInitialPerturbation
• uninitialized_energy : core::pack::annealer::MultiCoolAnnealer
• unique_basepairs_ : protocols::dna::DNAParameters
• unique_basestep_starts_ : protocols::dna::DNAParameters
• unique_id_ : protocols::motifs::IRCollection
• unique_match_names_ : protocols::match::output::CloudPDBWriter
• unique_ref_poses_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• unitsurfaceNormalVec : protocols::surface_docking::SurfaceParameters
• unixtime_creation_ : protocols::wum::WorkUnitBase::WU_Header , protocols::wum2::WorkUnit
• unixtime_start_ : protocols::wum::WorkUnitBase::WU_Header , protocols::wum2::WorkUnit
• unixtime_stop_ : protocols::wum::WorkUnitBase::WU_Header , protocols::wum2::WorkUnit
• unknown_pool_name_ : protocols::frag_picker::FragmentCandidate
• unknown_resonances_ : protocols::noesy_assign::CrossPeak
• unparsed_residue_ : protocols::seeded_abinitio::CoordinateCst
• unparsed_residues_ : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• unrecognized_atoms_ : core::pose::PDBInfo
• unrecognized_res_num2name_ : core::pose::PDBInfo
• unrecognized_res_size_ : core::pose::PDBInfo
• 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::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor
• unweighted_score_coeff : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• up_coll_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
• up_to_date_ : core::io::raw_data::DisulfideFile
• update_boinc_ : protocols::moves::MonteCarlo
• update_center_after_move_ : protocols::rigid::RigidBodyRandomizeMover
• update_energy_ : protocols::moves::PyMolMover
• update_interval_ : protocols::moves::PyMolMover
• update_movemap_ : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• update_rounds_ : protocols::antibody2::CDRsMinPackMin
• update_spin_axis_ : protocols::rigid::RigidBodySpinMover
• update_time : protocols::boinc::BoincSharedMemory
• upper : core::chemical::sdf::BondData
• upper_ : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
• upper_angle_ : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• upper_base_state_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• upper_bound : protocols::qsar::ColorGradient
• upper_bound_ : core::scoring::constraints::SOGFunc_Impl , core::scoring::nv::NVscore , core::scoring::PoissonBoltzmannPotential , protocols::simple_filters::RangeFilter
• upper_bound_dy_ : core::scoring::constraints::SplineFunc
• upper_bound_squared_ : core::scoring::nv::NVscore
• upper_bound_x_ : core::scoring::constraints::SplineFunc
• upper_bound_y_ : core::scoring::constraints::SplineFunc
• upper_chains_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• upper_connect_angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• upper_connect_id_ : core::chemical::ResidueType
• upper_edges_ : core::graph::UEVertex< V, E >
• upper_lower_ : core::chemical::SetPolymerConnectAtom
• upper_nblist_ : core::scoring::NeighborList
• upper_range_dof_jumps1_ : core::conformation::symmetry::SymDof
• upper_range_dof_jumps2_ : core::conformation::symmetry::SymDof
• upper_threshold_ : protocols::enzdes::LigDSasaFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter
• upper_trim_ : protocols::filters::ReplicateFilter
• upper_vertex_ : core::graph::UEEdge< V, E >
• upper_vertex_index_ : core::graph::UEEdge< V, E >
• uppers1_ : protocols::sic_dock::LinkerScore
• uppers2_ : protocols::sic_dock::LinkerScore
• upstream_builders_ : protocols::match::Matcher
• upstream_chains_ : protocols::analysis::InterfaceAnalyzerMover
• upstream_confs_ : protocols::match::output::UpstreamHitCacher
• upstream_downstream_atom_collision_tolerance_ : 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_rep_ : protocols::match::MatcherTask
• upstream_downstream_residue_collision_Wfa_sol_ : protocols::match::MatcherTask
• upstream_hits : protocols::match::match_dspos1
• upstream_kin_writer_ : protocols::match::output::WriteKinemageOutputter
• upstream_only_geom_cst_ : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• upstream_pose_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::Matcher , protocols::match::MatcherTask
• upstream_pose_name_ : 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_tolerance_ : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_atr_ : protocols::match::MatcherTask
• upstream_residue_collision_Wfa_rep_ : 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_stub_atoms_ : core::fragment::DownJumpSRFD
• ur_conn_ : core::conformation::PseudoBond
• us_ds_chemical_bond_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• us_hitset_end_its_ : protocols::match::output::CloudPDBWriter
• us_hitset_its_ : protocols::match::output::CloudPDBWriter
• use_2prime_OH_potential_ : core::scoring::rna::RNA_TorsionPotential
• use_abego_ : protocols::fldsgn::filters::SecondaryStructureFilter , protocols::jd2::parser::FragmentReader
• use_abego_bias_ : protocols::fldsgn::BluePrintBDR
• use_bp_seq_ : protocols::forge::remodel::RemodelMover::instruction_flags
• 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_charge : core::scoring::APBSConfig::I_PARAM
• use_chem_shift_data_ : protocols::rna::RNA_DeNovoProtocol
• use_constraints_ : protocols::docking::DockingLowResFilter
• use_coordinate_constraints_ : protocols::rna::RNA_Minimizer
• use_cstid_list_ : protocols::enzdes::DetectProteinLigandInterface
• use_cstids_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RepackWithoutLigandFilter
• use_csts_ : protocols::antibody2::AntibodyModelerProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• use_current_ : protocols::simple_moves::FavorSequenceProfile
• use_current_pose_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_custom_task_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• 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::GraftMoverBase
• use_default_pack_full_repack_ : protocols::relax::ClassicRelax
• use_default_pack_rottrial_ : protocols::relax::ClassicRelax
• use_diel : core::scoring::APBSConfig::I_PARAM
• use_distance_cst_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• use_dynamic_weights_for_sampling_ : protocols::abinitio::IterativeBase
• use_fast_relax_ : protocols::flxbb::FlxbbDesign
• use_fasta_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_filter_omega_ : protocols::anchored_design::AnchoredDesignMover
• use_filter_SASA_ : protocols::anchored_design::AnchoredDesignMover
• use_filter_score_ : protocols::anchored_design::AnchoredDesignMover
• use_frags_ : protocols::seeded_abinitio::SegmentHybridizer
• use_fullmer_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::forge::components::VarLengthBuild
• use_green_packer_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• use_hb_env_dep_ : core::scoring::hbonds::HBondOptions
• use_hb_env_dep_DNA_ : core::scoring::hbonds::HBondOptions
• use_hhpot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_hierarchical_clustering_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• use_hspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_icoor_geometry_ : protocols::swa::protein::StepWiseProteinLoopBridger
• use_incorrect_deriv_ : core::scoring::hbonds::HBondOptions
• use_increased_vdw_radii_ : protocols::relax::CentroidRelax
• use_input_ : protocols::jd2::AtomTreeDiffJobOutputter
• use_input_partners_ : protocols::scoring::Interface
• use_input_sc_ : protocols::match::Matcher , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::MatcherTask
• use_intra_dna_cp_crossover_4_ : core::scoring::methods::LK_BallEnergy
• use_jobname_ : protocols::analysis::InterfaceAnalyzerMover
• use_jumps_ : protocols::seeded_abinitio::CoordinateCst
• use_kappa : core::scoring::APBSConfig::I_PARAM
• use_legacy_protocol_ : protocols::docking::DockingProtocol
• use_local_distviol_ : protocols::noesy_assign::PeakAssignmentParameters
• use_log_score_ : core::scoring::constraints::GaussianFunc
• use_lowest_ : protocols::frag_picker::scores::FragmentScoringMethod
• use_mover_status_ : protocols::moves::SequenceMover
• use_multicool_annealer_ : core::pack::task::operation::OptH
• use_natro_ : protocols::toolbox::task_operations::JointSequenceOperation
• use_nblist_ : core::optimization::MinimizerOptions , core::scoring::Energies
• use_nblist_auto_update_ : core::scoring::Energies
• use_ncaa_rotlib_ : core::chemical::ResidueType
• use_new_potential_ : core::scoring::rna::RNA_TorsionPotential
• use_nobias_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• use_only_calpha_ : protocols::fldsgn::NcontactsCalculator
• use_original_ : protocols::flxbb::LayerDesignOperation
• use_original_seq_ : protocols::flxbb::DesignTask_Layer
• use_original_weights_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• use_origseq_for_not_dsgned_layer_ : protocols::flxbb::FlxbbDesign
• use_packer_instead_of_rotamer_trials_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• use_phenix_geo_ : protocols::rna::RNA_HelixAssembler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• use_phenix_sugar_close_ : core::scoring::rna::RNA_SugarCloseEnergy
• use_phipsi_dep_ : core::scoring::OmegaTether
• use_poly_val_ : protocols::fldsgn::BluePrintBDR
• use_pot : core::scoring::APBSConfig::I_PARAM
• use_predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• use_preset_task_ : protocols::simple_moves::DesignRepackMover
• 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_residue_type_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParamSet
• use_rt_ : protocols::forge::build::ConnectRight
• use_seq_ : protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SegmentHybridizer
• use_seqprof_constraints_ : protocols::simple_moves::ConsensusDesignMover
• use_sequence_bias_ : protocols::forge::components::BDR , protocols::fldsgn::BluePrintBDR
• use_sequence_profiles_ : protocols::protein_interface_design::movers::Splice
• use_single_residue_to_define_anchor_transfrom_ : protocols::features::LoopAnchorFeatures
• use_soft_rep_ : protocols::ligand_docking::LigandBaseProtocol
• use_sp2_chi_penalty_ : core::scoring::hbonds::HBondOptions
• use_sspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_symmetry_ : core::conformation::symmetry::SymmetryInfo
• use_transactions_ : protocols::features::ReportToDB
• use_triangle_inequality_ : protocols::swa::rna::StepWiseRNA_Clusterer
• use_unbound_for_sequence_profile_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• use_variance_archive_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• use_VDW_rep_pose_for_screening_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• used_for_calibration_ : protocols::noesy_assign::DistanceScoreMover
• used_for_searching_ : protocols::frag_picker::CSTalosIO
• used_tags_ : protocols::jobdist::PlainSilentFileJobDistributor , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainRawJobDistributor
• user_defined_ : protocols::antibody2::H3RefineCCD , protocols::antibody2::ModelCDRH3 , protocols::antibody2::H3PerturbCCD , protocols::docking::DockingProtocol , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::H3CterInsert , protocols::antibody2::RefineBetaBarrel , protocols::antibody2::LHRepulsiveRampLegacy
• user_defined_cycles_ : protocols::rna::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::protein_interface_design::movers::PlaceStubMover , protocols::filters::Filter
• user_input_VDW_bin_screener_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_Minimizer
• user_inputted_VDW_screen_pose_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• user_pos_ : protocols::hybridization::CartesianSampler
• user_provided_movers_ : protocols::forge::remodel::RemodelLoopMover , protocols::forge::components::VarLengthBuild
• user_provided_movers_apply_cycle_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• using_unfolded_energy_term_ : protocols::optimize_weights::IterativeOptEDriver
• uuid_ : protocols::moves::UDPSocketClient