- 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
ubr_ : protocols::toolbox::task_operations::JointSequenceOperation
unaligned_ : protocols::star::Extender
unassigned_ : protocols::loops::ResidueIndexDescription
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_total_energy_ : protocols::simple_moves::ddG
unboundrot_ : protocols::ligand_docking::LigandBaseProtocol , protocols::toolbox::task_operations::ImportUnboundRotamersOperation
undefined_coef1_ : protocols::branch_angle::BranchAngleOptimizer
undefined_coef2_ : protocols::branch_angle::BranchAngleOptimizer
undercount_sugar_rotamers_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
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
uniform_backrub_ : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
uniform_modeler_ : protocols::stepwise::sampler::MC_StepWiseSampler
uniform_trans_ : protocols::docking::DockingInitialPerturbation
unique_basepairs_ : protocols::dna::DNAParameters
unique_basestep_starts_ : protocols::dna::DNAParameters
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
unlocks_ : protocols::environment::ProtectedConformation
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
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_down_filt_ : protocols::match::output::MatchProcessor
up_jump_atom_ : protocols::simple_filters::JumpEvaluator
up_stub_ : protocols::simple_filters::JumpEvaluator
update_ : protocols::md::Rattle
update_boinc_ : protocols::moves::MonteCarlo
update_center_after_move_ : protocols::rigid::RigidBodyRandomizeMover
update_energy_ : protocols::moves::PyMolMover
update_fcalc_ : protocols::cryst::UpdateSolventMover
update_interval_ : protocols::moves::PyMolMover
update_mask_ : protocols::cryst::UpdateSolventMover
update_membrane_ : protocols::moves::PyMolMover
update_movemap_ : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
update_pdb_numbering_ : protocols::cyclic_peptide::PeptideStubMover
update_rounds_ : protocols::antibody::CDRsMinPackMin
update_spin_axis_ : protocols::rigid::RigidBodySpinMover
update_time : protocols::boinc::BoincSharedMemory
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_chains_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
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
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
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_all_pivot_res_ : protocols::simple_moves::BBGaussianMover
use_bp_seq_ : protocols::forge::remodel::RemodelMover::instruction_flags
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_constraints_ : protocols::docking::DockingLowResFilter
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_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::AnchoredGraftMover
use_default_pack_full_repack_ : protocols::relax::ClassicRelax
use_default_pack_rottrial_ : protocols::relax::ClassicRelax
use_defaults_ : protocols::helical_bundle::PerturbBundleOptions
use_deterministic_algorithm_ : protocols::antibody::design::AntibodyGraftDesignMover
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_frags_ : protocols::seeded_abinitio::SegmentHybridizer
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 , 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_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_partners_ : protocols::scoring::Interface
use_input_sc_ : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::upstream::ProteinUpstreamBuilder
use_jobname_ : protocols::analysis::InterfaceAnalyzerMover
use_jumps_ : protocols::seeded_abinitio::CoordinateCst
use_legacy_protocol_ : protocols::docking::DockingProtocol
use_light_chain_type_ : protocols::antibody::design::AntibodyGraftDesignMover
use_local_distviol_ : protocols::noesy_assign::PeakAssignmentParameters
use_loose_rep_cutoff_ : protocols::stepwise::screener::PartitionContactScreener
use_lowest_ : protocols::frag_picker::scores::FragmentScoringMethod
use_match_rt_ : protocols::forge::remodel::RemodelMover
use_mover_status_ : protocols::moves::SequenceMover
use_natro_ : protocols::toolbox::task_operations::JointSequenceOperation
use_nobias_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
use_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
use_omega_ : protocols::normalmode::NormalModeMultifunc
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::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker
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_precomputed_library_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
use_predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
use_preset_task_ : protocols::simple_moves::DesignRepackMover
use_psi_ : protocols::normalmode::NormalMode
use_rama_2b_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
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_seq_ : protocols::seeded_abinitio::SegmentHybridizer
use_seqprof_constraints_ : protocols::simple_moves::ConsensusDesignMover
use_sequence_bias_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
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_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_pos_ : protocols::hybridization::CartesianSampler
user_provided_movers_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
user_provided_movers_apply_cycle_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
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
uuid_ : protocols::moves::UDPSocketClient