- u -

• ub() : core::scoring::constraints::BoundFunc
• ubi_e2c_modeler() : protocols::ub_e2c::ubi_e2c_modeler
• UDPSocketClient() : protocols::moves::UDPSocketClient
• UEEdge() : core::graph::UEEdge< V, E >
• UEVertex() : core::graph::UEVertex< V, E >
• unaligned() : protocols::star::Extender
• unassigned() : protocols::loops::ResidueIndexDescription
• unbind() : protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter
• unblock_signals() : core::conformation::Conformation
• unbound() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::protein_interface_design::filters::FilterScanFilter
• unbound_score() : protocols::dna::DnaInterfacePacker
• unbound_struct() : protocols::optimize_weights::DGBindOptEData
• UnboundRotamersOperation() : core::pack::rotamer_set::UnboundRotamersOperation
• UnconstrainedTorsionsMover() : protocols::ligand_docking::UnconstrainedTorsionsMover
• undefined_positions() : protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• unfinished_batches() : protocols::jd2::archive::ArchiveManager
• unfolded_energies_type() : core::scoring::methods::EnergyMethodOptions
• unfolded_energy_emap_vector() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• UnfoldedStateEnergy() : core::scoring::methods::UnfoldedStateEnergy
• UnfoldedStateEnergyCalculatorJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor
• UnfoldedStateEnergyCalculatorMover() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• UnfoldedStatePotential() : core::scoring::UnfoldedStatePotential
• unfreeze() : protocols::rigid::RigidBodyMover
• ungapped_length() : core::sequence::Sequence
• ungapped_sequence() : core::sequence::Sequence
• uniform_translate_ligand() : protocols::ligand_docking::Translate
• UniformPolicy() : protocols::nonlocal::UniformPolicy
• UniformSphereTransMover() : protocols::rigid::UniformSphereTransMover
• unimplemented_method_error() : core::scoring::constraints::Constraint , core::sequence::ScoringScheme
• union_of_intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
• unique_id() : protocols::motifs::IRCollection
• unknown_tag() : protocols::topology_broker::TopologyClaimer
• unlock_semaphore() : protocols::boinc::Boinc
• unordered_object_pool() : boost::unordered_object_pool< T, UserAllocator >
• UnrecognizedAtomFeatures() : protocols::features::UnrecognizedAtomFeatures
• UnrecognizedAtomFeaturesCreator() : protocols::features::UnrecognizedAtomFeaturesCreator
• UnrecognizedAtomRecord() : core::pose::UnrecognizedAtomRecord
• up_coll_filt() : protocols::match::output::MatchProcessor
• up_down_filt() : protocols::match::output::MatchProcessor
• update() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::rna::RNA_CentroidInfo , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::toolbox::GreedyKCenter , protocols::viewer::triangle
• update_a_ik() : protocols::cluster::APCluster
• update_actcoord() : core::chemical::ResidueType , core::conformation::Conformation , core::conformation::Residue , core::pose::Pose
• update_actcoords() : core::conformation::Conformation , core::pose::Pose
• update_active_enmeths_for_residue() : core::scoring::MinimizationNode
• update_after_boltzmann() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::simple_moves::DOFHistogramRecorder
• update_allow_insert_with_extra_minimize_res() : protocols::rna::RNA_Minimizer
• update_allow_sc_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• update_alt_state_exphphobes() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• update_alternate_one_body_energy() : core::pack::interaction_graph::SimpleNode
• update_assignment_list() : protocols::noesy_assign::CrossPeakList
• update_atom_ids_from_atom_pointer() : core::kinematics::AtomTree
• update_atom_tree() : core::pack::scmin::ResidueAtomTreeCollection
• Update_base_stub_list() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• Update_base_stub_list_and_Check_centroid_interaction() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• Update_base_stub_list_and_Check_that_terminal_res_are_unstacked() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• update_bg_edge_vector() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• update_calc_chem_shift_list() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• update_chemshiftscore() : protocols::noesy_assign::CrossPeakList
• update_chemshiftscore_from_peak() : protocols::noesy_assign::PeakAssignment
• update_child_torsions() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• update_chunks() : protocols::rigid::RigidBodyMotionMover
• update_comm() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• update_commutative() : core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• update_component_energies() : core::scoring::Energies
• update_connections_to_residues() : core::conformation::Residue
• update_current_energy() : core::pack::interaction_graph::SimpleEdge
• update_current_one_body_energy() : core::pack::interaction_graph::SimpleNode
• update_cutpoints() : core::kinematics::FoldTree
• update_decoy_compatibility_score() : protocols::noesy_assign::CrossPeakList
• update_denovo_scorefxn_weights() : protocols::rna::RNA_DeNovoProtocol
• update_derived_data() : core::chemical::ResidueType
• update_derived_rna_data() : core::chemical::rna::RNA_ResidueType
• update_disjoint_sets_using_cache() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• update_domain_map() : core::kinematics::tree::Atom_ , core::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::tree::Atom
• update_domain_rot_trans_mag() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• update_domainmap_for_lr_energy_container() : core::scoring::Energies
• update_edge_label() : core::kinematics::FoldTree
• update_edge_labels() : core::kinematics::FoldTree
• update_edge_vector() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• update_energies_after_passive_change() : core::pack::interaction_graph::SimpleNode
• update_energy() : protocols::moves::PyMolMover
• update_entity_history() : protocols::pack_daemon::MultistateFitnessFunction
• update_frag_size() : protocols::rna::RNA_DeNovoProtocol
• update_fragment_library_pointers() : protocols::hybridization::CartesianSampler
• update_from_momento() : core::pack::scmin::ResidueAtomTreeCollection
• update_from_pose() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• update_from_wide_nblist() : core::scoring::NeighborList
• update_grids() : protocols::qsar::scoring_grid::GridManager
• update_hbevaltype() : core::scoring::hbonds::HBEvalTuple
• update_hydrogens() : protocols::simple_moves::oop::OopMover
• update_hydrogens_() : protocols::simple_moves::oop::OopMover
• update_indices() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• update_insert_map() : protocols::rna::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• update_internal_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• update_internal_energy_sums() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• update_internal_energy_totals() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• update_internal_energy_totals_hpatch() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• update_internal_energy_totals_surface() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• update_internal_vectors() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• update_intersection() : core::pack::task::ResidueLevelTask_
• update_interval() : protocols::moves::PyMolMover
• update_intrares_energy_status() : core::scoring::ScoreFunction
• update_jump_edge() : core::kinematics::FoldTree
• update_jump_points() : core::kinematics::FoldTree
• update_last_controlling_chi() : core::chemical::ResidueType
• update_matrix_A() : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• update_matrix_A_all() : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• 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_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
• update_my_A_matrix_for_cstyle() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• update_my_A_matrix_for_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• update_n_to_be_packed() : core::pack::task::PackerTask_
• update_neighbor_links() : core::scoring::Energies , core::scoring::symmetry::SymmetricEnergies
• update_neighbor_mass_sum() : core::scoring::TenANeighborNode
• update_nmonomer_jumps() : core::conformation::symmetry::SymmetryInfo
• update_noesy_filter_files() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• update_nres() : core::kinematics::FoldTree
• update_num_jump() : core::kinematics::FoldTree
• update_offset_data() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• update_one_body_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::PDNode
• update_one_body_energy() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• update_orbital_coords() : core::conformation::Conformation , core::conformation::Residue , core::pose::Pose
• update_original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• update_pct_complete() : protocols::boinc::Boinc
• 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_polymeric_connection() : core::conformation::Conformation
• update_pose_chains_from_pdb_chains() : core::pose::Pose
• update_pose_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• Update_pose_data_list() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• update_proposed_energy() : core::pack::interaction_graph::SimpleEdge
• update_r_ik() : protocols::cluster::APCluster
• update_range() : protocols::optimize_weights::OptEPositionData
• update_ranks() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• update_recent_history() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• update_residue() : core::pack::scmin::ResidueAtomTreeCollection
• update_residue_commutative() : core::pack::task::PackerTask_
• update_residue_connection_mapping() : core::chemical::ResidueType
• update_residue_coordinates() : core::conformation::Conformation
• update_residue_for_packing() : core::scoring::electron_density::PattersonCorrEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::GenBornPotential , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::PairEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction
• update_residue_intersection() : core::pack::task::PackerTask_
• update_residue_map() : protocols::noesy_assign::ResonanceList
• update_residue_maps() : core::chemical::ResidueTypeSet
• update_residue_neighbors() : core::pose::Pose , core::scoring::Energies
• update_residue_torsions() : core::conformation::Conformation
• update_residue_union() : core::pack::task::PackerTask_
• update_resonances_from_peak() : protocols::noesy_assign::PeakAssignment
• update_rhos_() : protocols::pockets::PlaidFingerprint
• update_rna_base_base_interactions() : core::scoring::rna::RNA_LowResolutionPotential
• update_rna_base_pair_list() : core::scoring::rna::RNA_LowResolutionPotential
• update_rna_centroid_info() : core::scoring::rna::RNA_LowResolutionPotential
• update_rot_trans_mag() : protocols::rna::MultipleDomainMover
• update_rotamer_offsets() : core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• update_sampler_weights() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• update_score() : core::io::silent::SilentStruct
• update_score_multiply_factor() : core::conformation::symmetry::SymmetryInfo
• update_segments() : protocols::backrub::BackrubSidechainMover
• update_sequence() : protocols::antibody::Antibody , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• update_sequence_numbering() : core::conformation::Conformation , core::conformation::Residue , core::id::AtomID_Map< T > , core::kinematics::AtomTree
• update_state_at_neighbor() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• update_state_for_neighbors_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G >
• update_state_for_substitution() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• update_stub() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• update_symmetry_score() : protocols::noesy_assign::CrossPeakList
• update_task_and_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
• update_to_next_rotamer() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• update_type() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• update_union() : core::pack::task::ResidueLevelTask_
• update_upperdistance_score() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignment
• update_value_from_list() : protocols::optimize_weights::OptEVariableExpression
• update_VDW_screen_bin() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• update_weighted_total() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• update_weights() : protocols::moves::RampingMover
• update_working_moving_suite() : protocols::swa::rna::StepWiseRNA_JobParameters
• update_working_sequence() : protocols::swa::rna::StepWiseRNA_JobParameters
• update_X_Y_Z_all() : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• update_xyz_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::kinematics::tree::BondedAtom
• updateCachedDensity() : core::scoring::electron_density::ElectronDensity
• updateChains() : protocols::flexpep_docking::FlexPepDockingFlags
• updateChainsAndAnchors_fromParamsFile() : protocols::flexpep_docking::FlexPepDockingFlags
• updateWithDsspAssignment() : protocols::forge::remodel::RemodelData
• UpJumpSRFD() : core::fragment::UpJumpSRFD
• upper() : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
• upper_atom_neighbors() : core::scoring::NeighborList
• upper_bound() : core::scoring::constraints::SOGFunc_Impl , core::scoring::PoissonBoltzmannPotential , core::scoring::constraints::SOGFunc_Impl
• upper_bound_score() : core::scoring::constraints::SOGFunc_Impl
• upper_chain() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• upper_connect() : core::chemical::ResidueType , core::conformation::Residue
• upper_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• upper_connect_atom() : core::conformation::Residue , core::chemical::ResidueType
• upper_connect_id() : core::chemical::ResidueType
• upper_edge_list_begin() : core::graph::Node , core::graph::UEVertex< V, E >
• upper_edge_list_end() : core::graph::Node , core::graph::UEVertex< V, E >
• upper_neighbor_id() : core::scoring::ResidueNeighborIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::constraints::CstResNeighbConstIterator
• upper_neighbor_iterator_begin() : core::scoring::DenseEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::constraints::CstEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• upper_neighbor_iterator_end() : core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::PeptideBondedEnergyContainer , core::scoring::LREnergyContainer
• upper_threshold() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• upper_vertex() : core::graph::UEEdge< V, E >
• UpperEdgeGraph() : core::graph::UpperEdgeGraph< V, E >
• upstream_atom() : core::kinematics::Edge , core::kinematics::FoldTree
• upstream_builder() : protocols::match::Matcher
• upstream_combine() : core::id::SequenceMapping
• upstream_conf_id() : protocols::match::Hit , protocols::match::upstream_hit
• upstream_conformation_for_hit() : 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_hit() : protocols::match::upstream_hit
• upstream_jump_residue() : core::kinematics::FoldTree
• upstream_jump_stub() : core::conformation::Conformation
• upstream_only() : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• upstream_only_geom_cst() : protocols::match::MatcherTask
• upstream_pose() : protocols::match::MatcherTask , protocols::match::Matcher
• upstream_pose_build_resids_for_geometric_constraint() : 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_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_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• UpstreamCollisionFilter() : protocols::match::output::UpstreamCollisionFilter
• UpstreamDownstreamCollisionFilter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• UpstreamHitCacher() : protocols::match::output::UpstreamHitCacher
• UpstreamResTypeGeometry() : protocols::match::upstream::UpstreamResTypeGeometry
• ur() : core::conformation::PseudoBond
• ur_conn_id() : core::conformation::PseudoBond
• ur_resconnid() : core::conformation::PseudoBond
• use_abego_bias() : protocols::fldsgn::BluePrintBDR
• use_all_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_backbone_only_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_coarse_vdw() : protocols::relax::ClassicRelax
• use_coordinate_constraints() : protocols::rna::RNA_Minimizer
• use_current_pose() : protocols::toolbox::task_operations::JointSequenceOperation
• use_custom_task() : protocols::simple_moves::ddG , protocols::simple_filters::DdgFilter
• use_cutpoints() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::CloseFold
• use_different_build_points_for_each_geometric_constraint() : protocols::match::MatcherTask
• use_extended_intrares_energy_interface() : core::scoring::methods::TwoBodyEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• use_extended_residue_energy_interface() : core::scoring::methods::OneBodyEnergy
• use_extended_residue_pair_energy_interface() : core::scoring::hackelec::RNAHackElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::constraints::ConstraintsEnergy
• use_fullmer() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild , protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• use_hb_env_dep() : core::scoring::hbonds::HBondOptions
• use_hb_env_dep_DNA() : core::scoring::hbonds::HBondOptions
• use_hierarchical_clustering() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• use_incorrect_deriv() : core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondDatabase
• use_input_for_ref() : protocols::jd2::AtomTreeDiffJobOutputter
• use_input_sc() : protocols::match::MatcherTask
• use_interface() : protocols::dna::DnaInterfaceMinMover
• use_job_pose() : protocols::topology_broker::TopologyBroker
• use_late_scoring_for_zeros() : protocols::frag_picker::scores::FragmentScoreManager
• use_loops_from_observer_cache() : protocols::loops::loop_mover::LoopMover
• use_loops_from_threading_job() : protocols::topology_broker::RigidChunkClaimer
• use_mean() : protocols::ddg::ddGMover
• use_min() : protocols::ddg::ddGMover
• use_mover_status() : protocols::moves::SequenceMover
• use_MPI_bcast() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• use_MPI_sync_pools() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• use_multicool_annealer() : core::pack::task::operation::OptH
• use_natro() : protocols::toolbox::task_operations::JointSequenceOperation
• use_nblist() : core::optimization::MinimizerOptions , core::scoring::Energies , core::optimization::MinimizerOptions
• use_nblist_auto_update() : core::scoring::Energies
• use_nobias() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• use_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• use_only_calpha() : protocols::fldsgn::NcontactsCalculator
• use_orientation_dep_rna_ch_o_bonds() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• use_original_seq() : protocols::flxbb::LayerDesignOperation
• use_original_weights() : protocols::toolbox::pose_metric_calculators::EnergiesData
• use_origseq_for_not_dsgned_layer() : protocols::flxbb::FlxbbDesign
• use_phenix_geo() : protocols::rna::RNA_HelixAssembler
• use_prefiltering() : protocols::loophash::LoopHashSampler
• use_preset_task() : protocols::simple_moves::DesignRepackMover
• use_random_conformer() : protocols::docking::ConformerSwitchMover
• use_residue_type_theta0() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• use_rt() : protocols::forge::build::ConnectRight
• use_sequence_bias() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::fldsgn::BluePrintBDR
• use_sp2_chi_penalty() : core::scoring::hbonds::HBondOptions
• use_ss_length_screen() : protocols::simple_moves::SmoothFragmentMover
• use_tracer() : protocols::analysis::InterfaceAnalyzerMover
• user_inputted_VDW_screen_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• user_options() : protocols::jd2::archive::Batch
• user_provided_movers_apply_cycle() : protocols::forge::remodel::RemodelLoopMover
• USOGFunc() : core::scoring::constraints::USOGFunc