- 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 >
• UltraLightResidue() : core::conformation::UltraLightResidue
• unaligned() : protocols::star::Extender
• unassigned() : core::pose::ResidueIndexDescription
• unbind() : protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_moves::ddG
• 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::simple_filters::TaskAwareScoreTypeFilter
• unbound_score() : protocols::dna::DnaInterfacePacker
• unbound_struct() : protocols::optimize_weights::DGBindOptEData
• UnboundRotamersOperation() : core::pack::rotamer_set::UnboundRotamersOperation
• unbuffer_observers() : core::pose::Pose
• UnconstrainedTorsionsMover() : protocols::ligand_docking::UnconstrainedTorsionsMover
• 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
• 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() : protocols::hybridization::FragmentBiasAssigner
• uniform_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• uniform_modeler() : protocols::stepwise::sampler::MC_StepWiseSampler
• uniform_phipsi_from_allowed_rama() : core::scoring::Ramachandran
• 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
• unimplemented_method_error() : core::scoring::constraints::Constraint , core::sequence::ScoringScheme
• union_of_intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
• UnionEdge() : protocols::pockets::UnionEdge
• uniq_refers_to_beta() : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMultiFunc
• unique_id() : protocols::motifs::IRCollection
• unknown_tag() : protocols::topology_broker::TopologyClaimer
• unlock_file() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• unlock_semaphore() : protocols::boinc::Boinc
• unordered_object_pool() : boost::unordered_object_pool< T, UserAllocator >
• unpack() : protocols::rpc::JSON_RPC
• unpaired_valence_electrons_sp() : core::chemical::ElectronConfiguration
• UnrecognizedAtomFeatures() : protocols::features::UnrecognizedAtomFeatures
• UnrecognizedAtomFeaturesCreator() : protocols::features::UnrecognizedAtomFeaturesCreator
• UnrecognizedAtomRecord() : core::pose::UnrecognizedAtomRecord
• unset_consideration() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• unvisit() : core::environment::FoldTreeSketch::Node
• 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::loop_graph::LoopGraph , core::scoring::rna::RNA_CentroidInfo , core::scoring::TMscoreStore , 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_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_sc_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• update_alt_state_exphphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< 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_information_based_on_occupancy() : core::io::pose_from_sfr::PoseFromSFRBuilder
• update_atom_level_domain_map() : protocols::farna::libraries::RNA_ChunkLibrary
• update_atom_level_domain_map_to_move_rosetta_library_chunks() : protocols::farna::movers::RNA_Minimizer
• update_atom_level_domain_map_with_extra_minimize_res() : protocols::farna::movers::RNA_Minimizer
• update_atom_tree() : core::pack::scmin::ResidueAtomTreeCollection
• update_bank() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• update_base_bin_map() : protocols::stepwise::screener::BaseBinMapUpdater
• update_base_residue_types_if_replaced() : core::chemical::ResidueTypeSet
• 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_bg_edge_vector() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• update_bond_connections() : protocols::noesy_assign::ResonanceList
• update_calc_chem_shift_list() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• update_calc_rms_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• update_center() : protocols::pockets::SmallMol
• update_centers() : core::pose::rna::RNA_SuiteName
• 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_com() : protocols::environment::CoMTrackerCM
• update_comm() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• update_commutative() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask_
• update_component_energies() : core::scoring::Energies
• update_conformation() : core::conformation::UltraLightResidue
• update_connections_to_other_residue() : core::conformation::Residue
• update_connections_to_residues() : core::conformation::Residue
• update_contiguous_monomers() : core::conformation::symmetry::SymmetryInfo
• update_coords_from_pose() : protocols::sewing::Assembly
• update_counting_last_PDR() : protocols::simple_moves::BBGaussianMover
• update_covalent_bonds_in_pose() : protocols::denovo_design::components::StructureData
• 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::farna::RNA_FragmentMonteCarlo
• 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::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , 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_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• 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 , protocols::pack_daemon::TopEntitySet
• update_enumeration_shell() : core::scoring::FACTSPoseInfo
• update_fold_tree_at_virtual_sugars() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• update_frag_size() : protocols::farna::RNA_FragmentMonteCarlo
• 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_full_model_info_and_switch_focus_to_new_pose() : protocols::stepwise::monte_carlo::mover::FromScratchMover
• update_full_model_parameters() : protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover
• update_grids() : protocols::qsar::scoring_grid::GridManager
• update_hbevaltype() : core::scoring::hbonds::HBEvalTuple
• update_hydrogens() : protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• update_hydrogens_() : protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• update_indices() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• update_inertia_tensor() : protocols::normalmode::NormalMode
• update_info_on_name3_and_interchangeability_group() : core::chemical::ResidueTypeSet
• update_insert_map() : protocols::farna::movers::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_jobs_list() : protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter
• update_jump_edge() : core::kinematics::FoldTree
• update_jump_points() : core::kinematics::FoldTree
• update_last_controlling_chi() : core::chemical::ResidueType
• update_last_template() : protocols::hybridization::HybridizeProtocol
• update_library_NSGAII() : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::MultiObjective
• update_links() : protocols::moves::PyMolObserver
• update_loop_atoms_and_lengths() : core::scoring::loop_graph::LoopCloseEnergy
• update_loops() : core::scoring::loop_graph::LoopGraph
• update_loops_and_cycles() : core::scoring::loop_graph::LoopGraph
• 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_position() : core::conformation::Conformation
• update_movable_groups_after_deletion() : protocols::denovo_design::components::StructureData
• 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_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_njumps_nres() : core::conformation::symmetry::MirrorSymmetricConformation
• update_nmonomer_jumps() : core::conformation::symmetry::SymmetryInfo
• update_noesy_filter_files() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• update_noncanonical_connection() : core::conformation::Conformation
• update_nres() : core::kinematics::FoldTree
• update_num_jump() : core::kinematics::FoldTree
• update_numbering() : protocols::denovo_design::components::StructureData
• 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_packer_task() : protocols::simple_moves::MSDMover
• update_pct_complete() : protocols::boinc::Boinc
• 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_polymeric_connection() : core::conformation::Conformation
• update_pose_and_cst_set_from_cst_string() : core::pose::full_model_info::FullModelParameters
• update_pose_chains_from_pdb_chains() : core::pose::Pose
• update_pose_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo
• update_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• 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_reference_pose_local() : protocols::stepwise::modeler::align::StepWisePoseAligner
• 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::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::GenBornPotential , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::MultipoleElecPotential , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction , core::scoring::VdWTinkerPotential
• update_residue_identities() : core::conformation::symmetry::MirrorSymmetricConformation
• update_residue_intersection() : core::pack::task::PackerTask_
• update_residue_links() : core::conformation::parametric::ParametersSet
• update_residue_map() : protocols::noesy_assign::ResonanceList
• update_residue_neighbors() : core::pose::Pose , core::scoring::Energies
• update_residue_torsions() : core::conformation::Conformation
• update_residue_type() : core::chemical::ResidueTypeSetCache
• update_residue_union() : core::pack::task::PackerTask_
• update_resonances_from_peak() : protocols::noesy_assign::PeakAssignment
• update_restraint() : protocols::md::CartesianMD
• 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::farna::MultipleDomainMover
• update_rotamer_ids() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• update_rotamer_offsets() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• 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_legacy::Antibody , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• update_sequence_numbering() : core::conformation::Conformation , core::conformation::Residue , core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::AtomTree
• update_state_at_neighbor() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< 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_submotif_info_list() : core::pose::full_model_info::FullModelInfo
• 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_to_move_chunks_with_domain() : protocols::toolbox::AtomLevelDomainMap
• update_to_move_internal_phosphates() : protocols::toolbox::AtomLevelDomainMap
• update_to_move_rosetta_library_chunks() : protocols::farna::libraries::RNA_ChunkLibrary
• update_to_not_move_last_virtual_residue() : protocols::toolbox::AtomLevelDomainMap
• update_to_not_move_virtual_phosphates() : protocols::toolbox::AtomLevelDomainMap
• update_tracking_residue() : protocols::environment::CoMTrackerCM
• 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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• update_virtual_base_if_necessary() : core::scoring::rna::data::RNA_DMS_Potential
• 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
• update_xyz_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• updateChains() : protocols::flexpep_docking::FlexPepDockingFlags
• updateChainsAndAnchors_fromParamsFile() : protocols::flexpep_docking::FlexPepDockingFlags
• UpdateEnzdesHeaderMover() : protocols::enzdes::UpdateEnzdesHeaderMover
• updateFcalc() : core::scoring::cryst::PhenixInterface
• updates_jobs_list() : protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter
• updateSolventMask() : core::scoring::cryst::PhenixInterface
• UpdateSolventMover() : protocols::cryst::UpdateSolventMover
• updateWithDsspAssignment() : protocols::forge::remodel::RemodelData
• UpJumpSRFD() : core::fragment::UpJumpSRFD
• upper() : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
• upper_anchor() : protocols::denovo_design::components::StructureData
• upper_atom_neighbors() : core::scoring::NeighborList
• upper_bound() : core::scoring::func::SOGFunc_Impl , core::scoring::PoissonBoltzmannPotential
• upper_bound_score() : core::scoring::func::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::chemical::ResidueType , core::conformation::Residue
• 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::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• upper_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• upper_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• upper_overlap() : protocols::denovo_design::connection::Connection
• upper_segment() : protocols::denovo_design::components::Segment
• upper_segment_id() : protocols::denovo_design::connection::Connection
• upper_threshold() : protocols::matdes::InterfacePackingFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter
• upper_value() : protocols::helical_bundle::PerturbBundleOptions
• 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::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_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• 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
• url() : core::SVNVersion
• use_abego_bias() : protocols::fldsgn::BluePrintBDR
• use_all_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_backbone_only_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
• use_cartesian() : protocols::loop_modeling::refiners::MinimizationRefiner
• use_chem_shift_data() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• use_coarse_vdw() : protocols::relax::ClassicRelax
• use_coordinate_constraints() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• 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_default_membrane() : protocols::membrane::TransformIntoMembraneMover
• use_default_movemap() : protocols::grafting::AnchoredGraftMover
• use_defaults() : protocols::helical_bundle::PerturbBundleOptions
• use_degrees() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• use_different_build_points_for_each_geometric_constraint() : protocols::match::MatcherTask
• use_distance_cst() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• use_extended_intrares_energy_interface() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy
• use_extended_residue_energy_interface() : core::scoring::methods::OneBodyEnergy
• use_extended_residue_pair_energy_interface() : core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::rna::StackElecEnergy
• use_fast_frame_heuristic() : protocols::magnesium::MgHydrater
• use_fast_heuristic() : protocols::magnesium::MgWaterHydrogenPacker
• use_first_jump_for_submotif() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_fragments() : protocols::loop_modeling::LoopBuilder
• use_fullmer() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild
• use_gen_kirkwood() : core::scoring::methods::EnergyMethodOptions
• use_green_packer() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• use_hb_env_dep() : core::scoring::hbonds::HBondOptions
• use_hb_env_dep_DNA() : core::scoring::hbonds::HBondOptions
• use_hb_env_dep_new() : core::scoring::hbonds::HBondOptions
• use_hierarchical_clustering() : protocols::canonical_sampling::CanonicalSamplingMover
• use_incorrect_deriv() : 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_light_chain_type() : protocols::antibody::AntibodyDatabaseManager
• 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
• use_MPI_sync_pools() : protocols::canonical_sampling::CanonicalSamplingMover
• 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_nblist_of_type() : core::scoring::Energies
• use_nbr() : protocols::ligand_docking::StartFrom
• 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_packer_instead_of_rotamer_trials() : protocols::stepwise::options::StepWiseBasicOptions
• use_pdb_format_HETNAM_records() : core::io::StructFileRepOptions
• use_pdb_info_for_num() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• use_phenix_geo() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_polarization() : core::scoring::methods::EnergyMethodOptions
• use_pose_sequence_as_native() : protocols::toolbox::task_operations::ConservativeDesignOperation
• use_precomputed_library() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• use_prefiltering() : protocols::loophash::LoopHashSampler
• use_preset_task() : protocols::simple_moves::DesignRepackMover
• use_pssm_features() : core::scoring::methods::NMerSVMEnergy
• use_rama_2B() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• use_rama_filter() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• use_random_conformer() : protocols::docking::ConformerSwitchMover
• use_rattle() : protocols::md::CartesianMD
• use_residue_type_theta0() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• use_rt() : protocols::forge::build::ConnectRight
• use_sc_neighbors() : core::select::residue_selector::LayerSelector
• use_sequence_bias() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• use_sidechain_neighbors() : core::select::util::SelectResiduesByLayer
• use_sp2_chi_penalty() : core::scoring::hbonds::HBondOptions
• use_ss_length_screen() : protocols::simple_moves::SmoothFragmentMover
• use_symmetry() : protocols::flxbb::LayerDesignOperation
• use_threeletter() : protocols::helical_bundle::BundleReporterFilter
• user() : protocols::hybridization::FragmentBiasAssigner
• user_chain1() : protocols::denovo_design::connection::Connection
• user_chain2() : protocols::denovo_design::connection::Connection
• user_defined_cycles() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• user_input() : protocols::farna::libraries::ChunkSet
• user_inputted_VDW_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• user_options() : protocols::jd2::archive::Batch
• user_provided_movers_apply_cycle() : protocols::forge::remodel::RemodelLoopMover
• useres1() : core::scoring::motif::ResPairMotifQuery
• useres1_ph() : core::scoring::motif::ResPairMotifQuery
• useres1_po() : core::scoring::motif::ResPairMotifQuery
• useres2() : core::scoring::motif::ResPairMotifQuery
• useres2_ph() : core::scoring::motif::ResPairMotifQuery
• useres2_po() : core::scoring::motif::ResPairMotifQuery
• using_parser() : protocols::jd2::JobDistributor
• USOGFunc() : core::scoring::func::USOGFunc