- u -

• ub() : core::scoring::constraints::BoundFunc
• UEEdge() : core::graph::UEEdge< V, E >
• UEVertex() : core::graph::UEVertex< V, E >
• UltraLightResidue() : core::conformation::UltraLightResidue
• unblock_signals() : core::conformation::Conformation
• UnboundRotamersOperation() : core::pack::rotamer_set::UnboundRotamersOperation
• unfolded_energies_type() : core::scoring::methods::EnergyMethodOptions
• UnfoldedStateEnergy() : core::scoring::methods::UnfoldedStateEnergy
• UnfoldedStatePotential() : core::scoring::UnfoldedStatePotential
• ungapped_length() : core::sequence::Sequence
• ungapped_sequence() : core::sequence::Sequence
• uniform_phipsi_from_allowed_rama() : core::scoring::Ramachandran
• unimplemented_method_error() : core::scoring::constraints::Constraint , core::sequence::ScoringScheme
• unpaired_valence_electrons_sp() : core::chemical::ElectronConfiguration
• UnrecognizedAtomRecord() : core::pose::UnrecognizedAtomRecord
• unvisit() : core::environment::FoldTreeSketch::Node
• 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
• 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_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_atom_ids_from_atom_pointer() : core::kinematics::AtomTree
• update_atom_information_based_on_occupancy() : core::io::pdb::FileData
• update_atom_tree() : core::pack::scmin::ResidueAtomTreeCollection
• 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_child_torsions() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• 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_residues() : core::conformation::Residue
• update_contiguous_monomers() : core::conformation::symmetry::SymmetryInfo
• update_current_energy() : core::pack::interaction_graph::SimpleEdge
• update_current_one_body_energy() : core::pack::interaction_graph::SimpleNode
• update_cutpoints() : core::kinematics::FoldTree
• 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_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_enumeration_shell() : core::scoring::FACTSPoseInfo
• 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_fullatom_info() : core::conformation::membrane::MembraneInfo
• update_hbevaltype() : core::scoring::hbonds::HBEvalTuple
• update_indices() : core::scoring::BB_Pos
• 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
• 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
• 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
• update_intersection() : core::pack::task::ResidueLevelTask_
• 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_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_lowres_info() : core::conformation::membrane::MembraneInfo
• 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_nres() : core::kinematics::FoldTree
• update_num_jump() : core::kinematics::FoldTree
• update_offset_data() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• 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
• update_orbital_coords() : core::conformation::Conformation , core::conformation::Residue , core::pose::Pose
• update_polymeric_connection() : core::conformation::Conformation
• update_pose_chains_from_pdb_chains() : core::pose::Pose
• update_proposed_energy() : core::pack::interaction_graph::SimpleEdge
• 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::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::GenBornPotential , core::scoring::hbonds::HBondEnergy , 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_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_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_rotamer_offsets() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• update_score() : core::io::silent::SilentStruct
• update_score_multiply_factor() : core::conformation::symmetry::SymmetryInfo
• 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::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_union() : core::pack::task::ResidueLevelTask_
• update_xyz_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• updateCachedDensity() : core::scoring::electron_density::ElectronDensity
• updateFcalc() : core::scoring::cryst::PhenixInterface
• updateSolventMask() : core::scoring::cryst::PhenixInterface
• UpJumpSRFD() : core::fragment::UpJumpSRFD
• 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_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::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , 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::PeptideBondedEnergyContainer
• 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::PeptideBondedEnergyContainer
• upper_vertex() : core::graph::UEEdge< V, E >
• UpperEdgeGraph() : core::graph::UpperEdgeGraph< V, E >
• upstream_atom() : core::kinematics::Edge , core::kinematics::FoldTree
• upstream_combine() : core::id::SequenceMapping
• upstream_jump_residue() : core::kinematics::FoldTree
• upstream_jump_stub() : core::conformation::Conformation
• ur() : core::conformation::PseudoBond
• ur_conn_id() : core::conformation::PseudoBond
• ur_resconnid() : core::conformation::PseudoBond
• url() : core::SVNVersion
• use_extended_intrares_energy_interface() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• 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::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::StackElecEnergy
• use_hb_env_dep() : core::scoring::hbonds::HBondOptions
• use_hb_env_dep_DNA() : core::scoring::hbonds::HBondOptions
• use_incorrect_deriv() : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• use_multicool_annealer() : core::pack::task::operation::OptH
• use_nblist() : core::optimization::MinimizerOptions , core::scoring::Energies
• use_nblist_auto_update() : core::scoring::Energies
• use_orientation_dep_rna_ch_o_bonds() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• use_pssm_features() : core::scoring::methods::NMerSVMEnergy
• use_residue_type_theta0() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• use_sp2_chi_penalty() : core::scoring::hbonds::HBondOptions
• USOGFunc() : core::scoring::func::USOGFunc