- n -

• N() : core::scoring::BB_Pos
• n() : core::scoring::elec::FAElecContextData
• n_active_score_types() : core::scoring::EnergyGraph
• n_alt_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• n_alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_atom() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_atomtypes() : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::scoring::etable::Etable
• n_bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• n_bins_i() : core::scoring::bin_transitions::BinTransitionData
• n_bins_iplus1() : core::scoring::bin_transitions::BinTransitionData
• n_bonded_neighbor_all_res() : core::conformation::Residue
• n_branches() : core::chemical::carbohydrates::CarbohydrateInfo
• n_carbons() : core::chemical::carbohydrates::CarbohydrateInfo
• n_chi() : core::io::silent::ProteinSilentStruct_Template< T >
• n_chi_bins() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_connected_residues() : core::scoring::etable::etrie::CountPairDataGeneric
• n_connection_pairs() : core::scoring::mm::MMBondAngleResidueTypeParam
• n_connpoints_for_entry() : core::scoring::trie::CPDataCorrespondence
• n_curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• n_curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_deriv_check_results() : core::optimization::NumericalDerivCheckResult
• n_derivs() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• n_disjoint_sets() : core::graph::DisjointSets
• n_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• n_elements() : core::chemical::ElementSet
• n_entries() : core::scoring::trie::CPDataCorrespondence
• n_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• n_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• n_hbond_acceptors() : core::chemical::ResidueType , core::conformation::Residue
• n_hbond_donors() : core::chemical::ResidueType , core::conformation::Residue
• n_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_mainchain_atoms() : core::conformation::Residue
• n_mainchain_torsions_i() : core::scoring::bin_transitions::BinTransitionData
• n_mainchain_torsions_iplus1() : core::scoring::bin_transitions::BinTransitionData
• n_nodes() : core::graph::DisjointSets
• n_non_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_nonjump_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_nus() : core::chemical::ResidueType , core::conformation::Residue
• n_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• n_packed_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_parameters() : core::conformation::parametric::ParametersSet
• n_parameters_sets() : core::conformation::Conformation
• n_phi_bins() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_possible_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_proton_chi() : core::chemical::ResidueType
• n_psi_bins() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_pssms() : core::scoring::methods::NMerPSSMEnergy
• n_residue() : core::conformation::parametric::Parameters , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::pose::Pose
• n_residue_connections() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::mm::MMBondAngleResidueTypeParam
• n_residue_connections_for_atom() : core::chemical::ResidueType
• n_residues() : core::fragment::picking_old::vall::VallLibrary
• n_rotamer_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_rotamer_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_rotamer_bins_for_aa_02() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_rotameric_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_sample_rotamers() : core::pack::rotamer_set::ContinuousRotamerSets
• n_scores() : core::fragment::picking_old::vall::VallLibrarian
• n_seqs() : core::sequence::CompositeSequence
• n_svms() : core::scoring::methods::NMerSVMEnergy
• n_types() : core::chemical::gasteiger::GasteigerAtomTypeSet
• n_unassigned() : core::pack::scmin::SidechainStateAssignment
• n_virtual_atoms() : core::chemical::ResidueType , core::conformation::Residue
• nactive_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• nallocated() : core::graph::ArrayPool< T >
• name() : core::chemical::Atom , core::chemical::AtomType , core::chemical::AtomTypeSet , core::chemical::MMAtomType , core::chemical::Orbital , core::chemical::orbitals::OrbitalType , core::chemical::Patch , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOMolecule , core::conformation::Residue , core::environment::EnvCore , core::io::rna::RDAT , core::io::silent::SilentEnergy , core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AUTO , core::pack::task::EMPTY , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NC , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::POLAR , core::pack::task::RESET , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC , core::pose::PDBInfo , core::scoring::methods::GoapRsdType , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::util::ABEGO
• name1() : core::chemical::ResidueType , core::conformation::Residue
• name2enum_() : core::pose::datacache::CacheableDataType
• name2suite() : core::pose::rna::RNA_SuiteName
• name3() : core::chemical::ResidueType , core::conformation::Residue , core::pack::interaction_graph::RotamerDots
• name3_map() : core::chemical::ResidueTypeSet
• name_from_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
• name_from_deriv_type() : core::scoring::hbonds::HBondTypeManager
• name_from_don_chem_type() : core::scoring::hbonds::HBondTypeManager
• name_from_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
• name_from_hybridization_type() : core::scoring::hbonds::HBondTypeManager
• name_from_score_type() : core::scoring::ScoreTypeManager
• name_from_seq_sep_type() : core::scoring::hbonds::HBondTypeManager
• name_from_weight_type() : core::scoring::hbonds::HBondTypeManager
• name_map() : core::chemical::ResidueTypeSet
• NamedAtomID() : core::id::NamedAtomID
• NamedAtomID_Map() : core::id::NamedAtomID_Map< T >
• NamedAtomPairConstraint() : core::scoring::constraints::NamedAtomPairConstraint
• NamedStubID() : core::id::NamedStubID
• nangles() : core::fragment::BBTorsionAndAnglesSRFD , core::optimization::MinimizerMap , core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::SymMinimizerMap
• natom() : core::scoring::methods::GoapRsdType , core::scoring::packstat::SimplePDB
• natoms() : core::chemical::ResidueType , core::conformation::Residue , core::conformation::UltraLightResidue , core::optimization::CartesianMinimizerMap , core::optimization::DOF_DataPoint , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pose::PDBInfo , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::FACTSResidueInfo , core::scoring::FACTSRsdTypeInfo , core::scoring::hbonds::HBondResidueMinData , core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• nb_weight() : core::scoring::packing::HolesParams
• nballs() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• nbb() : core::fragment::BBTorsionSRFD , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• nbhist() : core::scoring::packing::PoseBalls
• nblist() : core::scoring::Energies
• nblist_auto_update() : core::optimization::MinimizerOptions
• nblist_dis2_cutoff_HH() : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::mm::MMLJLibrary
• nblist_dis2_cutoff_XH() : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::mm::MMLJLibrary
• nblist_dis2_cutoff_XX() : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::mm::MMLJLibrary
• nblist_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• nblocks() : core::graph::ArrayPool< T >
• nbonds() : core::chemical::ResidueType , core::conformation::PseudoBond
• nbr_atom() : core::chemical::ResidueType , core::conformation::Residue
• nbr_atom_xyz() : core::conformation::Residue
• nbr_radius() : core::chemical::ResidueType , core::conformation::Residue
• nbr_vertex() : core::chemical::ResidueType
• nbrs() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::HBondSet
• nbrs1() : core::scoring::motif::ResPairMotif
• nbrs2() : core::scoring::motif::ResPairMotif
• NCAARotLibPath() : core::chemical::NCAARotLibPath
• NCaCaC_Dihedral_Func() : core::scoring::disulfides::NCaCaC_Dihedral_Func
• nchi() : core::chemical::ResidueType , core::conformation::Residue , core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• ndihe() : core::chemical::ResidueType
• ndofs() : core::optimization::CartesianMinimizerMap
• nearby_atom_cut() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• negative_better() : core::sequence::SequenceProfile
• negln_rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• NegSpaceElement() : core::graph::NegSpaceElement< T >
• neighbor_cutoff() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• neighbor_id() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• 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
• 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
• neighbor_mass() : core::scoring::TenANeighborNode
• neighbor_weight() : core::scoring::nv::NVscore
• NeighborhoodResidueSelector() : core::pack::task::residue_selector::NeighborhoodResidueSelector
• NeighborList() : core::scoring::NeighborList
• NelderMeadSimplex() : core::optimization::NelderMeadSimplex
• new_array() : core::graph::ArrayPool< T >
• new_chain_order() : core::io::pdb::PDB_DReaderOptions
• new_chemical_bond() : core::kinematics::FoldTree
• new_func() : core::scoring::func::FuncFactory
• new_icoor() : core::chemical::Orbital
• new_jump() : core::kinematics::FoldTree
• new_orbital_icoor_data() : core::chemical::ResidueType
• new_residue_group() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_residue_selector() : core::pack::task::residue_selector::ResidueSelectorFactory
• new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_sym_min() : core::optimization::symmetry::SymMinimizerMap
• newConstraint() : core::scoring::constraints::ConstraintFactory
• newNode() : core::environment::FoldTreeSketch::Node
• newResFilter() : core::pack::task::operation::ResFilterFactory
• newRLTO() : core::pack::task::operation::ResLvlTaskOperationFactory
• newTaskOperation() : core::pack::task::operation::TaskOperationFactory
• newTaskOperations() : core::pack::task::operation::TaskOperationFactory
• next() : core::chemical::AutomorphismIterator , core::graph::EdgeListElement , core::graph::NegSpaceElement< T > , core::sequence::Cell
• next_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• next_circle() : core::scoring::packstat::trace
• next_struct() : core::import_pose::pose_stream::SilentFilePoseInputStream
• ngaussians() : core::scoring::SmoothScoreTermCoeffs
• nhbonds() : core::scoring::hbonds::HBondSet
• nheavyatoms() : core::chemical::ResidueType , core::conformation::Residue
• njumps() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• nlr_gaussians() : core::scoring::CenHBPotential
• nmer_length() : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
• nmer_pssm_scorecut() : core::scoring::methods::NMerPSSMEnergy
• nmer_svm_scorecut() : core::scoring::methods::NMerSVMEnergy
• NMerPSSMEnergy() : core::scoring::methods::NMerPSSMEnergy
• NMerRefEnergy() : core::scoring::methods::NMerRefEnergy
• NMerSVMEnergy() : core::scoring::methods::NMerSVMEnergy
• nmissing() : core::scoring::loop_graph::LoopGraph
• nmoltenres() : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , core::pack::scmin::SidechainStateAssignment
• nmtr() : core::scoring::FACTSResidueInfo
• nneighbors() : core::scoring::hbonds::HBondResidueMinData
• no_dis_dep_die() : core::scoring::etable::coulomb::Coulomb
• no_optH() : core::import_pose::ImportPoseOptions
• no_residues_with_nonzero_change_id() : core::kinematics::ResidueCoordinateChangeList
• Node() : core::environment::FoldTreeSketch::Node
• node() : core::graph::DisjointSets
• Node() : core::graph::Node , core::kinematics::Node
• NodeBase() : core::pack::interaction_graph::NodeBase
• nodes_in_set() : core::graph::DisjointSets
• non_const_pose() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• non_hbonding_atom() : core::scoring::hbonds::hbtrie::HBAtom
• non_helix_in_membrane_penalty() : core::scoring::MembranePotential
• non_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• non_virtual_score() : core::scoring::constraints::CoordinateConstraint
• nonconst_atom_numbers_for_mg_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_begin() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet
• nonconst_cenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• nonconst_data_ptr() : core::conformation::Residue
• nonconst_dcenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• nonconst_end() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet
• nonconst_is_magnesium() : core::scoring::rna::RNA_ScoringInfo
• nonconst_long_range_container() : core::scoring::Energies
• nonconst_mindata_from_pose() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• nonconst_other_struct_list() : core::io::silent::SilentStruct
• nonconst_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• nonconst_residue_type_set() : core::chemical::ChemicalManager
• nonconst_residue_type_set_op() : core::chemical::ChemicalManager
• nonconst_rna_task() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• nonconst_rotamer() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• NonContinuousFrame() : core::fragment::NonContinuousFrame
• nondefault() : core::chemical::ResidueType
• nonjump_atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• nonmonotone() : core::optimization::LineMinimizationAlgorithm
• NonResidueTypeConstraint() : core::scoring::constraints::NonResidueTypeConstraint
• nonzero_deltas() : core::kinematics::Jump
• NoRepackDisulfides() : core::pack::task::operation::NoRepackDisulfides
• NoResFilter() : core::pack::task::operation::NoResFilter
• norm_factor() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• norm_squared() : core::scoring::EMapVector
• normal() : core::scoring::MembraneEmbed
• normalize() : core::chemical::sdf::MolFileIOMolecule
• not_using() : core::scoring::FACTSRsdTypeInfo
• not_valid() : core::conformation::membrane::Span
• note_chi_controls_atom() : core::chemical::ResidueType
• note_coordinate_change_registered() : core::kinematics::AtomTree
• note_current_network_state() : core::pack::annealer::FASTERAnnealer
• note_dof_change() : core::kinematics::tree::Atom_
• note_edge_deleted() : core::graph::UpperEdgeGraph< V, E >
• note_has_pseudobonds() : core::scoring::trie::CPDataCorrespondence
• note_long_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• note_long_range_interactions_exist_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• note_lower_edge_added() : core::graph::UEVertex< V, E >
• note_lower_edge_deleted() : core::graph::UEVertex< V, E >
• note_rpe_calculated() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• note_short_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• note_short_range_interactions_exist_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• note_submatrix_accessed() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• note_submatrix_added() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• note_upper_edge_deleted() : core::graph::UEVertex< V, E >
• note_vertex_reached() : core::pack::interaction_graph::InteractionGraphBase
• note_xyz_uptodate() : core::kinematics::tree::Atom_
• notify_conformation_obs() : core::pose::Pose
• notify_connection_obs() : core::conformation::Conformation
• notify_destruction_obs() : core::pose::Pose
• notify_energy_change() : core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator
• notify_energy_obs() : core::pose::Pose
• notify_general_obs() : core::conformation::Conformation , core::pose::Pose
• notify_identity_obs() : core::conformation::Conformation
• notify_length_obs() : core::conformation::Conformation
• notify_structure_change() : core::pose::metrics::PoseMetricCalculator , core::pose::metrics::StructureDependentCalculator
• notify_topological_change() : core::kinematics::AtomTree
• notify_xyz_obs() : core::conformation::Conformation
• NotResidueSelector() : core::pack::task::residue_selector::NotResidueSelector
• noutstanding() : core::graph::ArrayPool< T >
• npos() : core::sequence::SequenceCoupling
• npr() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nr_frags() : core::fragment::Frame
• nr_frames() : core::fragment::FragSet
• nr_res_affected() : core::fragment::Frame
• nrad() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nrchi_bin_id() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• nrchi_lower_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_sample() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_upper_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nres() : core::environment::FoldTreeSketch , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::silent::SilentFileData , core::io::silent::SilentStruct , core::kinematics::FoldTree , core::pose::PDBInfo
• nres_topo() : core::conformation::membrane::SpanningTopology
• nrotamer_offset_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• nrotamers() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• nrotamers_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• nsigmoids() : core::scoring::SmoothScoreTermCoeffs
• nspans() : core::conformation::membrane::SpanningTopology
• nsr_gaussians() : core::scoring::CenHBPotential
• nstep() : core::pack::rotamer_set::WaterAnchorInfo
• nsteps() : core::optimization::SimpleDerivCheckResult
• ntorsions() : core::optimization::CartesianMinimizerMap
• nu() : core::conformation::Residue
• nu0_components() : core::scoring::dna::DNATorsionPotential
• nu1_components() : core::scoring::dna::DNATorsionPotential
• nu1_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu1_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_components() : core::scoring::dna::DNATorsionPotential
• nu2_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu3_components() : core::scoring::dna::DNATorsionPotential
• nu4_components() : core::scoring::dna::DNATorsionPotential
• nu_atoms() : core::chemical::ResidueType , core::conformation::Residue
• num_base_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_bb_clones() : core::conformation::symmetry::SymmetryInfo
• num_bins() : core::scoring::motif::XformScore
• num_bondangles() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• num_chains() : core::conformation::Conformation
• num_chi_clones() : core::conformation::symmetry::SymmetryInfo
• num_cutpoint() : core::kinematics::FoldTree
• num_cuts() : core::environment::FoldTreeSketch
• num_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• num_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• num_edges() : core::graph::Graph , core::graph::Node , core::graph::UpperEdgeGraph< V, E >
• num_features_proq2() : core::scoring::ProQPotential
• num_features_proqm() : core::scoring::ProQPotential
• num_heavy_atoms() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_hits() : core::scoring::motif::MotifHits
• num_hits1() : core::scoring::motif::MotifHits
• num_hits2() : core::scoring::motif::MotifHits
• num_independent_residues() : core::conformation::symmetry::SymmetryInfo
• num_interfaces() : core::conformation::symmetry::SymmetryInfo
• num_jump() : core::kinematics::FoldTree , core::pose::Pose
• num_jump_clones() : core::conformation::symmetry::SymmetryInfo
• num_jumps() : core::environment::FoldTreeSketch
• num_loops() : core::scoring::loop_graph::LoopGraph
• num_lower_neighbors() : core::graph::UEVertex< V, E >
• num_motifs() : core::scoring::motif::MotifHash
• num_neighbors() : core::graph::UEVertex< V, E >
• num_neighbors_counting_self() : core::graph::Node , core::graph::UEVertex< V, E > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• num_neighbors_counting_self_static() : core::graph::Node
• num_nodes() : core::graph::Graph
• num_pairings() : core::scoring::dssp::Dssp
• num_possible_bins() : core::scoring::motif::XformScore
• num_residues() : core::scoring::disulfides::FullatomDisulfideEnergyContainer
• num_rings() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• num_rotamers() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• num_rotamers_in_subtree() : core::scoring::trie::TrieNode< AT, CPDATA >
• num_rots_to_pack() : core::pack::annealer::SimAnnealerBase
• num_sampling_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_selectors() : core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::OrResidueSelector
• num_slidablejumps() : core::conformation::symmetry::SymmetryInfo
• num_to_be_packed() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• num_total_residues() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_with_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_without_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_upper_neighbors() : core::graph::UEVertex< V, E >
• num_vertices() : core::graph::UpperEdgeGraph< V, E >
• num_virtuals() : core::conformation::symmetry::SymmetryInfo
• num_water() : core::scoring::packstat::SimplePDB
• number() : core::pose::PDBInfo
• number_bonded_heavyatoms() : core::chemical::ResidueType
• number_bonded_hydrogens() : core::chemical::ResidueType
• NumDerivCheckData() : core::optimization::NumDerivCheckData
• numeric_properties() : core::chemical::ResidueProperties
• NumericalDerivCheckResult() : core::optimization::NumericalDerivCheckResult
• numGaussians() : core::scoring::func::USOGFunc
• NumNeighborsSelector() : core::pack::task::residue_selector::NumNeighborsSelector
• nus() : core::conformation::Residue
• nusing() : core::scoring::methods::GoapRsdType
• NVlookup() : core::scoring::nv::NVlookup
• NVscore() : core::scoring::nv::NVscore
• NWAligner() : core::sequence::NWAligner