Here is a list of all class members with links to the classes they belong to:

- n -

• n : core::io::raw_data::DisulfideFile::ResNum
• N() : core::scoring::BB_Pos
• n() : core::scoring::elec::FAElecContextData , core::scoring::fiber_diffraction::Hankel
• N1_ : core::scoring::constraints::BigBinConstraint
• N2_ : core::scoring::constraints::BigBinConstraint
• N_ : core::scoring::BB_Pos
• n_ : core::scoring::elec::FAElecContextData , core::scoring::func::MinMultiHarmonicFunc
• n_aa_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_acceptor : core::scoring::elec::ElecGroup
• n_active_dof_nodes_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• 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_ANGLE1_BINS : core::scoring::methods::GoapEnergy
• N_ANGLE2_BINS : core::scoring::methods::GoapEnergy
• n_assigned_at_start_ : core::pack::annealer::RotamerAssigningAnnealer
• N_ATMTYPES : core::scoring::methods::GoapEnergy
• 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_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint
• n_atomtypes() : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• n_atomtypes_ : core::scoring::etable::Etable
• n_backbone_heavyatoms_ : core::chemical::ResidueType
• n_baserotamers_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• n_baserots_total_ : core::pack::rotamer_set::ContinuousRotamerSet
• n_bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• n_bins_i() : core::scoring::bin_transitions::BinTransitionData
• n_bins_i_ : core::scoring::bin_transitions::BinTransitionData
• n_bins_iplus1() : 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_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_chi_bins_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_chi_products_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_connect_ : core::scoring::etable::count_pair::CountPairGeneric
• 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_cut : core::scoring::TMscoreStore
• n_cuts_ : core::environment::FoldTreeSketch
• n_deriv_check_results() : core::optimization::NumericalDerivCheckResult
• n_derivs() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• n_derivs_ : core::pack::dunbrack::BBDepScoreInterpData< N > , core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• n_disjoint_sets() : core::graph::DisjointSets
• N_DISTANCE_BINS : core::scoring::methods::GoapEnergy
• n_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• n_donor : core::scoring::elec::ElecGroup
• n_elements() : core::chemical::ElementSet
• n_entries() : core::scoring::trie::CPDataCorrespondence
• 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_full_updates_ : core::scoring::NeighborList
• n_GDT05 : core::scoring::TMscoreStore
• n_GDT05_max : core::scoring::TMscoreStore
• n_GDT1 : core::scoring::TMscoreStore
• n_GDT1_max : core::scoring::TMscoreStore
• n_GDT2 : core::scoring::TMscoreStore
• n_GDT2_max : core::scoring::TMscoreStore
• n_GDT4 : core::scoring::TMscoreStore
• n_GDT4_max : core::scoring::TMscoreStore
• n_GDT8 : core::scoring::TMscoreStore
• n_GDT8_max : core::scoring::TMscoreStore
• n_grid_ : core::scoring::PoissonBoltzmannPotential
• n_hbond_acceptors() : core::chemical::ResidueType , core::conformation::Residue
• n_hbond_acceptors_ : core::chemical::ResidueType
• n_hbond_donors() : core::chemical::ResidueType , core::conformation::Residue
• n_hbond_donors_ : core::chemical::ResidueType
• n_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_independent_dof_nodes_ : core::optimization::symmetry::SymMinimizerMap
• N_index_ : core::scoring::BB_Pos
• n_jumps_ : core::environment::FoldTreeSketch
• n_mainchain_atoms() : core::conformation::Residue
• n_mainchain_torsions_i() : core::scoring::bin_transitions::BinTransitionData
• n_mainchain_torsions_i_ : core::scoring::bin_transitions::BinTransitionData
• n_mainchain_torsions_iplus1() : core::scoring::bin_transitions::BinTransitionData
• n_mainchain_torsions_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• n_mappings_ : core::io::pdb::GeometricRenameIsomorphismCallback
• n_nodes() : core::graph::DisjointSets
• n_non_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_non_polymeric_residue_connections_ : core::chemical::ResidueType
• n_nonjump_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_nrchi_sample_bins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• n_nus() : core::chemical::ResidueType , core::conformation::Residue
• n_nv_dist_sd_ : core::scoring::methods::ProClosureEnergy
• N_OMG_BINS : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• n_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• n_orbitals_ : core::chemical::orbitals::AssignOrbitals
• N_p_sp2 : core::scoring::orbitals::OrbitalsStatistics
• n_packed_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_packed_rots_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_parameters() : core::conformation::parametric::ParametersSet
• n_parameters_sets() : core::conformation::Conformation
• n_pconnect_ : core::scoring::etable::count_pair::CountPairGeneric
• n_periodic_ : core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::PeriodicFunc
• n_phi_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• N_PHI_BINS : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• n_phi_bins() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• N_PHIPSI_BINS : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• N_pi_sp2 : core::scoring::orbitals::OrbitalsStatistics
• n_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_polymeric_residue_connections_ : core::chemical::ResidueType
• n_possible_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_possible_rots_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_prepare_for_scorings_ : core::scoring::NeighborList
• n_proton_chi() : core::chemical::ResidueType
• n_psi_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• N_PSI_BINS : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• 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_residue_groups_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_residue_types_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_residues() : core::fragment::picking_old::vall::VallLibrary
• n_restypes_ : core::pack::rotamer_set::ContinuousRotamerSet
• 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_rotameric_chi_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• n_rotamers_for_resgroup_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_rotamers_for_restype_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_sample_rotamers() : core::pack::rotamer_set::ContinuousRotamerSets
• n_sample_rotamers_ : core::pack::rotamer_set::ContinuousRotamerSets
• n_samplingrots_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• n_samplingrots_total_ : core::pack::rotamer_set::ContinuousRotamerSet
• n_scores() : core::fragment::picking_old::vall::VallLibrarian
• n_seqs() : core::sequence::CompositeSequence
• n_svms() : core::scoring::methods::NMerSVMEnergy
• N_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• N_term_inside_ : core::scoring::MembraneTopology
• n_to_be_packed_ : core::pack::task::PackerTask_
• n_to_be_packed_up_to_date_ : core::pack::task::PackerTask_
• n_torsions_ : core::scoring::rna::RNA_SuitePotential
• n_types() : core::chemical::gasteiger::GasteigerAtomTypeSet
• n_unassigned() : core::pack::scmin::SidechainStateAssignment
• n_unassigned_ : core::pack::scmin::SidechainStateAssignment
• n_update_from_wide_ : core::scoring::NeighborList
• n_valid_left_pp_bins_by_ppo_torbin_ : core::scoring::Ramachandran2B
• n_valid_pp_bins_by_ppo_torbin_ : core::scoring::Ramachandran
• n_valid_right_pp_bins_by_ppo_torbin_ : core::scoring::Ramachandran2B
• n_virtual_atoms() : core::chemical::ResidueType , core::conformation::Residue
• na_allowed_ : core::pack::task::PIKAA
• NACCESS_SASA_radii_ : core::pack::interaction_graph::RotamerDotsRadiusData
• NACCESS_SASA_radii_with_expanded_polars_ : core::pack::interaction_graph::RotamerDotsRadiusData
• nAccessibleDots : core::scoring::sc::_RESULTS
• nactive_moving_atoms_ : core::pack::scmin::CartSCMinMinimizerMap
• nactive_moving_atoms_total_ : core::pack::scmin::CartSCMinMinimizerMap
• nactive_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• nactive_residues_ : core::pack::scmin::SCMinMinimizerMap
• nAllDots : core::scoring::sc::_RESULTS
• 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::pdb::AtomInformation , core::io::rna::RDAT , core::io::silent::SilentEnergy , core::kinematics::Node , 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::pose::rna::RNA_SuiteAssignment , core::pose::rna::RNA_SuiteInfo , core::scoring::methods::GoapRsdType , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::util::ABEGO , update_ResidueType_enum_files.EnumInfo
• name1() : core::chemical::ResidueType , core::conformation::Residue , core::io::pdb::LinkInformation
• name1_ : core::chemical::ResidueType , core::chemical::Selector_NAME1 , core::chemical::SetIO_String
• name2 : core::io::pdb::LinkInformation
• name2abego_ : core::util::ABEGOManager
• name2acc_chem_type_ : core::scoring::hbonds::HBondTypeManager
• Name2Calculator : core::pose::metrics::PoseMetricContainer
• name2component_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• name2deriv_type_ : core::scoring::hbonds::HBondTypeManager
• name2don_chem_type_ : core::scoring::hbonds::HBondTypeManager
• name2enum_() : core::pose::datacache::CacheableDataType
• name2geo_dim_type_ : core::scoring::hbonds::HBondTypeManager
• name2hybridization_type_ : core::scoring::hbonds::HBondTypeManager
• name2score_type_ : core::scoring::ScoreTypeManager
• name2seq_sep_type_ : core::scoring::hbonds::HBondTypeManager
• name2suite() : core::pose::rna::RNA_SuiteName
• name2weight_type_ : core::scoring::hbonds::HBondTypeManager
• name3() : core::chemical::ResidueType , core::conformation::Residue , core::pack::interaction_graph::RotamerDots
• name3_ : core::chemical::ResidueType , core::chemical::SetIO_String
• name3_map() : core::chemical::ResidueTypeSet
• name3_map_ : core::chemical::ResidueTypeSet
• name3_set : core::pack::task::operation::ResidueName3Is
• name3s_ : core::chemical::Selector_NAME3
• name_ : core::chemical::Atom , core::chemical::AtomType , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::MMAtomType , core::chemical::Orbital , core::chemical::Patch , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOMolecule , core::environment::EnvCore , core::grid::CartGrid< T > , core::io::rna::RDAT , core::io::silent::SilentEnergy , core::pose::PDBInfo , core::scoring::hbonds::FadeInterval , core::scoring::methods::GoapRsdType , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::util::ABEGO
• 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
• name_map_ : core::chemical::ResidueTypeSet
• name_of_InterfaceNeighborDefinitionCalculator_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• named_atom1_ : core::scoring::constraints::NamedAtomPairConstraint
• named_atom2_ : core::scoring::constraints::NamedAtomPairConstraint
• NamedAtomID() : core::id::NamedAtomID , core::pose::Pose , core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• NamedAtomID_Map() : core::id::NamedAtomID_Map< T >
• NamedAtomPairConstraint() : core::scoring::constraints::NamedAtomPairConstraint
• NamedStubID() : core::id::NamedStubID
• names_to_indexes_ : core::scoring::saxs::FormFactorManager
• nangles() : core::fragment::BBTorsionAndAnglesSRFD , core::optimization::MinimizerMap , core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::SymMinimizerMap
• native_pose_ : core::scoring::methods::RMS_Energy
• native_task_ : core::pack::task::operation::ReplicateTask
• natom() : core::scoring::methods::GoapRsdType , core::scoring::packing::HolesResult , core::scoring::packstat::SimplePDB , core::scoring::sc::Atom
• natom_ : core::scoring::methods::GoapRsdType
• 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::APBSConfig , 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
• nAtoms : core::scoring::sc::_RESULTS
• natoms() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• natoms_ : core::chemical::AutomorphismIterator , core::optimization::DOF_DataPoint , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::scoring::FACTSResidueInfo , core::scoring::FACTSRsdTypeInfo , core::scoring::hbonds::HBondResidueMinData , core::scoring::PQR , core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• nb_weight() : core::scoring::packing::HolesParams
• nb_weights_ : core::scoring::packing::HolesParams
• nballs() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• 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
• nbhist_ : core::scoring::packing::PoseBalls
• nblist() : core::scoring::Energies
• nblist_ : core::scoring::Energies , core::scoring::NeighborList
• nblist_auto_update() : core::optimization::MinimizerOptions
• 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_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_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_dis2_cutoff_XX_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::mm::MMLJLibrary
• nblist_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• nBlockedAtoms : core::scoring::sc::_RESULTS
• nblocks() : core::graph::ArrayPool< T >
• nblocks_ : core::graph::ArrayPool< T >
• nbonds() : core::chemical::ResidueType , core::conformation::PseudoBond
• nbonds_ : core::conformation::PseudoBond
• nbr_atom() : core::chemical::ResidueType , core::conformation::Residue
• nbr_atom_ : core::chemical::ResidueType
• nbr_atom_indices_ : core::chemical::ResidueType
• nbr_atom_xyz() : core::conformation::Residue
• nbr_distance_squared_ : core::scoring::orbitals::OrbitalsScore
• nbr_radius() : core::chemical::ResidueType , core::conformation::Residue
• nbr_radius_ : core::chemical::ResidueType
• nbr_vertex() : core::chemical::ResidueType
• nbrs() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::HBondSet
• nbrs1() : core::scoring::motif::ResPairMotif
• nbrs1_ : core::scoring::motif::ResPairMotif
• nbrs2() : core::scoring::motif::ResPairMotif
• nbrs2_ : core::scoring::motif::ResPairMotif
• nbrs_ : core::scoring::hbonds::HBondSet
• nBuriedAtoms : core::scoring::sc::_RESULTS
• nBuriedDots : core::scoring::sc::_RESULTS
• nc_to_include_ : core::pack::task::NC
• ncaa_rotlib_n_bins_per_rot_ : core::chemical::ResidueType
• ncaa_rotlib_n_rots_ : core::chemical::ResidueType
• ncaa_rotlib_path_ : core::chemical::ResidueType
• ncaa_rotlibs_ : core::pack::dunbrack::RotamerLibrary
• NCAARotLibPath() : core::chemical::NCAARotLibPath
• NCaCaC_Dihedral_Func() : core::scoring::disulfides::NCaCaC_Dihedral_Func
• ncacac_dihedral_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• 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
• nchi_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nconnections_for_entry_ : core::scoring::trie::CPDataCorrespondence
• ncopies_ : core::fragment::FragmentIO
• NCS_RESIDUE_MAPPING : core::pose::datacache::CacheableDataType
• ndihe() : core::chemical::ResidueType
• ndofs() : core::optimization::CartesianMinimizerMap
• ndofs_added_for_focused_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• nearby_atom_cut() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• nearby_atom_cut_ : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• neg_begin_ : core::graph::ArrayPool< T >
• neg_ptr_ : core::graph::ArrayPoolElement< T >
• neg_space_blocks_ : core::graph::ArrayPool< T >
• negative_better() : core::sequence::SequenceProfile
• negative_better_ : core::sequence::SequenceProfile
• negln_rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• negln_rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• NegSpaceElement() : core::graph::NegSpaceElement< T >
• neighbor_atoms_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• neighbor_cutoff() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• neighbor_cutoff_ : core::scoring::solid_surface::SurfaceEnergies
• 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_mass_ : core::scoring::TenANeighborNode
• neighbor_relaxed_in_sBR_ : core::pack::interaction_graph::FASTERNode
• neighbor_weight() : core::scoring::nv::NVscore
• NeighborhoodResidueSelector() : core::pack::task::residue_selector::NeighborhoodResidueSelector
• NeighborList : core::scoring::Energies , core::scoring::NeighborList
• neighbors : core::scoring::sc::Atom
• neighbors_curr_state_ : 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
• neighbors_curr_state_plus_offset_ : core::pack::interaction_graph::DoubleDensePDNode
• neighbors_curr_state_sparse_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• neighbors_num_states_ : core::pack::interaction_graph::DoubleDensePDNode
• neighbors_rotindex_offset_ : core::pack::interaction_graph::DoubleDensePDNode
• neighbors_state_recent_history_index_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• NelderMeadSimplex() : core::optimization::NelderMeadSimplex
• netstate_duplicated_ : core::pack::annealer::FASTERAnnealer
• NEUTRAL_OMG : core::pack::dunbrack::SingleResiduePeptoidLibrary
• NEUTRAL_PHI : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• NEUTRAL_PSI : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• NEUTRON_DIFFRACTION : core::io::pdb::HeaderInformation
• new_array() : core::graph::ArrayPool< T >
• new_cache_ : core::fragment::CacheWrapper< T, XCacheUnit >
• new_chain_order() : core::io::pdb::PDB_DReaderOptions
• 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_icoor_ : core::chemical::Orbital
• new_jump() : core::kinematics::FoldTree
• new_orbital_icoor_data() : core::chemical::ResidueType
• new_order : core::kinematics::FoldTree
• 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
• new_sym_min_ : core::optimization::symmetry::SymMinimizerMap
• new_topology : core::kinematics::FoldTree
• 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
• nex_ : core::scoring::ResidualDipolarCoupling
• next() : core::chemical::AutomorphismIterator , core::graph::EdgeListElement , core::graph::NegSpaceElement< T > , core::sequence::Cell
• next_ : core::graph::EdgeListElement , core::graph::NegSpaceElement< T >
• next_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• next_circle() : core::scoring::packstat::trace
• next_struct() : core::import_pose::pose_stream::SilentFilePoseInputStream
• next_trace_ : core::scoring::packstat::trace
• ngaussians() : core::scoring::SmoothScoreTermCoeffs
• nhbonds() : core::scoring::hbonds::HBondSet
• nheavyatoms() : core::chemical::ResidueType , core::conformation::Residue
• nheavyatoms_ : core::chemical::ResidueType
• nions : core::scoring::APBSConfig::I_PARAM
• njump_monomer_ : core::conformation::symmetry::SymmetryInfo
• njumps() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• nkbins_ : core::scoring::electron_density::ElectronDensity
• nlev : core::scoring::APBSConfig::I_PARAM
• nlr_gaussians() : core::scoring::CenHBPotential
• nmer_cterm_ : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
• nmer_length() : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
• nmer_length_ : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
• nmer_pssm_ : core::scoring::methods::NMerSVMEnergy
• nmer_pssm_scorecut() : core::scoring::methods::NMerPSSMEnergy
• nmer_pssm_scorecut_ : core::scoring::methods::NMerPSSMEnergy
• nmer_ref_energies_ : core::scoring::methods::NMerRefEnergy
• nmer_svm_scorecut() : core::scoring::methods::NMerSVMEnergy
• 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
• nmoltenres_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::scmin::SidechainStateAssignment
• NMR : core::io::pdb::HeaderInformation
• nmtr() : core::scoring::FACTSResidueInfo
• nmtr_ : core::scoring::FACTSResidueInfo
• nnegative_ : core::graph::ArrayPool< T >
• nneighbors() : core::scoring::hbonds::HBondResidueMinData
• nneighbors_ : core::scoring::hbonds::HBondResidueMinData
• nneighbs_ : core::io::sequence_comparation::DesignContrast , core::scoring::methods::LK_hack
• no_dis_dep_die() : core::scoring::etable::coulomb::Coulomb
• no_dis_dep_die_ : core::scoring::etable::coulomb::Coulomb
• NO_DISULFIDE : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• no_index_ : core::chemical::AddChi , core::chemical::AddChiRotamer
• no_interpolate_mpair_ : core::scoring::membrane::MPPairEnergy
• no_interpolate_Mpair_ : core::scoring::MembranePotential
• no_lk_polar_desolvation : core::scoring::etable::EtableOptions
• no_lk_polar_desolvation_ : core::scoring::etable::Etable
• no_optH() : core::import_pose::ImportPoseOptions
• 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::Graph , core::graph::Node , core::kinematics::Node , core::scoring::constraints::ConstraintNode
• node_changing_ : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• node_considering_alt_state_ : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• node_dist_ : core::kinematics::ShortestPathInFoldTree
• node_index_ : core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::exposed_hydrophobic_data , core::pack::interaction_graph::NodeBase
• node_indices_ : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• node_not_changing_ : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• node_state_offsets_ : core::pack::interaction_graph::InteractionGraphBase
• node_states_coverage_of_bg_res_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• node_states_overlap_with_bg_res_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• NodeAP : core::environment::FoldTreeSketch
• NodeBase : core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase
• NodeCAP : core::environment::FoldTreeSketch
• NodeCOP : core::environment::FoldTreeSketch
• NodeOP : core::environment::FoldTreeSketch
• nodes_ : core::environment::FoldTreeSketch , core::graph::DisjointSets , core::graph::Edge , core::graph::Graph , core::pack::interaction_graph::EdgeBase
• nodes_alt_pair_dot_counts_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• nodes_alt_state_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• nodes_alt_states_ : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• nodes_curr_pair_dot_counts_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• nodes_curr_state_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• nodes_curr_states_ : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• nodes_in_set() : core::graph::DisjointSets
• NodeVector : core::graph::Graph
• 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_main_chain_sugar_coords_ : core::io::silent::RNA_SilentStruct
• non_main_chain_sugar_coords_defined_ : core::io::silent::RNA_SilentStruct
• non_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• non_residue_pair_constraints_ : core::scoring::constraints::ConstraintSet
• non_standard_residues_ : core::pose::full_model_info::FullModelParameters
• non_surface_ranges_ : core::scoring::solid_surface::SurfaceEnergies
• non_virtual_score() : core::scoring::constraints::CoordinateConstraint
• noncanonical_residue_connections_ : core::io::silent::BinarySilentStruct
• 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_name_map_ : core::chemical::ResidueTypeSet
• 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
• nondefault_ : core::chemical::ResidueType
• nondegenerate_conformers_ : core::chemical::RingConformerSet
• None : core::chemical::gasteiger::GasteigerAtomTypeData
• nonideal_ : core::pack::RTMin , core::pack::scmin::SCMinMinimizerMap
• nonjump_atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• nonmonotone() : core::optimization::LineMinimizationAlgorithm
• nonprepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• NonResidueTypeConstraint() : core::scoring::constraints::NonResidueTypeConstraint
• nonstandard_polymer_ : core::conformation::Residue
• 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_factor_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• norm_squared() : core::scoring::EMapVector
• normal() : core::scoring::MembraneEmbed
• normal_ : core::scoring::hbonds::HBondEnergy , core::scoring::MembraneEmbed
• normalization : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• normalize() : core::chemical::sdf::MolFileIOMolecule
• not_using() : core::scoring::FACTSRsdTypeInfo
• not_using_ : core::scoring::FACTSRsdTypeInfo
• not_valid() : core::conformation::membrane::Span
• NOT_YET_COMPUTED_ENERGY : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge
• 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 >
• npEnergy : core::scoring::APBSResult
• npoints_ : core::grid::CartGrid< T >
• npos() : core::sequence::SequenceCoupling
• npr() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• npr_ : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• npseudo_ : core::conformation::symmetry::SymmetryInfo
• npx : core::scoring::APBSResult
• npy : core::scoring::APBSResult
• npz : core::scoring::APBSResult
• nr_frags() : core::fragment::Frame
• nr_frames() : core::fragment::FragSet
• nr_res_ : core::fragment::Frame
• nr_res_affected() : core::fragment::Frame
• nrad() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nrad_ : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nrchi_bin_ : core::pack::dunbrack::BBDepNRChiSample< P >
• nrchi_bin_id() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• nrchi_bin_id_ : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• nrchi_lower_angle_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• nrchi_lower_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_lower_boundary_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_mean_ : core::pack::dunbrack::BBDepNRChiSample< P >
• nrchi_periodicity_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• nrchi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_probability_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_sample() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_sample_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_sd_ : core::pack::dunbrack::BBDepNRChiSample< P >
• nrchi_start_angle_ : core::chemical::ResidueType
• nrchi_symmetric_ : core::chemical::ResidueType
• nrchi_upper_boundary() : 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_ : core::io::raw_data::RawStruct , core::io::silent::SilentStruct , core::kinematics::FoldTree , core::kinematics::ShortestPathInFoldTree , core::pack::task::IGEdgeReweightContainer , core::pack::task::PackerTask_ , core::scoring::methods::ProQ_Energy
• nres_monomer_ : core::conformation::symmetry::SymmetryInfo , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy
• nres_scored : core::scoring::methods::RG_MinData
• nres_topo() : core::conformation::membrane::SpanningTopology
• nres_topo_ : core::conformation::membrane::SpanningTopology
• nreses : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::PattersonCorrEnergy
• nresidue : core::scoring::sc::Atom
• nrotamer_offset_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• nrotamer_offsets_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• nrotamers() : 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::RotamerSubsets
• nrotamers_for_moltenres() : 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::RotamerSubsets
• nrows_ : core::scoring::ResidualDipolarCoupling
• nsdie : core::scoring::APBSConfig::R_PARAM
• nseq_ : core::scoring::TMscore , core::scoring::TMscoreStore
• nseq_ref_ : core::scoring::TMscoreStore
• nsigmoids() : core::scoring::SmoothScoreTermCoeffs
• nsims : core::scoring::APBSConfig
• nspans() : core::conformation::membrane::SpanningTopology
• nsr_gaussians() : core::scoring::CenHBPotential
• nstep() : core::pack::rotamer_set::WaterAnchorInfo
• nstep_ : core::pack::rotamer_set::WaterAnchorInfo
• nsteps() : core::optimization::SimpleDerivCheckResult
• nsteps_ : core::pack::annealer::MultiCoolAnnealer
• nsteps_for_rot_ : core::pack::annealer::MultiCoolAnnealer
• ntimes_ : core::import_pose::pose_stream::ExtendedPoseInputStream
• ntorsions() : core::optimization::CartesianMinimizerMap
• nTrimmedDots : core::scoring::sc::_RESULTS
• nu() : core::conformation::Residue
• nu0_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu0_components() : core::scoring::dna::DNATorsionPotential
• nu0_components_ : core::scoring::dna::DNATorsionPotential
• nu1_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu1_components() : core::scoring::dna::DNATorsionPotential
• nu1_components_ : core::scoring::dna::DNATorsionPotential
• nu1_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu1_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu1_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu1_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu2_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu2_components() : core::scoring::dna::DNATorsionPotential
• nu2_components_ : core::scoring::dna::DNATorsionPotential
• nu2_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu2_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu3_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu3_components() : core::scoring::dna::DNATorsionPotential
• nu3_components_ : core::scoring::dna::DNATorsionPotential
• nu4_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu4_components() : core::scoring::dna::DNATorsionPotential
• nu4_components_ : core::scoring::dna::DNATorsionPotential
• nu_angles : core::chemical::RingConformer
• nu_atoms() : core::chemical::ResidueType , core::conformation::Residue
• nu_atoms_ : core::chemical::ResidueType
• nu_atoms_indices_ : core::chemical::ResidueType
• nuchemics_mode_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• null_vertex : core::chemical::ResidueType
• nullaa : core::scoring::Ramachandran2B
• num : core::pose::RemarkInfo , core::scoring::packstat::SimplePDB_Atom
• num_aa_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• num_aa_types_ : core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode
• num_atoms_ : core::pack::interaction_graph::RotamerDots
• num_base_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_bb_clones() : core::conformation::symmetry::SymmetryInfo
• num_bg_nodes_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• num_bins() : core::scoring::motif::XformScore
• num_bins_ : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::func::CircularGeneral1D_Func
• num_bondangles() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• num_bytes_ : core::pack::interaction_graph::RotamerDots , core::scoring::sasa::LeGrandSasa
• NUM_BYTES_IN_DOT_SPHERE_OVERLAP_ARRAYS : core::pack::interaction_graph::DotSphere
• num_cacheable_data_types : core::pose::datacache::CacheableDataType , core::pose::datacache::CacheableObserverType
• num_carbon_donor_atoms_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• num_cav_ball_layers : core::scoring::packstat::SasaOptions
• num_chain1_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• num_chain2_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• num_chains() : core::conformation::Conformation
• num_chi_clones() : core::conformation::symmetry::SymmetryInfo
• num_commits_since_last_update_ : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• num_components_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• NUM_COUNTS_TO_ALLOCATE : core::pack::interaction_graph::DotSphere
• num_covered_ : core::pack::interaction_graph::DotSphere
• num_covered_current_ : core::pack::interaction_graph::DotSphere
• num_cutpoint() : core::kinematics::FoldTree
• num_cutpoint_ : core::kinematics::FoldTree
• num_cuts() : core::environment::FoldTreeSketch
• num_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• num_deriv_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• NUM_DERIV_H : core::scoring::electron_density::ElectronDensity
• NUM_DERIV_H_CEN : core::scoring::electron_density::ElectronDensity
• num_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• NUM_DOTS_TOTAL : core::pack::interaction_graph::DotSphere
• num_edges() : core::graph::Graph , core::graph::Node , core::graph::UpperEdgeGraph< V, E >
• num_edges_ : core::graph::Graph , core::graph::UpperEdgeGraph< V, E >
• num_edges_to_bg_nodes_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• num_edges_to_larger_indexed_nodes_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• NUM_EDGES_TO_RESERVE : core::conformation::PointGraphVertexData
• num_edges_to_smaller_indexed_nodes_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• num_energy_sum_groups_ : core::pack::interaction_graph::InteractionGraphBase
• num_features_proq2() : core::scoring::ProQPotential
• num_features_proq2_ : core::scoring::ProQPotential
• num_features_proqm() : core::scoring::ProQPotential
• num_features_proqm_ : core::scoring::ProQPotential
• num_file_aa_types_ : core::pack::interaction_graph::PDInteractionGraph
• num_file_states_for_aa_for_node_ : core::pack::interaction_graph::PDInteractionGraph
• num_hbonds : core::pose::rna::BasePair
• num_hbonds_ : core::scoring::hbonds::HBondEnergy
• num_heavy_atoms() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_heavyatoms_ : 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_hpatch_comps_later_made_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• num_hpatch_comps_procrastinated_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• num_ig_nodes_ : core::pack::interaction_graph::InteractionGraphBase
• num_incident_edges_ : core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• num_independent_residues() : core::conformation::symmetry::SymmetryInfo
• num_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• num_interfaces() : core::conformation::symmetry::SymmetryInfo
• num_jump() : core::kinematics::FoldTree , core::pose::Pose
• num_jump_ : core::kinematics::FoldTree
• num_jump_clones() : core::conformation::symmetry::SymmetryInfo
• num_jumps() : core::environment::FoldTreeSketch
• num_loops() : core::scoring::loop_graph::LoopGraph
• num_lower_edges_ : core::graph::UEVertex< V, E >
• num_lower_neighbors() : core::graph::UEVertex< V, E >
• num_models_ : core::scoring::ProQPotential
• 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_ : 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_neighbors_counting_self_static_ : core::graph::Node
• num_node_states_ : core::pack::interaction_graph::EdgeBase
• num_nodes() : core::graph::Graph
• num_nodes_ : core::graph::Graph , core::pack::annealer::FASTERAnnealer
• num_nodes_in_file_ : core::pack::interaction_graph::PDInteractionGraph
• num_orientations_ : core::scoring::sasa::LeGrandSasa
• num_overlaps_ : core::scoring::sasa::LeGrandSasa
• num_pairings() : core::scoring::dssp::Dssp
• num_pairs : core::scoring::dna::DirectReadoutPotential
• num_phi_ : core::scoring::sasa::LeGrandSasa
• num_possible_bins() : core::scoring::motif::XformScore
• num_recently_accepted_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• num_res_types_ : core::pack::interaction_graph::SymmOnTheFlyNode
• num_residues() : core::scoring::disulfides::FullatomDisulfideEnergyContainer
• num_residues_assigned_as_background_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• num_restype_groups_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode
• num_rings() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• num_rings_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• num_RNA_backbone_oxygen_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• num_RNA_base_pair_orientations_ : core::scoring::rna::RNA_LowResolutionPotential
• num_RNA_res_types_ : core::scoring::rna::RNA_LowResolutionPotential
• 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_rots_to_pack_ : core::pack::annealer::SimAnnealerBase
• num_rpe_calcs_ : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• num_sa_trajectories_ : core::pack::annealer::FASTERAnnealer
• 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_state_substitutions_considered_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• num_states_ : core::pack::interaction_graph::NodeBase
• num_states_for_aa_type_for_higher_indexed_neighbor_ : core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• num_states_for_aatype_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• num_states_for_restype_group_ : core::pack::interaction_graph::SymmOnTheFlyNode
• num_substitutions_since_hpatch_min_update_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• num_substitutions_since_surface_min_update_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• num_surface_comps_later_made_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• num_surface_comps_procrastinated_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• num_surface_deltaE_observations_since_update_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• num_surrounding_sasa_bins : core::scoring::packstat::SasaOptions
• num_theta_ : core::scoring::sasa::LeGrandSasa
• num_to_be_packed() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• num_top_kept_ : core::pack::annealer::MultiCoolAnnealer
• num_total_atoms_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_total_residues() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• num_total_residues_with_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_without_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_total_rotamers_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_total_states_ : core::pack::interaction_graph::InteractionGraphBase
• num_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_unique_rotamers_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_unrecognized_atoms_ : core::pose::PDBInfo
• num_unrecognized_res_ : core::pose::PDBInfo
• num_upper_edges_ : core::graph::UEVertex< V, E >
• num_upper_neighbors() : core::graph::UEVertex< V, E >
• num_vertices() : core::graph::UpperEdgeGraph< 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
• number_bonds_ : core::chemical::gasteiger::GasteigerAtomTypeData
• number_electrons_in_bonds_ : core::chemical::gasteiger::GasteigerAtomTypeData
• number_elements_ : core::scoring::orbitals::OrbitalsLookup
• number_hybrid_orbitals_nonbinding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• number_hybrid_orbitals_sigma_binding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• number_of_histograms_ : core::scoring::orbitals::OrbitalsStatistics
• number_stats_ : core::scoring::orbitals::OrbitalsLookup
• NumberBondingPOrbitals : core::chemical::gasteiger::GasteigerAtomTypeData
• NumberBondingSOrbitals : core::chemical::gasteiger::GasteigerAtomTypeData
• NumberHybridOrbitalType : core::chemical::gasteiger::GasteigerAtomTypeData
• NumberingSystem : core::io::raw_data::DisulfideFile
• NumberLonePairOrbitals : core::chemical::gasteiger::GasteigerAtomTypeData
• NumberOfAtomicOrbitalTypes : core::chemical::gasteiger::GasteigerAtomTypeData
• NumberOfProperties : core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData
• NumberTypeDifferences : core::chemical::gasteiger::GasteigerAtomTypeData
• NumDerivCheckData() : core::optimization::NumDerivCheckData
• numEdges_ : core::sequence::SequenceCoupling
• numeric_properties() : core::chemical::ResidueProperties
• numeric_properties_ : core::chemical::ResidueProperties
• NumericalDerivCheckResult() : core::optimization::NumericalDerivCheckResult
• numGaussians() : core::scoring::func::USOGFunc
• NumMap : core::environment::SequenceAnnotation
• NumNeighborsSelector() : core::pack::task::residue_selector::NumNeighborsSelector
• numVerts_ : core::sequence::SequenceCoupling
• nus() : core::conformation::Residue
• nus_ : core::conformation::Residue
• nusing() : core::scoring::methods::GoapRsdType
• NV_lookup_table_ : core::scoring::ScoringManager
• nvals : core::scoring::fiber_diffraction::FiberDiffraction
• NVlookup() : core::scoring::nv::NVlookup
• NVscore() : core::scoring::nv::NVscore
• NWAligner() : core::sequence::NWAligner
• nwrites : core::scoring::APBSResult
• nX_ : core::grid::CartGrid< T >
• Nx_ : core::scoring::packstat::Array2D
• nY_ : core::grid::CartGrid< T >
• Ny_ : core::scoring::packstat::Array2D
• nZ_ : core::grid::CartGrid< T >