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

- n -

• N() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• n : core::io::raw_data::DisulfideFile::ResNum
• N1_ : core::scoring::constraints::BigBinConstraint
• N1_NODE_H : protocols::sparta::ANN
• N1_NODE_I : protocols::sparta::ANN
• N1_NODE_O : protocols::sparta::ANN
• N2_ : core::scoring::constraints::BigBinConstraint
• N2_NODE_H : protocols::sparta::ANN
• N2_NODE_I : protocols::sparta::ANN
• N2_NODE_O : protocols::sparta::ANN
• N_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• n_ : core::scoring::constraints::MinMultiHarmonicFunc
• n_aa_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_actcoord_atoms_ : core::chemical::ResidueType
• n_active_dof_nodes_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• n_active_score_types() : core::scoring::EnergyGraph
• n_ali8_ : protocols::hybridization::TMalign
• n_alt_state_exp_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_anchor() : protocols::sic_dock::Rose
• n_ang_U1D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_ang_U2D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_assigned() : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::CrossPeak
• n_assigned_at_start_ : core::pack::annealer::RotamerAssigningAnnealer
• n_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T >
• N_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• N_atom_id_ : core::scoring::constraints::BackboneStubConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• n_atoms() : protocols::toolbox::DecoySetEvaluation , protocols::toolbox::InteratomicVarianceMatrix
• n_atoms_ : protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::PhiPsiRmsd , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::InteratomicVarianceMatrix
• n_atoms_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_atomtypes : core::scoring::etable::MembEtable , core::chemical::AtomTypeSet , core::chemical::CSDAtomTypeSet , core::chemical::MMAtomTypeSet , core::scoring::etable::Etable
• 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_batchrelax_ : protocols::loophash::MPI_LoopHashRefine
• n_best_ : protocols::enzdes::PackRotamersMoverPartGreedy
• n_bonded_neighbor_all_res() : core::conformation::Residue
• n_branches() : core::chemical::carbohydrates::CarbohydrateInfo
• n_build_sets() : protocols::match::upstream::ProteinUpstreamBuilder
• n_ca_atom_ : protocols::toolbox::KClusterData
• n_candidates_ : protocols::frag_picker::FragmentPicker
• 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
• n_chi_bins_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_chi_products_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_classes_ : protocols::frag_picker::scores::ABEGO_SS_Score
• n_cluster_ : protocols::toolbox::KCluster
• n_collision_check_atoms() : protocols::toolbox::match_enzdes_util::LigandConformer
• n_columns() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_comm_ : protocols::jd2::MPIMultiCommJobDistributor
• n_confs_to_cache_ : protocols::match::output::UpstreamHitCacher
• 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_construct() : protocols::swa::rna::RNA_LoopCloseSampler
• n_construct_ : protocols::swa::rna::RNA_LoopCloseSampler
• n_curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_cycles_ : protocols::docking::TemperedDocking , protocols::enzdes::EnzRepackMinimize
• n_data_ : protocols::toolbox::KClusterElement
• n_decoys() : protocols::toolbox::DecoySetEvaluation
• n_decoys_ : protocols::toolbox::DecoySetEvaluation
• n_decoys_max() : protocols::toolbox::DecoySetEvaluation
• n_decoys_max_ : protocols::toolbox::DecoySetEvaluation
• n_denied : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• n_denied_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• n_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• n_deriv_check_results() : core::optimization::NumericalDerivCheckResult
• n_dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_disjoint_sets() : core::graph::DisjointSets
• n_dof_angle_ : protocols::simple_moves::BBGaussianMover
• n_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• n_dof_nodes_ : core::optimization::symmetry::SymMinimizerMap
• n_doublebins_per_supervoxel : protocols::match::Bool3DGrid
• n_downstream_to_output_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• n_elements() : core::chemical::ElementSet
• n_end_atom_ : protocols::simple_moves::BBGaussianMover
• n_entries() : core::scoring::trie::CPDataCorrespondence
• n_entries_ : core::scoring::trie::CPDataCorrespondence
• n_euler_bins_ : protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• n_external_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• n_extra_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• n_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• n_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• n_frags_ : protocols::frag_picker::FragmentPicker
• n_full_updates_ : core::scoring::NeighborList
• n_geom_csts_ : protocols::match::MatchCounter
• n_geometric_constraints() : protocols::match::Matcher
• n_geometric_constraints_ : protocols::match::output::SameSequenceGrouper , protocols::match::output::UpstreamHitCacher , protocols::match::Matcher , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper
• n_geometric_constraints_per_match_ : protocols::match::HitHasher
• n_grid_ : core::scoring::PoissonBoltzmannPotential
• N_HASH_MAPS : protocols::match::HitHasher
• 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_high_entropy_decoys_ : protocols::optimize_weights::PNatStructureOptEData
• 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 , protocols::fldsgn::topology::BB_Pos
• n_inserts_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• n_interface_res_ : protocols::analysis::InterfaceAnalyzerMover
• n_kept_matches() : protocols::match::output::BestMatchesCollection
• n_lanthanides_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• n_loophash_ : protocols::loophash::MPI_LoopHashRefine
• n_loops() : protocols::loophash::LoopHashMap
• n_mainchain_atoms() : core::conformation::Residue
• n_max_cluster_ : protocols::toolbox::ClusterPhilStyle
• n_mutants() : protocols::pmut_scan::PointMutScanDriver
• n_mutations() : protocols::pmut_scan::Mutant
• n_new_dofs_ : protocols::optimize_weights::WrapperOptEMultifunc
• n_nodes() : core::graph::DisjointSets
• n_nodes_left_to_spin_down_ : protocols::jd2::MPIFileBufJobDistributor
• n_non_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_non_polymeric_residue_connections_ : core::chemical::ResidueType
• n_nonchitip_atoms_for_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• n_nonjump_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_npd_properties() : protocols::pack_daemon::DaemonSet
• n_npd_properties_ : protocols::pack_daemon::DaemonSet
• n_nrchi_sample_bins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• n_nv_dist_sd_ : core::scoring::methods::ProClosureEnergy
• n_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• n_orbitals_ : core::chemical::orbitals::AssignOrbitals , core::chemical::ResidueType
• n_output_so_far_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• N_p_sp2 : core::scoring::orbitals::OrbitalsStatistics
• n_packed_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_packed_rots_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_pconnect_ : core::scoring::etable::count_pair::CountPairGeneric
• n_pcs_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs2::PcsDataLanthanide
• n_pcs_spin_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• n_periodic_ : core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::constraints::PeriodicFunc
• n_pert_res_ : protocols::simple_moves::BBGaussianMover
• n_phi_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• N_PHIPSI_BINS : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• 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_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• N_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• n_poses_ : protocols::contact_map::ContactMap
• n_possible_hits_per_at3frame() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• n_possible_hits_per_upstream_conformation() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage
• n_possible_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_possible_rots_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_prepare_for_scorings_ : core::scoring::NeighborList
• n_proton_chi() : core::chemical::ResidueType
• n_psi_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• n_rank() : protocols::jd2::MPIFileBufJobDistributor
• n_rank_ : protocols::jd2::MPIFileBufJobDistributor
• n_real_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• n_real_dofs_ : protocols::optimize_weights::WrapperOptEMultifunc
• n_rebuild_tries() : protocols::comparative_modeling::LoopRelaxMover
• n_rebuild_tries_ : protocols::comparative_modeling::LoopRelaxMover
• n_res_ : protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::PCS_FragDistance
• n_resi_ : protocols::protein_interface_design::movers::BestHotspotCstMover
• n_residue() : core::id::AtomID_Map< T > , core::id::DOF_ID_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_residues_for_entity() : protocols::pack_daemon::EntityCorrespondence
• n_restypes() : protocols::match::downstream::TargetRotamerCoords
• n_restypes_ : core::pack::rotamer_set::ContinuousRotamerSet
• n_restypes_to_build() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• n_rotamer_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamer_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamer_bins_for_aa_02() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotameric_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotameric_chi_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamers_for_resgroup_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_rotamers_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_rotamers_for_restype_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• n_rotamers_per_target_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• n_rots_total() : protocols::match::downstream::TargetRotamerCoords
• n_rots_total_ : protocols::match::downstream::TargetRotamerCoords
• n_rows() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_sample_ : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• n_sample_rotamers() : core::pack::rotamer_set::ContinuousRotamerSets
• n_sample_rotamers_ : core::pack::rotamer_set::ContinuousRotamerSets
• n_samples_per_chi() : protocols::match::upstream::FullChiSampleSet
• n_samples_per_chi_ : protocols::match::upstream::FullChiSampleSet
• n_samples_per_side_of_nrchi_bin() : protocols::match::upstream::SampleStrategyData
• n_samples_per_side_of_nrchi_bin_ : protocols::match::upstream::SampleStrategyData
• n_samples_wi_sd_range() : protocols::match::upstream::SampleStrategyData
• n_samples_wi_sd_range_ : protocols::match::upstream::SampleStrategyData
• 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_small_moves_ : protocols::antibody2::H3RefineCCD
• n_sorts : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• n_sorts_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• n_stubs_ : protocols::protein_interface_design::movers::HotspotHasherMover
• n_swap_dead_ : protocols::wum::WorkUnitQueue_Swapped
• n_swap_total_ : protocols::wum::WorkUnitQueue_Swapped
• N_target_ : core::scoring::constraints::BackboneStubConstraint
• n_temp_levels() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• N_term_inside_ : core::scoring::MembraneTopology
• n_terminus_ : protocols::swa::protein::StepWiseProteinPoseSetup
• n_tied_for_worst_ : protocols::pack_daemon::MultistateFitnessFunction
• n_to_be_packed_ : core::pack::task::PackerTask_
• n_to_be_packed_up_to_date_ : core::pack::task::PackerTask_
• n_to_buffer_ : protocols::jd2::SilentFileJobOutputter
• n_to_output_per_group() : protocols::match::MatcherTask
• n_to_output_per_group_ : protocols::match::MatcherTask , protocols::match::output::MatchConsolidator
• n_top_matches_to_keep_ : protocols::match::output::BestMatchesCollection
• n_top_natives_to_score() : protocols::optimize_weights::PNatStructureOptEData
• n_top_natives_to_score_ : protocols::optimize_weights::PNatStructureOptEData
• n_tor_U1D3_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_trial_min_ : protocols::scoring::methods::pcs2::PcsEnergyParameter
• n_trial_min_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• n_trial_min_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• n_trial_min_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• n_trial_min_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• n_unassigned() : core::pack::scmin::SidechainStateAssignment
• n_unassigned_ : core::pack::scmin::SidechainStateAssignment
• n_update_from_wide_ : core::scoring::NeighborList
• n_viable_target_hits_since_last_pruning_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• n_Vmin_assignments() : protocols::noesy_assign::CrossPeak
• n_wells_ : protocols::optimize_weights::PNatRotOptEPositionData
• n_worker() : protocols::jd2::MPIFileBufJobDistributor
• n_worker_ : protocols::jd2::MPIFileBufJobDistributor
• n_xyz_bins_ : protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• na_allowed_ : core::pack::task::PIKAA
• NA_calculate() : protocols::scoring::Interface
• naccepted_ : protocols::dna::RotamerDNAHBondFilter
• 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
• nali() : protocols::frag_picker::VallResidue
• nali_ : protocols::frag_picker::VallResidue
• nAllDots : core::scoring::sc::_RESULTS
• nallocated() : core::graph::ArrayPool< T >
• name : core::io::pdb::AtomInformation , core::kinematics::Node , protocols::rna::suite_info , protocols::swa::rna::Residue_info , core::chemical::Atom , core::chemical::AtomType , core::chemical::AtomTypeSet , core::chemical::CSDAtomType , core::chemical::Element , core::chemical::MMAtomType , core::chemical::Orbital , core::chemical::orbitals::OrbitalType , core::chemical::Patch , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::coarse::Translator , core::conformation::Residue , core::io::silent::SilentEnergy , core::pack::task::NATRO , core::pack::task::NATAA , core::pack::task::ALLAA , core::pack::task::ALLAAxc , core::pack::task::ALLAAwc , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::NOTAA , core::pack::task::EMPTY , core::pack::task::POLAR , core::pack::task::APOLAR , core::pack::task::APOLA , core::pack::task::EX , core::pack::task::NC , core::pack::task::EX_CUTOFF , core::pack::task::USE_INPUT_SC , core::pack::task::AUTO , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::NO_ADDUCTS , core::pack::task::FIX_HIS_TAUTOMER , core::pose::PDBInfo , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::util::ABEGO , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::Template , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::evaluation::MetaPoseEvaluator , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::FilterStructs , protocols::genetic_algorithm::EntityElement , protocols::inputter::FastaInputter , protocols::inputter::Inputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter , protocols::jd2::archive::AbstractArchiveBase , protocols::match::upstream::UpstreamResTypeGeometry , protocols::moves::Mover , protocols::moves::PDBDumpMover , protocols::multistate_design::PosType , protocols::noesy_assign::Resonance , protocols::outputter::FormatStringOutputter , protocols::outputter::Outputter , protocols::outputter::PDBOutputter , protocols::outputter::ResFileOutputter , protocols::outputter::SilentFileOutputter , protocols::pack_daemon::VectorExpression , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::BatchEvaluator , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_moves::O2M_MutateMover , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::viewer::ConformationViewer , protocols::wum2::WorkUnit_ElScripts
• name1() : core::chemical::ResidueType , core::conformation::Residue
• name1_ : core::chemical::SetIO_String , core::chemical::Selector_NAME1 , core::chemical::ResidueType , core::io::pdb::LinkInformation
• 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
• name2foldtype_ : protocols::fldsgn::topology::SheetFoldTypeManager
• 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() : protocols::rna::RNA_suite_list
• name2weight_type_ : core::scoring::hbonds::HBondTypeManager
• name3 : protocols::dna::DnaDesignDef , core::chemical::ResidueType , core::conformation::Residue , core::pack::interaction_graph::RotamerDots
• name3_ : core::chemical::SetIO_String , core::chemical::ResidueType
• 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::CSDAtomType , core::chemical::Element , core::chemical::MMAtomType , core::chemical::Orbital , core::chemical::Patch , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::coarse::Translator::BeadAtom , core::grid::CartGrid< T > , core::io::silent::SilentEnergy , core::pose::PDBInfo , core::scoring::hbonds::FadeInterval , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::util::ABEGO , protocols::abinitio::Template , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::features::ReportToDB , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::StrandPairing , protocols::flxbb::FilterStructs , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::scores::MakeFragmentScoringMethod , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity , protocols::jd2::archive::AbstractArchiveBase , protocols::moves::PDBDumpMover , protocols::moves::PyMolMover , protocols::pack_daemon::VectorExpression , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::viewer::ConformationViewer , protocols::wum2::WorkUnit_ElScripts
• 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_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• name_from_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
• name_from_hybridization_type() : core::scoring::hbonds::HBondTypeManager
• name_from_loop_configuration() : protocols::loops::JSONFormattedLoopsFileReader
• name_from_residue_identifier() : protocols::loops::JSONFormattedLoopsFileReader
• 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_hbond_calc() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• name_of_hbond_calc_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• name_of_InterfaceNeighborDefinitionCalculator_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• name_of_ResidueDecompositionCalculator_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• name_of_sasa_calc() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• name_of_sasa_calc_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• name_wo_rgstr() : protocols::fldsgn::topology::StrandPairingSet
• named_atom1_ : core::scoring::constraints::NamedAtomPairConstraint
• named_atom2_ : core::scoring::constraints::NamedAtomPairConstraint
• named_atom_id_map_ : protocols::toolbox::AllowInsert
• named_distmap_ : protocols::noesy_assign::FragsToAtomDist
• named_state_data_file_names_ : protocols::pack_daemon::DynamicAggregateFunction
• named_state_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• NamedAtomID : core::pose::Pose , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::id::NamedAtomID
• NamedAtomPairConstraint() : core::scoring::constraints::NamedAtomPairConstraint
• NamedAtomPairConstraintCreator() : protocols::constraints_additional::NamedAtomPairConstraintCreator
• NamedAtomPairConstraintList : protocols::abinitio::Template
• NamedDistanceMap : protocols::noesy_assign::FragsToAtomDist
• NamedInnerMap : protocols::noesy_assign::FragsToAtomDist
• NamedStubID : protocols::forge::build::ConnectRight , core::id::NamedStubID
• names_to_indexes_ : core::scoring::saxs::FormFactorManager
• names_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• NameTable : protocols::noesy_assign::MethylNames
• nangleA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nangleB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nangles() : core::fragment::BBTorsionAndAnglesSRFD , core::optimization::MinimizerMap , core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::SymMinimizerMap
• nat_bb_bins_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• nat_chis_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• nat_rots_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• NatbiasHelicesSheetPotential : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• NatbiasHelicesSheetPotentialOP : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• NatbiasHelixPairPotential : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• NatbiasHelixPairPotentialOP : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• NatbiasSecondaryStructureEnergy() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• NatbiasSheetPotential() : protocols::fldsgn::potentials::sspot::NatbiasSheetPotential
• NatbiasStrandPairPotential() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• NatbiasStrandPairPotentialOP : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• native_ : protocols::abinitio::Templates , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDockMain , protocols::simple_filters::ContactMapEvaluator , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• native_aa() : protocols::optimize_weights::PNatAAOptEPositionData
• native_aa_ : protocols::optimize_weights::PNatAAOptEPositionData
• native_alignment() : protocols::swa::rna::StepWiseRNA_JobParameters
• native_alignment_ : protocols::swa::rna::StepWiseRNA_JobParameters
• native_chi_ : protocols::optimize_weights::PNatRotOptEPositionData
• native_chi_periodicity_ : protocols::optimize_weights::PNatRotOptEPositionData
• native_comp_ : protocols::enzdes::EnzdesScorefileFilter
• native_compare_calculators_ : protocols::enzdes::EnzdesScorefileFilter
• native_comparison_ : protocols::enzdes::EnzdesScorefileFilter
• native_conf_ : protocols::enzdes::EnzdesFlexibleRegion
• native_distance_viol() : protocols::noesy_assign::PeakAssignment
• native_distance_viol_ : protocols::noesy_assign::PeakAssignment
• native_down_ : protocols::simple_filters::JumpEvaluator
• native_edensity_score_cutoff_ : protocols::swa::rna::StepWiseRNA_Minimizer
• native_edensity_score_screener() : protocols::swa::rna::StepWiseRNA_Minimizer
• native_filename_ : protocols::antibody::AntibodyModeler
• native_fragment_bb_energies_ : protocols::enzdes::EnzdesFlexBBProtocol
• native_id_ : protocols::jobdist::BasicJob
• native_pdbs_ : protocols::optimize_weights::IterativeOptEDriver
• native_pose() : protocols::evaluation::AlignEvaluator
• native_pose_ : core::scoring::methods::RMS_Energy , protocols::abinitio::AbrelaxApplication , protocols::abinitio::JumpingFoldConstraints , protocols::antibody::AntibodyModeler , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::forge::remodel::RemodelMover , protocols::jumping::JumpSelector , protocols::moves::_BoolMover , protocols::moves::Mover , protocols::relax::WorkUnit_BatchRelax , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::swa::PoseFilter_RMSD_Screen , protocols::swa::RigidBodySampler
• native_pose_buf : protocols::boinc::BoincSharedMemory
• native_pose_exists : protocols::boinc::BoincSharedMemory
• native_poses_ : protocols::enzdes::DesignVsNativeComparison , protocols::optimize_weights::IterativeOptEDriver
• native_present_ : protocols::antibody::AntibodyModeler
• native_residue_bonus_ : protocols::protein_interface_design::FavorNativeResidue
• native_rmsd_screen_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• native_rotamer_index_ : protocols::optimize_weights::PNatRotOptEPositionData
• native_screen_ : protocols::swa::rna::StepWiseRNA_Minimizer
• native_screen_rmsd_cutoff_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• native_secstruct() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native_secstruct_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native_sequence_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• native_spairset_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• native_tag() : protocols::jobdist::BasicJob
• native_task_ : core::pack::task::operation::ReplicateTask
• native_topology_ : protocols::abinitio::PairingStatistics
• native_up_ : protocols::simple_filters::JumpEvaluator
• native_virtual_res_list_ : protocols::swa::rna::StepWiseRNA_PoseSetup
• NativeEvaluatorCreator() : protocols::simple_filters::NativeEvaluatorCreator
• nativeness() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_high() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_low() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_rms_high_ : protocols::optimize_weights::PNatStructureOptEData
• nativeness_rms_low_ : protocols::optimize_weights::PNatStructureOptEData
• nativeness_sum_ : protocols::optimize_weights::PNatStructureOptEData
• natives_ : protocols::ddg::ddGMover , protocols::optimize_weights::PNatStructureOptEData
• natom : core::scoring::packing::HolesResult , core::scoring::sc::Atom , core::scoring::packstat::SimplePDB , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• natom_ : protocols::toolbox::KClusterData
• nAtoms : core::scoring::sc::_RESULTS
• natoms : core::scoring::APBSConfig , core::chemical::ResidueType , core::conformation::Residue , 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::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::hbonds::HBondResidueMinData , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::match::upstream::UpstreamResTypeGeometry , protocols::pockets::PocketConstraint
• natoms_ : core::chemical::AutomorphismIterator , core::chemical::ResidueType , core::optimization::DOF_DataPoint , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::scoring::PQR , core::scoring::FACTSResidueInfo , core::scoring::hbonds::HBondResidueMinData , core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• natro_movemap_ : protocols::forge::remodel::RemodelData
• nb_list : protocols::relax::ClassicRelax , protocols::simple_moves::MinMover
• nb_list_ : protocols::ub_e2c::ubi_e2c_modeler , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• nb_weight() : core::scoring::packing::HolesParams
• nb_weights_ : core::scoring::packing::HolesParams
• nbackbone_conformations() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nballs() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• nballs_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• nbb() : core::fragment::BBTorsionSRFD , protocols::frags::TorsionFragment
• nbbconfs_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_flexseg() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_flexseg_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbhist() : core::scoring::packing::PoseBalls
• nbhist_ : core::scoring::packing::PoseBalls
• nbins_ : protocols::features::AtomAtomPairFeatures
• nblist() : core::scoring::Energies
• nblist_ : core::scoring::Energies , core::scoring::NeighborList , core::scoring::symmetry::NBListCache
• 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
• NBListCache() : core::scoring::symmetry::NBListCache
• nBlockedAtoms : core::scoring::sc::_RESULTS
• nblocks() : core::graph::ArrayPool< T >
• nblocks_ : core::graph::ArrayPool< T >
• nbonds() : core::conformation::PseudoBond
• nbonds_ : core::conformation::PseudoBond
• nbonds_from_bb_atom() : protocols::match::upstream::BuildSet
• nbonds_from_bb_atom_ : protocols::match::upstream::BuildSet
• nbr_atom() : core::chemical::ResidueType , core::conformation::Residue
• nbr_atom_ : core::chemical::ResidueType
• nbr_atom_xyz() : core::conformation::Residue
• nbr_cutoff_ : protocols::ddg::ddGMover
• nbr_distance_squared_ : core::scoring::orbitals::OrbitalsScore
• nbr_list_begin() : core::optimization::AtomNode
• nbr_list_end() : core::optimization::AtomNode
• nbr_radius() : core::chemical::ResidueType , core::conformation::Residue
• nbr_radius_ : core::chemical::ResidueType
• nbrs : core::optimization::AtomNode , core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::HBondSet
• nbrs_ : core::scoring::hbonds::HBondSet
• nBuriedAtoms : core::scoring::sc::_RESULTS
• nBuriedDots : core::scoring::sc::_RESULTS
• nc_allatm_ : protocols::fldsgn::NcontactsCalculator
• nc_hpatm_ : protocols::fldsgn::NcontactsCalculator
• nc_hpres_ : protocols::fldsgn::NcontactsCalculator
• 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
• ncentroid_ : protocols::loophash::LoopHashMoverWrapper
• nchi() : core::chemical::ResidueType , core::conformation::Residue , core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary , protocols::match::upstream::UpstreamResTypeGeometry
• nchi_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nchi_aa : core::pack::dunbrack::CoarseRotamer
• nchi_max_ : protocols::simple_filters::ChiWellRmsdEvaluator
• ncluster() : protocols::toolbox::KClusterElement
• ncol() : protocols::noesy_assign::PeakFileFormat
• nconnections_for_entry_ : core::scoring::trie::CPDataCorrespondence
• NcontactsCalculator() : protocols::fldsgn::NcontactsCalculator
• NcontactsFilter() : protocols::fldsgn::filters::NcontactsFilter
• nContinuousSegments() : protocols::rbsegment_relax::RBSegment
• ncopies_ : core::fragment::FragmentIO
• ncsts() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• ncycle() : protocols::flxbb::DesignTask
• ncycle_ : protocols::flxbb::DesignTask
• ncycles_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler
• ndaemons() : protocols::pack_daemon::DaemonSet
• ndaemons_ : protocols::pack_daemon::DaemonSet
• ndata_ : protocols::toolbox::KClusterData
• ndihe() : core::chemical::ResidueType
• ndihe_ : core::chemical::ResidueType
• ndisAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ndofs() : core::optimization::CartesianMinimizerMap
• ndofs_added_for_focused_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• ndruns_ : protocols::simple_moves::SetReturningPackRotamersMover
• ne_ : protocols::frag_picker::quota::TorsionBinPool
• near_interface : protocols::ligand_docking::ligand_options::InterfaceInfo
• Near_Native_Rotamer_Count : protocols::swa::rna::SillyCountStruct
• nearby_atom_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• nearby_atom_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• need_to_initialize_ : protocols::swa::StepWiseCombineSampleGenerator , protocols::swa::StepWisePoseCombineSampleGenerator
• NEED_TO_KNOW : protocols::topology_broker::DofClaim
• neg_begin_ : core::graph::ArrayPool< T >
• neg_ptr_ : core::graph::ArrayPoolElement< T >
• neg_space_blocks_ : core::graph::ArrayPool< T >
• negate() : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• negate_ : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• negative_better() : core::sequence::SequenceProfile
• negative_better_ : core::sequence::SequenceProfile
• negative_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• negln_rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• negln_rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• negmask_from_offsets() : protocols::match::Bool3DGrid
• NegSpaceElement() : core::graph::NegSpaceElement< T >
• neighbor_addresses_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• neighbor_count : protocols::qsar::scoring_grid::ChargeAtom , protocols::optimize_weights::PNatAAOptEPositionData
• neighbor_count_ : protocols::optimize_weights::PNatAAOptEPositionData
• neighbor_count_cutoff_ : protocols::toolbox::task_operations::ProteinCore
• neighbor_counts() : protocols::frag_picker::ContactCounts
• neighbor_counts_ : protocols::frag_picker::ContactCounts
• neighbor_counts_exist() : protocols::frag_picker::ContactCounts
• neighbor_cutoff() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::ddg::ddGMover , protocols::simple_filters::NonSequentialNeighborsFilter
• neighbor_cutoff_ : core::scoring::solid_surface::SurfaceEnergies , protocols::scoring::ImplicitFastClashCheck , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::toolbox::task_operations::ProteinCore
• neighbor_cutoff_ca_ : protocols::scoring::ImplicitFastClashCheck
• neighbor_cutoff_sq_ : protocols::scoring::ImplicitFastClashCheck
• neighbor_cutoff_sq_ca_ : protocols::scoring::ImplicitFastClashCheck
• neighbor_design_ : protocols::forge::remodel::RemodelMover::instruction_flags
• neighbor_dist_ : protocols::antibody2::H3RefineCCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• neighbor_distance_cutoff_ : protocols::features::UnrecognizedAtomFeatures
• neighbor_hits() : protocols::match::HitNeighborFinder
• neighbor_id() : core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator
• 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_repack_ : protocols::forge::remodel::RemodelMover::instruction_flags
• neighbor_strands() : protocols::fldsgn::topology::StrandPairingSet
• neighbor_strands_ : protocols::fldsgn::topology::StrandPairingSet
• neighbor_weight() : core::scoring::nv::NVscore
• NeighborDependentTabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• NeighborDependentTorsionSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber
• neighborhood_buns_polar_calc_name() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• neighborhood_calc() : protocols::anchored_design::AnchorMoversData
• neighborhood_calc_ : protocols::anchored_design::AnchorMoversData
• neighborhood_calc_name() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• neighborhood_of_mutations() : protocols::ddg::ddGMover
• NeighborhoodByDistanceCalculator() : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• NeighborList : core::scoring::Energies , protocols::sparta::PDB , core::scoring::NeighborList
• neighbors : core::scoring::sc::Atom
• neighbors_ : protocols::enzdes::LigBurialFilter , protocols::simple_filters::ResidueBurialFilter , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• 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
• NeighborsByDistanceCalculator() : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• NeighborTypeFilter() : protocols::simple_filters::NeighborTypeFilter
• Nend_orient() : protocols::fldsgn::topology::SS_Base
• Nend_orient_ : protocols::fldsgn::topology::SS_Base
• Nend_pos() : protocols::fldsgn::topology::SS_Base
• Nend_pos_ : protocols::fldsgn::topology::SS_Base
• NestedEnergyTermDDGMutationOptEData() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• NestedEnergyTermPNatAAOptEPositionData() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• netstate_duplicated_ : core::pack::annealer::FASTERAnnealer
• netTargetPocketVolume() : protocols::pockets::PocketGrid
• network_allow_same_residue_connect_ : protocols::noesy_assign::PeakAssignmentParameters
• network_analysis() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignmentResidueMap
• network_analysis2() : protocols::noesy_assign::PeakAssignmentResidueMap
• network_anchoring() : protocols::noesy_assign::PeakAssignment
• network_anchoring_ : protocols::noesy_assign::PeakAssignment
• network_anchoring_per_residue() : protocols::noesy_assign::PeakAssignment
• network_anchoring_per_residue_ : protocols::noesy_assign::PeakAssignment
• network_atom_min_ : protocols::noesy_assign::PeakAssignmentParameters
• network_include_reverse_dir_ : protocols::noesy_assign::PeakAssignmentParameters
• network_mode_ : protocols::noesy_assign::PeakAssignmentParameters
• network_reswise_high_ : protocols::noesy_assign::PeakAssignmentParameters
• network_reswise_min_ : protocols::noesy_assign::PeakAssignmentParameters
• network_use_all_covalent_atoms_ : protocols::noesy_assign::PeakAssignmentParameters
• NEUTRAL_PHI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• NEUTRAL_PSI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• NEUTRON_DIFFRACTION : core::io::pdb::HeaderInformation
• never_switched_noe_filter_ : protocols::abinitio::IterativeBase
• new_array() : core::graph::ArrayPool< T >
• new_cache_ : core::fragment::CacheWrapper< T, XCacheUnit >
• new_calculator() : protocols::pack_daemon::NPDPropCalculatorCreator
• new_chain_order() : core::io::pdb::PDB_DReaderOptions
• new_chain_order_ : core::io::pdb::PDB_DReaderOptions
• new_chemical_bond() : core::kinematics::FoldTree
• new_conformation_ : protocols::viewer::ConformationViewer
• new_decoy() : protocols::topology_broker::JumpClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TopologyClaimer , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DisulfJumpClaimer
• new_decoys_out_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• new_dof_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• new_entity() : protocols::genetic_algorithm::EntityElementCreator , protocols::genetic_algorithm::GeneticAlgorithm , protocols::multistate_design::PosTypeCreator
• new_func() : core::scoring::constraints::FuncFactory
• new_grid() : protocols::qsar::scoring_grid::GridFactory
• new_icoor() : core::chemical::Orbital
• new_icoor_ : core::chemical::Orbital
• new_jump() : core::kinematics::FoldTree
• new_kinematics() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::LoopJumpFoldCst
• new_level_begins_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• new_nr_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• new_orbital_icoor_data() : core::chemical::ResidueType
• new_order : core::kinematics::FoldTree
• new_phi() : protocols::simple_moves::BackboneMover
• new_phi_ : protocols::simple_moves::BackboneMover
• new_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• new_psi() : protocols::simple_moves::BackboneMover
• new_psi_ : protocols::simple_moves::BackboneMover
• new_rama_score_ : protocols::simple_moves::BackboneMover
• new_residue_group() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_rots_ : protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• new_secondary_structure_override() : protocols::forge::components::VarLengthBuild
• new_secondary_structure_override_ : protocols::forge::components::VarLengthBuild
• new_sequence_override() : protocols::forge::components::VarLengthBuild
• new_sequence_override_ : protocols::forge::components::VarLengthBuild
• new_structures_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• new_terminal_pos() : protocols::fldsgn::CircularPermutation
• new_terminal_pos_ : protocols::fldsgn::CircularPermutation
• new_topology : core::kinematics::FoldTree
• newConstraint() : core::scoring::constraints::ConstraintFactory
• newDataLoader() : protocols::jd2::parser::DataLoaderFactory
• newFilter() : protocols::filters::FilterFactory , protocols::protein_interface_design::DockDesignFilterFactory
• newMover() : protocols::moves::MoverFactory
• newResFilter() : core::pack::task::operation::ResFilterFactory
• newRLTO() : core::pack::task::operation::ResLvlTaskOperationFactory
• newSearch() : protocols::pockets::PocketGrid
• newTaskOperation() : core::pack::task::operation::TaskOperationFactory
• newTaskOperations() : core::pack::task::operation::TaskOperationFactory
• newTopologyClaimer() : protocols::topology_broker::TopologyClaimerFactory
• nex_ : core::scoring::ResidualDipolarCoupling
• next() : core::graph::EdgeListElement , core::chemical::AutomorphismIterator , core::graph::NegSpaceElement< T > , core::graph::EdgeListElement , core::sequence::Cell , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::viewer::triangleIterator , protocols::wum::WorkUnitQueue
• next_ : core::graph::NegSpaceElement< T > , core::graph::EdgeListElement
• next_batch() : protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
• next_center() : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA
• next_child() : core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• next_circle() : core::scoring::packstat::trace
• next_exchange_schedule() : protocols::canonical_sampling::HamiltonianExchange
• next_free_address_index_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• next_from_pool() : protocols::frag_picker::quota::QuotaSelector
• next_iteration_pdbs_ : protocols::optimize_weights::IterativeOptEDriver
• next_job() : protocols::jobdist::BaseJobDistributor
• next_job_to_assign_ : protocols::jd2::MPIWorkPoolJobDistributor
• next_job_to_try_assigning_ : protocols::jd2::MPIWorkPartitionJobDistributor
• next_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• next_level_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• next_move_ : protocols::moves::CycleMover
• next_nodes_ : protocols::toolbox::match_enzdes_util::InvrotTarget
• next_random_job() : protocols::jd2::ShuffleFileSystemJobDistributor
• next_random_job_ : protocols::jd2::ShuffleFileSystemJobDistributor
• next_resnum() : protocols::simple_moves::sidechain_moves::SidechainMover
• next_resnum_ : protocols::simple_moves::sidechain_moves::SidechainMover
• next_segment_id() : protocols::backrub::BackrubMover
• next_segment_id_ : protocols::backrub::BackrubMover
• next_struct() : core::import_pose::pose_stream::SilentFilePoseInputStream
• next_suite_atoms_ : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• NEXT_Tab : protocols::sparta::Sparta::SpartaLib
• next_to_return_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator
• next_torsion_string() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• next_trace_ : core::scoring::packstat::trace
• next_trigger_id_ : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• nextFileName : protocols::sparta::Sparta::SpartaLib
• nextof() : boost::unordered_object_pool< T, UserAllocator >
• nextX : protocols::viewer::triangleIterator
• nextY : protocols::viewer::triangleIterator
• nextZ : protocols::viewer::triangleIterator
• nfile_ : protocols::toolbox::KClusterData
• nfiltered_ : protocols::dna::RotamerDNAHBondFilter
• nfit_ : protocols::evaluation::PCA
• nflexible_segments() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nflxbb_cycles_ : protocols::flxbb::FlxbbDesign
• nfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• nFrags_ : protocols::frag_picker::QuotaDebug
• nfrags_ : protocols::jd2::parser::FragmentReader , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::PlaceFragments
• nfullatom_ : protocols::loophash::LoopHashMoverWrapper
• ngaussians() : core::scoring::SmoothScoreTermCoeffs
• nh_ : protocols::frag_picker::quota::TorsionBinPool
• nhbonds() : core::scoring::hbonds::HBondSet
• nheavyatoms() : core::chemical::ResidueType , core::conformation::Residue
• nheavyatoms_ : core::chemical::ResidueType
• ninner_cycles_ : protocols::rbsegment_relax::AutoRBMover
• nions : core::scoring::APBSConfig::I_PARAM
• nirotamers() : protocols::motifs::IRCollection
• njobs : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• njump_ : protocols::jumping::JumpSample
• njump_monomer_ : core::conformation::symmetry::SymmetryInfo
• njumps() : core::io::silent::ProteinSilentStruct_Template< T >
• nkins_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• nl_ : protocols::frag_picker::quota::TorsionBinPool
• nlcontacts_graph_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• nlev : core::scoring::APBSConfig::I_PARAM
• nlevels() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• nlevels_ : protocols::canonical_sampling::mc_convergence_checks::PoolData , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• nloop() : protocols::simple_moves::PackRotamersMover
• nloop_ : protocols::simple_moves::PackRotamersMover
• nlr_gaussians() : core::scoring::CenHBPotential
• nmax_ : protocols::noesy_assign::PeakAssignmentParameters
• nmer_cterm_ : core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerPSSMEnergy
• nmer_length() : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy
• nmer_length_ : core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerPSSMEnergy
• nmer_pssm_scorecut() : core::scoring::methods::NMerPSSMEnergy
• nmer_pssm_scorecut_ : core::scoring::methods::NMerPSSMEnergy
• nmer_ref_energies_ : core::scoring::methods::NMerRefEnergy
• NMerPSSMEnergy() : core::scoring::methods::NMerPSSMEnergy
• NMerPSSMEnergyFilter() : protocols::simple_filters::NMerPSSMEnergyFilter
• NMerRefEnergy() : core::scoring::methods::NMerRefEnergy
• nmolten_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmoltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::ContinuousRotamerSets
• nmoltenres_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::scmin::SidechainStateAssignment
• nmotifs() : protocols::motifs::MotifLibrary
• nmoves() : protocols::simple_moves::BackboneMover
• nmoves_ : protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::moves::RandomMover , protocols::moves::WhileMover , protocols::relax::ClassicRelax , protocols::simple_moves::BackboneMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover , protocols::moves::RepeatMover
• NMR : core::io::pdb::HeaderInformation
• nmr2rosetta() : protocols::noesy_assign::MethylNames
• nmr2rosetta_ : protocols::noesy_assign::MethylNames
• NmrConstraint : protocols::noesy_assign::PeakAssignment
• NmrConstraintOP : protocols::noesy_assign::PeakAssignment
• nmtr() : core::scoring::FACTSResidueInfo
• nmtr_ : core::scoring::FACTSResidueInfo
• nnegative_ : core::graph::ArrayPool< T >
• nneigh : core::scoring::SelfNeighInfo
• nneighbors() : core::scoring::hbonds::HBondResidueMinData
• nneighbors_ : core::scoring::hbonds::HBondResidueMinData
• nneighbs_ : core::io::sequence_comparation::DesignContrast , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack
• NO_CONTACT : protocols::noesy_assign::FragsToAtomDist
• no_design() : protocols::flxbb::FlxbbDesign
• no_design_ : protocols::flxbb::FlxbbDesign , protocols::forge::remodel::RemodelMover::instruction_flags
• no_design_cys_ : protocols::enzdes::DetectProteinLigandInterface
• no_dis_dep_die_ : core::scoring::hackelec::HackElecEnergy
• NO_DISULFIDE : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• no_filters_ : protocols::docking::DockingProtocol
• no_frags_ : protocols::anchored_design::AnchoredPerturbMover , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::anchored_design::AnchorMoversData
• no_global_frame_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• no_interpolate_Mpair_ : core::scoring::MembranePotential
• no_lr_ : protocols::rbsegment_relax::RBSegmentRelax
• no_modified_ddG_ : protocols::simple_filters::RotamerBoltzmannWeight
• no_network_ : protocols::noesy_assign::PeakAssignmentParameters
• no_optH() : core::import_pose::ImportPoseOptions
• no_optH_ : core::import_pose::ImportPoseOptions
• no_packstat_calc_ : protocols::enzdes::EnzdesScorefileFilter
• no_prepack1 : protocols::flexpep_docking::FlexPepDockingFlags
• no_prepack2 : protocols::flexpep_docking::FlexPepDockingFlags
• no_progress_init_cnt_ : protocols::boinc::Boinc
• no_ranked_frags() : protocols::enzdes::EnzdesFlexibleRegion
• no_relax() : protocols::flxbb::FlxbbDesign
• no_relax_ : protocols::flxbb::FlxbbDesign
• no_repack_ : protocols::forge::remodel::RemodelMover::instruction_flags
• no_repack_ddG() : protocols::simple_moves::ddG
• no_residues_with_nonzero_change_id() : core::kinematics::ResidueCoordinateChangeList
• nocst_scorefxn_ : protocols::seeded_abinitio::SegmentHybridizer , protocols::hybridization::CartesianHybridize
• Node : core::scoring::constraints::ConstraintNode , core::graph::Graph , core::graph::Node , core::kinematics::Node
• node() : core::graph::DisjointSets
• Node() : core::graph::Node
• node_changing_ : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• node_considering_alt_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• 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::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• 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_name() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• 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 >
• NodeBase : core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase
• nodes_ : core::graph::DisjointSets , core::graph::Edge , core::pack::interaction_graph::EdgeBase , core::graph::Graph
• nodes_alt_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_info_ : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_pair_dot_counts_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• nodes_alt_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_state_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_states_ : core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• nodes_considering_bb_move() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_considering_bb_move_ : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_info_ : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_state_ : protocols::flexpack::interaction_graph::FlexbbEdge
• 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_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• nodes_from_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• nodes_in_set() : core::graph::DisjointSets
• nodes_num_bb_ : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_part_of_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_part_of_same_flexseg_ : protocols::flexpack::interaction_graph::FlexbbEdge
• NodeVector : core::graph::Graph
• noesy_assign_float_cycle_ : protocols::abinitio::IterativeBase
• noesy_assign_hash_ : protocols::abinitio::IterativeBase
• noesy_module_ : protocols::abinitio::IterativeBase
• NOESY_PHASEII_S2_RESAMPLING : protocols::abinitio::IterativeBase
• NOESY_PHASEII_TOPO : protocols::abinitio::IterativeBase
• NoesyModule() : protocols::noesy_assign::NoesyModule
• nojumps_ : protocols::forge::remodel::RemodelMover::instruction_flags
• nominal_depth() : protocols::qsar::scoring_grid::ChargeGrid
• non_clash_ribose : protocols::swa::rna::SillyCountStruct
• non_collision_detection_atoms_reqd_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• non_const_pose() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• non_CSP_ : protocols::ub_e2c::ubi_e2c_modeler
• non_CSP_swap_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• non_CSP_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• non_default_positions_ : protocols::forge::remodel::RemodelDesignMover
• non_hbonding_atom() : core::scoring::hbonds::hbtrie::HBAtom
• non_helix_in_membrane_penalty() : core::scoring::MembranePotential
• non_ideal() : protocols::loophash::FastGapMover
• non_ideal_ : protocols::loophash::FastGapMover
• non_interface : protocols::ligand_docking::ligand_options::InterfaceInfo
• non_main_chain_sugar_coords : protocols::rna::TorsionSet , protocols::rna::RNA_Fragments , protocols::rna::FullAtomRNA_Fragments
• non_main_chain_sugar_coords_ : core::io::silent::RNA_SilentStruct
• non_main_chain_sugar_coords_defined : protocols::rna::TorsionSet , protocols::rna::RNA_Fragments , protocols::rna::FullAtomRNA_Fragments
• non_main_chain_sugar_coords_defined_ : core::io::silent::RNA_SilentStruct
• non_native_residue_bonus_ : protocols::protein_interface_design::FavorNonNativeResidue
• non_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• non_residue_pair_constraints_ : core::scoring::constraints::ConstraintSet
• non_surface_ranges_ : core::scoring::solid_surface::SurfaceEnergies
• non_virtual_score() : core::scoring::constraints::CoordinateConstraint
• nonadduct_variants_match() : core::chemical::ResidueType
• nonchi_atom_id_2_restype_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• nonchi_atoms_in_ideal_frame_ : protocols::match::upstream::UpstreamResTypeGeometry
• nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• nonchitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• nonconst_atom_numbers_for_mg_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_cenlist_from_pose() : core::scoring::SmoothEnvPairPotential , core::scoring::EnvPairPotential
• nonconst_dcenlist_from_pose() : core::scoring::SmoothEnvPairPotential
• nonconst_downstream_algorithms() : protocols::match::Matcher
• nonconst_interface_from_pose() : protocols::scoring::InterchainPotential
• nonconst_is_magnesium() : core::scoring::rna::RNA_ScoringInfo
• nonconst_long_range_container() : core::scoring::Energies
• nonconst_MembraneEmbed_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_MembraneTopology_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_mindata_from_pose() : core::scoring::methods::RG_Energy_Fast
• nonconst_monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover
• nonconst_name_map() : core::chemical::ResidueTypeSet
• nonconst_name_map_ : core::chemical::ResidueTypeSet
• nonconst_pose() : protocols::multistate_design::SingleState
• nonconst_resA() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nonconst_resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nonconst_residue_task() : core::pack::task::PackerTask_ , core::pack::task::PackerTask
• nonconst_residue_type_set() : core::chemical::ChemicalManager
• 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
• none : protocols::rotamer_recovery::RRReporterSQLite::OutputLevel
• None : protocols::hotspot_hashing::movers::PlaceProbeMover
• nonideal_ : core::pack::scmin::SCMinMinimizerMap , protocols::loophash::LoopHashSampler , protocols::rotamer_recovery::RRProtocolRTMin , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::MinPackMover , core::pack::RTMin
• nonjump_atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• nonlocal_min_contacts_per_res_ : protocols::frag_picker::FragmentPicker
• nonlocal_pairs() : protocols::frag_picker::FragmentPicker
• nonlocal_pairs_at_positions() : protocols::frag_picker::FragmentPicker
• NonlocalContactsCalculator() : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• NonlocalFrags() : protocols::frag_picker::nonlocal::NonlocalFrags
• NonlocalPair() : protocols::frag_picker::nonlocal::NonlocalPair
• nonmonotone() : core::optimization::LineMinimizationAlgorithm
• nonpivot_res_to_sweep_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• nonpivot_torsion_sampling_ : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• NonPlaidFingerprint : protocols::pockets::EggshellGrid , protocols::pockets::NonPlaidFingerprint
• nonpolarF2() : core::scoring::FACTSResidueInfo
• nonpolarF2_ : core::scoring::FACTSResidueInfo
• nonprepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• NonResidueTypeConstraint() : core::scoring::constraints::NonResidueTypeConstraint
• NonSequentialNeighborsFilter() : protocols::simple_filters::NonSequentialNeighborsFilter
• nonstandard_polymer_ : core::conformation::Residue
• nonzero_deltas() : core::kinematics::Jump
• nonzero_energies() : protocols::jd2::ScoreMap
• nonzero_weight_score_types() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• nook_finder() : protocols::vip::VIP_Mover
• nooutput() : protocols::jobdist::BaseJobDistributor
• nooutput_ : protocols::jobdist::BaseJobDistributor
• NoOutputJobOutputter() : protocols::jd2::NoOutputJobOutputter
• norepack1_ : protocols::docking::DockMCMCycle , protocols::docking::DockTaskFactory
• norepack2_ : protocols::docking::DockMCMCycle , protocols::docking::DockTaskFactory
• norepack_res_ : protocols::seeded_abinitio::SeedSetupMover
• NoRepackDisulfides() : core::pack::task::operation::NoRepackDisulfides
• NoResFilter() : core::pack::task::operation::NoResFilter
• norm : protocols::sparta::RingData
• norm_ : protocols::scoring::methods::saxs::PDDFEnergy
• norm_neg() : protocols::protein_interface_design::filters::BoltzmannFilter
• norm_neg_ : protocols::protein_interface_design::filters::BoltzmannFilter
• norm_query_E_ : protocols::frag_picker::scores::PartialSecondarySimilarity
• norm_query_H_ : protocols::frag_picker::scores::PartialSecondarySimilarity
• norm_query_L_ : protocols::frag_picker::scores::PartialSecondarySimilarity
• norm_squared() : core::scoring::EMapVector
• Normal : protocols::nonlocal::Chunk
• normal() : core::scoring::MembraneEmbed
• normal_ : core::scoring::hbonds::HBondEnergy , core::scoring::MembraneEmbed
• normalization : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• normalization_1_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• normalization_2_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs2::PcsDataLanthanide
• normalization_3_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs2::PcsDataLanthanide
• normalization_factor_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs2::PcsDataLanthanide
• normalization_factor_inversed_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• normalize_by_sasa_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• normalize_decoy_stddev_ : protocols::optimize_weights::PNatStructureOptEData
• normalize_template_wts() : protocols::hybridization::FoldTreeHybridize
• normalized_ : protocols::qsar::scoring_grid::GridManager
• normalized_peak_volume() : protocols::noesy_assign::PeakAssignment
• NormalizedEvaluatedArchive() : protocols::jd2::archive::NormalizedEvaluatedArchive
• normals_ : protocols::viewer::triangle
• norme_vector_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator
• NOT_ELIMINATED : protocols::noesy_assign::CrossPeak
• not_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• not_in_pose_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• not_using() : core::scoring::FACTSResidueInfo
• not_using_ : core::scoring::FACTSResidueInfo
• NOT_YET_COMPUTED_ENERGY : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LinearMemEdge
• note_all_jobs_finished() : protocols::jd2::JobDistributor
• note_bbjump_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_chi_controls_atom() : core::chemical::ResidueType
• note_coordinate_change_registered() : core::kinematics::AtomTree
• note_current_network_state() : core::pack::annealer::FASTERAnnealer
• note_designed_residues() : protocols::dna::PDBOutput
• note_dof_change() : core::kinematics::tree::Atom_
• note_edge_deleted() : core::graph::UpperEdgeGraph< V, E >
• note_filter_fail() : protocols::match::output::MatchProcessor
• note_fixedbb_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_has_pseudobonds() : core::scoring::trie::CPDataCorrespondence
• note_hit_geometry() : protocols::match::OccupiedSpaceHash
• note_last_considered_substitution_resolved() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_long_range_interactions_exist() : protocols::flexpack::interaction_graph::OTFFlexbbEdge , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• note_long_range_interactions_exist_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph
• note_lower_edge_added() : core::graph::UEVertex< V, E >
• note_lower_edge_deleted() : core::graph::UEVertex< V, E >
• note_match_accepted() : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::StateAccumulatingMatchFilter
• note_match_processed() : protocols::match::output::MatchProcessor
• note_output_match() : protocols::match::MatchOutputTracker
• note_packertask_settings() : protocols::simple_moves::PackRotamersMover
• note_primary_change_to_geom_csts_hitlist() : protocols::match::Matcher
• note_rpe_calculated() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph
• note_short_range_interactions_exist() : core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::OnTheFlyEdge
• note_short_range_interactions_exist_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph
• note_state_substitution_accepted() : protocols::flexpack::interaction_graph::FlexbbEdge
• 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_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• notify_conformation_obs() : core::pose::Pose
• notify_connection_obs() : core::conformation::Conformation
• notify_destruction_obs() : core::pose::Pose
• notify_energy_change() : core::pose::metrics::PoseMetricCalculator , core::pose::metrics::EnergyDependentCalculator
• notify_energy_obs() : core::pose::Pose
• notify_general_obs() : core::pose::Pose , core::conformation::Conformation
• notify_identity_obs() : core::conformation::Conformation
• notify_length_obs() : core::conformation::Conformation
• notify_structure_change() : core::pose::metrics::StructureDependentCalculator , core::pose::metrics::PoseMetricCalculator
• notify_topological_change() : core::kinematics::AtomTree
• notify_xyz_obs() : core::conformation::Conformation
• nouter_cycles_ : protocols::rbsegment_relax::AutoRBMover
• noutstanding() : core::graph::ArrayPool< T >
• nparams : protocols::relax::RelaxScriptCommand
• npca_ : protocols::evaluation::PCA
• npd_calcs_for_poses_ : protocols::pack_daemon::DaemonSet
• npd_calculator_creators_ : protocols::pack_daemon::DaemonSet
• npd_properties() : protocols::pack_daemon::MultistateFitnessFunction
• npd_properties_ : protocols::pack_daemon::MultistateFitnessFunction
• npd_properties_for_state_variables_ : protocols::pack_daemon::DynamicAggregateFunction
• npd_property_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• npd_property_vector_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• npd_variable_indices_for_states_ : protocols::pack_daemon::DynamicAggregateFunction
• NPDIndAndCalc : protocols::pack_daemon::DaemonSet
• NPDPropCalculator() : protocols::pack_daemon::NPDPropCalculator
• NPDPropCalculatorCreator() : protocols::pack_daemon::NPDPropCalculatorCreator
• npEnergy : core::scoring::APBSResult
• npes_ : protocols::jd2::MPIWorkPoolJobDistributor , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::jd2::MPIWorkPartitionJobDistributor
• npoints_ : core::grid::CartGrid< T >
• npos() : core::sequence::SequenceCoupling
• npr() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• npr_ : core::scoring::packstat::PackingScoreResData , core::scoring::packstat::PackingScore
• nprefilter_ : protocols::loophash::LoopHashSampler , protocols::loophash::LoopHashMoverWrapper
• nproc_ : protocols::jobdist::BaseJobDistributor
• npseudo_ : core::conformation::symmetry::SymmetryInfo
• npx : core::scoring::APBSResult
• npy : core::scoring::APBSResult
• npz : core::scoring::APBSResult
• nr_assignments_ : protocols::noesy_assign::DistanceScoreMover
• nr_bad_ : protocols::jd2::archive::MPIArchiveJobDistributor
• nr_batches() : protocols::jd2::JobDistributor
• nr_completed_ : protocols::jd2::archive::MPIArchiveJobDistributor
• nr_conformers_violatable_ : protocols::noesy_assign::PeakAssignmentParameters
• nr_fragments() : protocols::loops::loop_closure::ccd::LoopClosure
• nr_fragments_ : protocols::loops::loop_closure::ccd::LoopClosure
• nr_frags() : core::fragment::Frame
• nr_frags_ : protocols::hybridization::WeightedFragmentTrialMover , protocols::hybridization::WeightedFragmentSmoothTrialMover
• nr_frames() : core::fragment::FragSet
• nr_jobs_ : protocols::jd2::archive::MPIArchiveJobDistributor
• nr_jump_cycles_ : protocols::abinitio::JumpingFoldConstraints
• nr_jumps_max_ : protocols::jumping::JumpSelector
• nr_jumps_min_ : protocols::jumping::JumpSelector
• nr_models() : protocols::abinitio::PairingStatistics
• nr_moves() : protocols::moves::MoverContainer
• nr_new_completed_ : protocols::jd2::archive::MPIArchiveJobDistributor
• nr_notify_ : protocols::jd2::archive::MPIArchiveJobDistributor
• nr_open_slaves() : protocols::jd2::SingleFileBuffer
• nr_recepients() : protocols::topology_broker::ClaimerMessage
• nr_res_ : core::fragment::Frame , protocols::topology_broker::SequenceClaimer
• nr_res_affected() : core::fragment::Frame
• nr_residues() : protocols::loops::Loops
• nr_scored_fragments_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• nr_scored_sampling_passes_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• nrad() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nrad_ : core::scoring::packstat::PackingScoreResData , core::scoring::packstat::PackingScore
• nrchi_bin_ : core::pack::dunbrack::BBDepNRChiSample< P >
• nrchi_bin_id() : core::pack::dunbrack::BBIndSemiRotamericData< T >
• nrchi_bin_id_ : core::pack::dunbrack::BBIndSemiRotamericData< T >
• nrchi_lower_angle_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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 >
• nrchi_prob_minimum_for_extra_samples() : protocols::match::upstream::SampleStrategyData
• nrchi_prob_minimum_for_extra_samples_ : protocols::match::upstream::SampleStrategyData
• 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_upper_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_upper_boundary_ : core::pack::dunbrack::DunbrackRotamerSampleData
• nreplica_frequency_ : protocols::moves::ReplicaExchangeMC
• nres() : core::io::silent::SilentFileData , core::io::silent::SilentStruct , core::pose::PDBInfo , core::io::raw_data::RawStruct , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::kinematics::FoldTree , protocols::toolbox::AllowInsert
• nres_ : protocols::simple_filters::TruncatedScoreEvaluator , core::kinematics::ShortestPathInFoldTree , core::pack::task::IGEdgeReweightContainer , core::io::raw_data::RawStruct , core::kinematics::FoldTree , protocols::toolbox::AllowInsert , protocols::topology_broker::TopologyBroker , core::io::silent::SilentStruct , core::pack::task::PackerTask_ , protocols::analysis::InterfaceAnalyzerMover , protocols::antibody2::LHRepulsiveRampLegacy , protocols::swa::protein::StepWiseProteinPoseSetup
• nres_monomer_ : core::conformation::symmetry::SymmetryInfo , core::scoring::hackelec::HackElecEnergy
• nres_peptide_ : protocols::flexpep_docking::FlexPepDockingProtocol
• nres_receptor_ : protocols::flexpep_docking::FlexPepDockingProtocol
• nres_scored : core::scoring::methods::RG_MinData
• nres_template_ : protocols::comparative_modeling::ThreadingJob
• nreses : core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy
• nresidue : core::scoring::sc::Atom
• nresidues_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• nrmlQueue : protocols::viewer::triangleIterator
• nrotamer_offset_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamer_offsets_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• nrotamers() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSetsBase
• nrotamers_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• nrotamers_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSubsets
• nrotamers_for_moltenres_ : core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_moltenres_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_resid_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotoffset_for_moltenres_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotoffset_for_moltenres_bbconf_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrots_for_moltenres_bbconf_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrounds : protocols::simple_moves::ShakeStructureMover
• nrows() : protocols::frag_picker::TorsionBinIO , protocols::frag_picker::LAMBEGO_IO
• nrows_ : core::scoring::ResidualDipolarCoupling
• nsdie : core::scoring::APBSConfig::R_PARAM
• nsegs_ : protocols::simple_filters::SymmetricMotifFilter
• nseq_ : protocols::hybridization::DDomainParse
• nsequence_ : protocols::seeded_abinitio::GrowPeptides
• nsigmoids() : core::scoring::SmoothScoreTermCoeffs
• nsims : core::scoring::APBSConfig
• nsol() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• nsol_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• 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
• nstruct() : protocols::jd2::archive::Batch , protocols::jobdist::BasicJob , protocols::jd2::archive::Batch , protocols::jd2::archive::ArchiveBase
• nstruct_ : protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::rna::RNA_DeNovoProtocol , protocols::jobdist::BasicJob , protocols::jd2::archive::Batch , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• nstruct_centroid_ : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• nstruct_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• nstruct_index() : protocols::jd2::Job
• nstruct_index_ : protocols::jd2::Job
• nstruct_iter_ : protocols::design_opt::GreedyOptMutationMover
• nstruct_max() : protocols::jd2::InnerJob , protocols::jd2::Job
• nstruct_max_ : protocols::jd2::InnerJob
• Nter_insert_flexibility_ : protocols::grafting::GraftMoverBase
• Nter_loop_end_ : protocols::grafting::GraftMoverBase
• Nter_loop_start_ : protocols::grafting::GraftMoverBase
• Nter_overhang_ : protocols::grafting::GraftMoverBase
• Nter_scaffold_flexibility_ : protocols::grafting::GraftMoverBase
• nterm_length_ : protocols::match::RemoveNorCTermMPM
• nth_dna_base() : protocols::dna::DNAParameters
• ntimes_ : core::import_pose::pose_stream::ExtendedPoseInputStream
• NtoC_RCG() : protocols::forge::constraints::NtoC_RCG
• ntorsionA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntorsionAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntorsionB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntorsions() : core::optimization::CartesianMinimizerMap
• ntrial_ : protocols::flxbb::FilterStructs
• ntrials() : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::canonical_sampling::CanonicalSamplingMover
• ntrials_ : protocols::moves::ReplicaExchangeMC , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• nTrimmedDots : core::scoring::sc::_RESULTS
• nu0_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu0_components() : core::scoring::dna::DNATorsionPotential
• nu0_components_ : core::scoring::dna::DNATorsionPotential
• nu1() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• nu1_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• NU1_A_FORM : protocols::rna::RNA_HelixAssembler
• nu1_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu1_components() : core::scoring::dna::DNATorsionPotential
• nu1_components_ : core::scoring::dna::DNATorsionPotential
• nu1_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu1_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• nu2() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• nu2_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• NU2_A_FORM : protocols::rna::RNA_HelixAssembler
• nu2_atom_names_ : core::scoring::dna::DNATorsionPotential
• nu2_components() : core::scoring::dna::DNATorsionPotential
• nu2_components_ : core::scoring::dna::DNATorsionPotential
• nu2_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• 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_id() : core::chemical::carbohydrates::CarbohydrateInfo
• nu_id_ : core::chemical::carbohydrates::CarbohydrateInfo
• nudge_distance_bound() : protocols::noesy_assign::CrossPeak
• nullaa : core::scoring::Ramachandran2B
• NullDesignMover() : protocols::protein_interface_design::movers::NullDesignMover
• NullMover() : protocols::moves::NullMover
• num : core::scoring::packstat::SimplePDB_Atom , core::pose::RemarkInfo
• num_ : protocols::moves::PDBDumpMover , protocols::simple_moves::BackboneMover
• num_aa_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• num_aa_types() : protocols::flexpack::interaction_graph::FlexbbNode
• num_aa_types_ : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDNode
• num_accepted() : protocols::moves::MoverStatistics
• num_accepts() : protocols::moves::TrialMover
• num_active_constraints_ : protocols::constraints_additional::AmbiguousMultiConstraint
• num_atom_pos_bin_out_of_range_message_outputted_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• num_atoms_ : core::pack::interaction_graph::RotamerDots
• num_base_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• num_base_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_base_std_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• num_bb() : protocols::flexpack::interaction_graph::FlexbbEdge
• num_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• num_bb_alternatives_for_flexseg_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_bb_clones() : core::conformation::symmetry::SymmetryInfo
• num_bbconfs() : protocols::flexpack::interaction_graph::FlexbbNode
• num_bg_nodes_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• num_bins() : protocols::simple_moves::DOFHistogramRecorder
• num_bins_ : protocols::simple_moves::DOFHistogramRecorder , core::scoring::constraints::CircularGeneral1D_Func , core::scoring::carbon_hbonds::CarbonHBondPotential
• num_bondangles() : core::scoring::mm::MMBondAngleResidueTypeParam , core::chemical::ResidueType
• num_bytes_ : core::pack::interaction_graph::RotamerDots
• 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::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• num_chains() : core::conformation::Conformation
• num_chi_ : protocols::MakeRotLib::RotData
• num_chi_clones() : core::conformation::symmetry::SymmetryInfo
• num_chi_samples_total() : protocols::match::upstream::FullChiSampleSet
• num_chi_samples_total_ : protocols::match::upstream::FullChiSampleSet
• num_chunk_sets() : protocols::rna::RNA_ChunkLibrary
• num_chunks() : protocols::rna::ChunkSet , protocols::rna::RNA_ChunkLibrary
• num_claimers() : protocols::topology_broker::TopologyBroker
• num_clash_atom_cutoff_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• num_clash_cutoff_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• num_clusters_ : protocols::MakeRotLib::RotData
• num_clusters_in_level_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• num_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_coef2() : protocols::branch_angle::BranchAngleOptimizer
• num_commits_since_last_update_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph
• num_components() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_components_ : core::conformation::symmetry::SymmData
• num_cons_ : protocols::simple_filters::RegionalConnections
• num_considered_muliple_origins : protocols::match::MatcherOutputStats
• num_contact_cutoff_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• 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_cycles1_ : protocols::antibody2::H3PerturbCCD
• num_cycles_ : protocols::ligand_docking::HighResDocker , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• num_decoys_used_in_calculations_ : protocols::ddg::ddGMover
• num_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• num_deriv_ : core::optimization::DOF_DataPoint , core::optimization::DerivCheckDataPoint
• NUM_DERIV_H : core::scoring::electron_density::ElectronDensity
• NUM_DERIV_H_CEN : core::scoring::electron_density::ElectronDensity
• num_designable() : protocols::simple_moves::GenericMonteCarloMover
• num_disulfides() : core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer
• num_domains() : protocols::rna::MultipleDomainMover
• num_domains_ : protocols::rna::MultipleDomainMover
• NUM_DOTS_TOTAL : core::pack::interaction_graph::DotSphere
• num_ds_hit_incompatible : protocols::match::MatcherOutputStats
• num_edges() : core::graph::Graph , core::graph::Node , core::graph::UpperEdgeGraph< V, E >
• num_edges_ : core::graph::UpperEdgeGraph< V, E > , core::graph::Graph
• num_edges_to_bg_nodes_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• num_edges_to_larger_indexed_nodes_ : core::pack::interaction_graph::NodeBase , core::graph::Node
• NUM_EDGES_TO_RESERVE : core::conformation::PointGraphVertexData , protocols::toolbox::pose_metric_calculators::EmptyVertexData
• num_edges_to_smaller_indexed_nodes_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• num_empty_uplist : protocols::match::MatcherOutputStats
• num_energy_dofs_ : protocols::optimize_weights::OptEMultifunc
• num_energy_sum_groups_ : core::pack::interaction_graph::InteractionGraphBase
• num_entities() : protocols::pack_daemon::EntityCorrespondence
• num_entities_ : protocols::pack_daemon::DaemonSet
• num_entity_elements_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• num_enz_cst_template_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• num_file_aa_types_ : core::pack::interaction_graph::PDInteractionGraph
• num_file_states_for_aa_for_node_ : core::pack::interaction_graph::PDInteractionGraph
• num_filter_tries_ : protocols::antibody2::RefineOneCDRLoop
• num_find_fragment_tries_ : protocols::rna::RNA_Relaxer
• num_flexible_segments_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_frag_moves : protocols::forge::remodel::RemodelMover::instruction_flags
• num_fragpick() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild , protocols::fldsgn::BluePrintBDR
• num_fragpick_ : protocols::forge::components::VarLengthBuild , protocols::fldsgn::BluePrintBDR
• num_geom_cst() : protocols::match::output::PDBWriter
• num_geom_cst_ : protocols::match::output::PDBWriter
• num_hbonds : core::scoring::rna::Base_pair
• num_heavy_atoms() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_heavyatoms_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_helices_ : protocols::fldsgn::topology::HelixPairingSet
• 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_inner_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_insertable_residues_ : protocols::rna::RNA_FragmentMover
• num_interactions() : protocols::toolbox::match_enzdes_util::ResInteractions
• num_interactions_ : protocols::toolbox::match_enzdes_util::ResInteractions
• num_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• num_interfaces() : core::conformation::symmetry::SymmetryInfo
• num_iterations() : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_iterations_ : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_jump() : core::kinematics::FoldTree , core::pose::Pose , protocols::scoring::InterfaceInfo
• num_jump_ : protocols::scoring::InterfaceInfo , core::kinematics::FoldTree
• num_jump_clones() : core::conformation::symmetry::SymmetryInfo
• num_loop() : protocols::loops::Loops
• num_loops() : protocols::anchored_design::AnchorMoversData , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• num_lower_edges_ : core::graph::UEVertex< V, E >
• num_lower_neighbors() : core::graph::UEVertex< V, E >
• num_masters_ : protocols::inputter::InputterStream
• num_matches_processed_ : protocols::match::output::MatchProcessor
• num_matching_levels() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• num_mcfi_lists() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• num_mcfis() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• num_negative_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_neighbors() : core::graph::UEVertex< V, E >
• num_neighbors_ : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator
• num_neighbors_counting_self() : core::graph::Node , core::graph::UEVertex< V, E > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< 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_neighbors_map_ : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• num_new_neighbors_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• num_node_states_ : core::pack::interaction_graph::EdgeBase
• num_nodes() : core::graph::Graph
• num_nodes_ : core::pack::annealer::FASTERAnnealer , core::graph::Graph
• num_nodes_changing_state_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_nodes_in_file_ : core::pack::interaction_graph::PDInteractionGraph
• num_non_up_only_incompatible : protocols::match::MatcherOutputStats
• num_nonvirt_residues_ : protocols::hybridization::HybridizeFoldtreeDynamic
• num_npd_properties() : protocols::pack_daemon::DynamicAggregateFunction
• num_of_first_cycle_ : protocols::docking::DockMCMProtocol
• num_of_pairings_ : protocols::jumping::PairingLibrary , protocols::jumping::DisulfPairingLibrary
• num_of_second_cycle_ : protocols::docking::DockMCMProtocol
• num_outer_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_packs_ : protocols::multistate_design::MultiStatePacker , protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• num_pairs : core::scoring::dna::DirectReadoutPotential
• num_partitions_ : protocols::loophash::LoopHashLibrary
• num_perturb_steps_ : protocols::swa::protein::StepWiseProteinLoopBridger
• num_pose_in_cluster_ : protocols::swa::StepWiseClusterer
• num_pose_kept_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• num_pose_minimize_ : protocols::swa::rna::StepWiseRNA_Minimizer
• num_positions() : protocols::optimize_weights::OptEData
• num_positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_potential_matches : protocols::match::MatcherOutputStats
• num_protein_residues_ : protocols::hybridization::HybridizeFoldtreeDynamic
• num_pts() : protocols::cluster::APCluster
• num_recently_accepted_ : core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::LinearMemNode
• num_ref_dofs_ : protocols::optimize_weights::OptEMultifunc
• num_rejections_ : protocols::simple_moves::GenericMonteCarloMover
• num_repacks_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• num_repeats_ : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy
• num_report : protocols::forge::remodel::RemodelMover::instruction_flags
• num_res_types_ : core::pack::interaction_graph::SymmOnTheFlyNode
• num_residues() : core::scoring::disulfides::FullatomDisulfideEnergyContainer , protocols::pack_daemon::EntityCorrespondence
• num_residues_ : protocols::star::Extender
• num_residues_assigned_as_background_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• num_restype_groups_ : core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• 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_rotamer_centers() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• num_rotamers() : core::pack::rotamer_set::RotamerSet_ , protocols::optimize_weights::OptEData , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSubset , core::conformation::RotamerSetBase
• 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_ROUNDS_ : protocols::rna::RNA_LoopCloser
• num_rpe_calcs_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph
• num_sa_ : protocols::pack_daemon::FASTER_IG_Repacker
• num_sa_trajectories_ : core::pack::annealer::FASTERAnnealer
• num_samples_ : protocols::swa::protein::StepWiseProteinFragmentSampleGenerator , protocols::swa::protein::StepWiseProteinMainChainSampleGenerator , protocols::swa::protein::StepWiseProteinJumpSampleGenerator
• num_sampling_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_segments() : protocols::backrub::BackrubMover
• num_sent_to_proc : protocols::match::MatcherOutputStats
• num_seqpos_lists() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• num_sets() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_sheets() : protocols::fldsgn::topology::SheetSet
• 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() : protocols::multistate_design::MultiStateFitnessFunction , protocols::pack_daemon::DynamicAggregateFunction
• num_states_ : core::pack::interaction_graph::NodeBase
• num_states_for_aa_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_for_aa_for_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• 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_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_for_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_for_restype_group_ : core::pack::interaction_graph::SymmOnTheFlyNode
• num_states_per_backbone_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• num_steps() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• num_steps_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• num_strands() : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairingSet
• num_strands_ : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairingSet
• num_strings_ : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• num_structures_added_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• 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::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• num_surrounding_sasa_bins : core::scoring::packstat::SasaOptions
• num_target_states() : protocols::toolbox::match_enzdes_util::InvrotTree
• num_templates() : protocols::comparative_modeling::ThreadingJobInputter
• 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_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_total_dofs_ : protocols::optimize_weights::OptEMultifunc
• num_total_rbconfs_ : protocols::enzdes::GenerateStoredRBConfs
• 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_trajectory : protocols::forge::remodel::RemodelMover::instruction_flags
• num_trials() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• num_trials_ : protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::ligand_docking::RigidSearchMover
• num_triggers() : protocols::simple_moves::GenericMonteCarloMover
• num_try_div() : protocols::loophash::LoopHashDiversifier
• num_try_div_ : protocols::loophash::LoopHashDiversifier
• num_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• 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_up_only_incompatible : protocols::match::MatcherOutputStats
• 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
• num_written_ : protocols::match::output::PDBWriter
• number() : core::pose::PDBInfo
• number_bonded_heavyatoms() : core::chemical::ResidueType
• number_bonded_hydrogens() : core::chemical::ResidueType
• number_cavities : protocols::vip::VIP_Mover
• number_designable_ : protocols::simple_moves::GenericMonteCarloMover
• number_elements_ : core::scoring::orbitals::OrbitalsLookup
• number_of_basepairs() : protocols::dna::DNAParameters
• number_of_bases() : protocols::dna::DNAParameters
• number_of_basesteps() : protocols::dna::DNAParameters
• number_of_high_resolution_cycles() : protocols::antibody2::SnugDock
• number_of_high_resolution_cycles_ : protocols::antibody2::SnugDock
• number_of_histograms_ : core::scoring::orbitals::OrbitalsStatistics
• number_of_moves() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• number_of_patchdock_entries() : protocols::protein_interface_design::PatchdockReader
• number_of_processors() : protocols::jd2::MPIFileBufJobDistributor
• number_stats_ : core::scoring::orbitals::OrbitalsLookup
• number_to_propagate_ : protocols::genetic_algorithm::GeneticAlgorithm
• NumberHBonds_ : protocols::analysis::InterfaceAnalyzerMover
• NumberHBondsCalculator() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• numbering_scheme_ : protocols::antibody2::AntibodyInfo
• NumberingSystem : core::io::raw_data::DisulfideFile
• numBonds_ : core::chemical::sdf::atomTyper
• NumDerivCheckData() : core::optimization::NumDerivCheckData
• numEdges_ : core::sequence::SequenceCoupling
• NumericalDerivCheckResult() : core::optimization::NumericalDerivCheckResult
• numGaussians() : core::scoring::constraints::USOGFunc
• NumNeighborsMPM() : protocols::match::NumNeighborsMPM
• numresults_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• numVerts_ : core::sequence::SequenceCoupling
• NV_lookup_table_ : core::scoring::ScoringManager
• nv_score_ : protocols::features::ResidueBurialFeatures
• nvec_ : protocols::evaluation::PCA
• NVlookup() : core::scoring::nv::NVlookup
• NVscore() : core::scoring::nv::NVscore
• NWAligner() : core::sequence::NWAligner
• NWDP_TM() : protocols::hybridization::TMalign
• nwrites : core::scoring::APBSResult
• Nx_ : core::scoring::packstat::Array2D
• nX_ : core::grid::CartGrid< T >
• Ny_ : core::scoring::packstat::Array2D
• nY_ : core::grid::CartGrid< T >
• nZ_ : core::grid::CartGrid< T >