- n -

• N() : protocols::fldsgn::topology::BB_Pos
• 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 , protocols::noesy_assign::CrossPeak::Spin
• N_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• n_atoms() : protocols::toolbox::DecoySetEvaluation , protocols::toolbox::InteratomicVarianceMatrix
• n_atoms_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_build_sets() : protocols::match::upstream::ProteinUpstreamBuilder
• n_ca() : protocols::kinematic_closure::ClosureProblem
• n_ca_c() : protocols::kinematic_closure::ClosureProblem
• n_closure_attempts_is_a_maximum() : protocols::generalized_kinematic_closure::GeneralizedKIC
• n_collision_check_atoms() : protocols::toolbox::match_enzdes_util::LigandConformer
• n_columns() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_decoys() : protocols::toolbox::DecoySetEvaluation
• n_decoys_max() : protocols::toolbox::DecoySetEvaluation
• n_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• n_dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_dof() : protocols::md::MDBase
• n_external_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• n_geometric_constraints() : protocols::match::Matcher
• n_helices() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::parameters::BundleParametersSet
• n_kept_matches() : protocols::match::output::BestMatchesCollection
• n_loops() : protocols::loophash::LoopHashMap
• n_mutants() : protocols::pmut_scan::PointMutScanDriver
• n_mutations() : protocols::pmut_scan::Mutant
• n_nonchitip_atoms_for_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• n_npd_properties() : protocols::pack_daemon::DaemonSet
• N_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• 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_rank() : protocols::jd2::MPIFileBufJobDistributor
• n_real_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• n_rebuild_tries() : protocols::comparative_modeling::LoopRelaxMover
• n_req_res_in_seq() : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• n_rerelaxed() : protocols::mpi_refinement::Scheduler
• n_residues_for_entity() : protocols::pack_daemon::EntityCorrespondence
• n_restypes() : protocols::match::downstream::TargetRotamerCoords
• n_restypes_to_build() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• n_rotamers_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_rots_total() : protocols::match::downstream::TargetRotamerCoords
• n_rows() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_sample() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• n_samples_per_chi() : protocols::match::upstream::FullChiSampleSet
• n_samples_per_side_of_nrchi_bin() : protocols::match::upstream::SampleStrategyData
• n_samples_wi_sd_range() : protocols::match::upstream::SampleStrategyData
• n_temp_levels() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• n_to_gen() : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Scheduler
• n_to_output_per_group() : protocols::match::MatcherTask
• n_to_rerelax() : protocols::mpi_refinement::Scheduler
• 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_torsion_sets() : protocols::simple_moves::SetTorsion
• n_torsions() : protocols::helical_bundle::BackboneGridSamplerHelper
• n_Vmin_assignments() : protocols::noesy_assign::CrossPeak
• n_worker() : protocols::jd2::MPIFileBufJobDistributor
• NA_calculate() : protocols::scoring::Interface
• nali() : protocols::frag_picker::VallResidue
• name() : protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::abinitio::Template , protocols::analysis::PeptideDeriverFilter , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::evaluation::MetaPoseEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::farna::FullAtomRNA_Fragments , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , 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::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , 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::indexed_structure_store::filters::FragmentLookupFilter , protocols::inputter::FastaInputter , protocols::inputter::Inputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter , protocols::jd2::archive::AbstractArchiveBase , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::match::upstream::UpstreamResTypeGeometry , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , 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::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::pose_selectors::AndSelector , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::OrSelector , protocols::pose_selectors::TopNByProperty , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::rigid::UniformRigidBodyCM , protocols::rosetta_scripts::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::BatchEvaluator , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::O2M_MutateMover , protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BaseBinMapUpdater , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::BulgeApplier , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::FastForwardToNextResidueAlternative , protocols::stepwise::screener::FastForwardToNextRigidBody , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::StepWiseResiduePairScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubApplier , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::viewer::ConformationViewer , protocols::wum2::WorkUnit_ElScripts
• name3() : protocols::simple_moves::IonizableResidue
• name_from_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• name_from_loop_configuration() : protocols::loops::JSONFormattedLoopsFileReader
• name_from_residue_identifier() : protocols::loops::JSONFormattedLoopsFileReader
• name_of_hbond_calc() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• name_of_sasa_calc() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• name_wo_rgstr() : protocols::fldsgn::topology::StrandPairingSet
• NamedAtomPairConstraintCreator() : protocols::constraints_additional::NamedAtomPairConstraintCreator
• names_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• NatbiasHelicesSheetPotential() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• NatbiasHelixPairPotential() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• NatbiasSecondaryStructureEnergy() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• NatbiasStrandPairPotential() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• native() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• native_aa() : protocols::optimize_weights::PNatAAOptEPositionData
• native_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• native_distance_viol() : protocols::noesy_assign::PeakAssignment
• native_edensity_score_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• native_edensity_score_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• native_pose() : protocols::evaluation::AlignEvaluator
• native_secstruct() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native_tag() : protocols::jobdist::BasicJob
• NativeEvaluatorCreator() : protocols::simple_filters::NativeEvaluatorCreator
• nativeness() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_high() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_low() : protocols::optimize_weights::PNatStructureOptEData
• natm() : protocols::normalmode::NormalMode
• natom() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• natoms() : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::match::upstream::UpstreamResTypeGeometry , protocols::pockets::PocketConstraint
• natoms_rmsd() : protocols::stepwise::modeler::align::StepWisePoseAligner
• natoms_superimpose_rmsd() : protocols::stepwise::modeler::align::StepWisePoseAligner
• nb_list() : protocols::simple_moves::MinMover
• nbackbone_conformations() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbb() : protocols::frags::TorsionFragment
• nbbconfs_for_flexseg() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbbconfs_for_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbonds_from_bb_atom() : protocols::match::upstream::BuildSet
• ncap_prob_from_svm() : protocols::helix_capper::HelixNCapperMover
• NcbbDockDesignProtocol() : protocols::ncbb::NcbbDockDesignProtocol
• nchi() : protocols::match::upstream::UpstreamResTypeGeometry
• ncluster() : protocols::toolbox::KClusterElement
• ncol() : protocols::noesy_assign::PeakFileFormat
• NcontactsCalculator() : protocols::fldsgn::NcontactsCalculator
• NcontactsFilter() : protocols::fldsgn::filters::NcontactsFilter
• nContinuousSegments() : protocols::rbsegment_relax::RBSegment
• NCSResMapping() : protocols::simple_moves::symmetry::NCSResMapping
• ncst() : protocols::md::Rattle
• ncsts() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• ncycle() : protocols::flxbb::DesignTask
• ndaemons() : protocols::pack_daemon::DaemonSet
• nDoFs() : protocols::helical_bundle::BundleGridSamplerHelper
• nearby_atom_cut() : protocols::simple_filters::DomainInterfaceFilter
• nearby_atom_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• negate() : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• negmask_from_offsets() : protocols::match::Bool3DGrid
• neighbor_count() : protocols::optimize_weights::PNatAAOptEPositionData
• neighbor_counts() : protocols::frag_picker::ContactCounts
• neighbor_counts_exist() : protocols::frag_picker::ContactCounts
• neighbor_cutoff() : protocols::ddg::ddGMover , protocols::simple_filters::NonSequentialNeighborsFilter
• neighbor_detection_dis() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator
• neighbor_dis() : protocols::grafting::AnchoredGraftMover
• neighbor_distance() : protocols::simple_filters::StemFinder
• neighbor_hits() : protocols::match::HitNeighborFinder
• neighbor_min() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_min_add() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_min_clear() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_separation() : protocols::simple_filters::StemFinder
• neighbor_strands() : protocols::fldsgn::topology::StrandPairingSet
• NeighborDependentTabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• NeighborDependentTorsionSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber
• Neighborhood() : protocols::neighbor::Neighborhood
• neighborhood_buns_polar_calc_name() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• 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
• neighbors() : protocols::simple_filters::ResidueBurialFilter
• NeighborsByDistanceCalculator() : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• NeighborTypeFilter() : protocols::simple_filters::NeighborTypeFilter
• Nend_orient() : protocols::fldsgn::topology::SS_Base
• Nend_pos() : protocols::fldsgn::topology::SS_Base
• NestedEnergyTermDDGMutationOptEData() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• NestedEnergyTermPNatAAOptEPositionData() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• NetChargeFilter() : protocols::simple_filters::NetChargeFilter
• netTargetPocketVolume() : protocols::pockets::PocketGrid
• network_analysis() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignmentResidueMap
• network_analysis2() : protocols::noesy_assign::PeakAssignmentResidueMap
• network_anchoring() : protocols::noesy_assign::PeakAssignment
• network_anchoring_per_residue() : protocols::noesy_assign::PeakAssignment
• neutral_restypes() : protocols::simple_moves::IonizableResidue
• new_calculator() : protocols::pack_daemon::NPDPropCalculatorCreator
• new_chain() : protocols::simple_moves::AddChainMover
• new_decoy() : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TopologyClaimer
• new_entity() : protocols::genetic_algorithm::EntityElementCreator , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::multistate_design::PosTypeCreator
• new_grid() : protocols::qsar::scoring_grid::GridFactory
• new_kinematics() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::LoopJumpFoldCst
• new_move_selector() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_secondary_structure_override() : protocols::forge::components::VarLengthBuild
• new_sequence_override() : protocols::forge::components::VarLengthBuild
• new_tasks() : protocols::matdes::MatDesPointMutationCalculator
• new_terminal_pos() : protocols::fldsgn::CircularPermutation
• newDataLoader() : protocols::jd2::parser::DataLoaderFactory
• newFilter() : protocols::filters::FilterFactory , protocols::protein_interface_design::DockDesignFilterFactory
• newMover() : protocols::moves::MoverFactory
• newPosePropertyReporter() : protocols::rosetta_scripts::PosePropertyReporterFactory
• newPoseSelector() : protocols::rosetta_scripts::PoseSelectorFactory
• newSearch() : protocols::pockets::PocketGrid
• newTopologyClaimer() : protocols::topology_broker::TopologyClaimerFactory
• next() : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::viewer::triangleIterator , protocols::wum::WorkUnitQueue
• next_angle() : protocols::backrub::BackrubMover
• next_batch() : protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
• next_center() : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• next_exchange_level() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::HamiltonianExchange
• next_exchange_schedule() : protocols::canonical_sampling::HamiltonianExchange
• next_from_pool() : protocols::frag_picker::quota::QuotaSelector
• next_job() : protocols::jobdist::BaseJobDistributor
• next_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• next_random_job() : protocols::jd2::ShuffleFileSystemJobDistributor
• next_resnum() : protocols::simple_moves::sidechain_moves::SidechainMover
• next_segment_id() : protocols::backrub::BackrubMover
• next_torsion_string() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• nflexible_segments() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• ngroups() : protocols::simple_moves::symmetry::NCSResMapping
• nhashlookups() : protocols::sic_dock::scores::MotifHashRigidScore
• nirotamers() : protocols::motifs::IRCollection
• nlevels() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• nlevels_per_dim() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::TemperatureController
• nloop() : protocols::simple_moves::PackRotamersMover
• NM() : protocols::normalmode::NormalModeRelaxMover
• NMerPSSMEnergyFilter() : protocols::simple_filters::NMerPSSMEnergyFilter
• NMerSVMEnergyFilter() : protocols::simple_filters::NMerSVMEnergyFilter
• nmode() : protocols::normalmode::NormalMode
• nmodes() : protocols::normalmode::NormalModeMultifunc
• nmolten_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmoltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmotifs() : protocols::motifs::MotifLibrary
• nmoves() : protocols::simple_moves::BackboneMover
• nmr2rosetta() : protocols::noesy_assign::MethylNames
• no_design() : protocols::flxbb::FlxbbDesign
• no_ranked_frags() : protocols::enzdes::EnzdesFlexibleRegion
• no_relax() : protocols::flxbb::FlxbbDesign
• nobjs() : protocols::mpi_refinement::MultiObjective
• Node() : protocols::toolbox::Node
• node_considering_alt_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• node_name() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• nodes() : protocols::toolbox::ResidueNetwork
• nodes_alt_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_considering_bb_move() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_cur_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_from_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• nodes_part_of_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbEdge
• NoesyModule() : protocols::noesy_assign::NoesyModule
• nominal_depth() : protocols::qsar::scoring_grid::ChargeGrid
• non_ideal() : protocols::loophash::FastGapMover
• non_main_chain_sugar_coords() : protocols::farna::FullAtomRNA_Fragments
• non_main_chain_sugar_coords_defined() : protocols::farna::FullAtomRNA_Fragments
• nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• nonconst_downstream_algorithms() : protocols::match::Matcher
• nonconst_interface_from_pose() : protocols::scoring::InterchainPotential
• nonconst_MembraneEmbed_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_MembraneTopology_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover
• nonconst_pose() : protocols::multistate_design::SingleState
• nonconst_resA() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nonconst_resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• 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
• nonpivot_residues() : protocols::kinematic_closure::ClosureProblem
• NonPlaidFingerprint() : protocols::pockets::NonPlaidFingerprint
• NonSequentialNeighborsFilter() : protocols::simple_filters::NonSequentialNeighborsFilter
• nonzero_energies() : protocols::jd2::ScoreMap
• nonzero_weight_score_types() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• nook_finder() : protocols::vip::VIP_Mover
• NoOpStepWiseSampler() : protocols::stepwise::sampler::NoOpStepWiseSampler
• nooutput() : protocols::jobdist::BaseJobDistributor
• NoOutputJobOutputter() : protocols::jd2::NoOutputJobOutputter
• NoPoseXYX_Func() : protocols::sic_dock::NoPoseXYX_Func
• norm_neg() : protocols::protein_interface_design::filters::BoltzmannFilter
• normal() : protocols::membrane::geometry::EmbeddingDef
• normal_to_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• normalize_isc() : protocols::analysis::PeptideDeriverFilter
• normalize_probabilities() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• normalize_template_wts() : protocols::hybridization::FoldTreeHybridize
• normalized_distance_in_degrees() : protocols::antibody::clusters::CDRCluster
• normalized_peak_volume() : protocols::noesy_assign::PeakAssignment
• NormalizedEvaluatedArchive() : protocols::jd2::archive::NormalizedEvaluatedArchive
• NormalMode() : protocols::normalmode::NormalMode
• NormalModeMinimizer() : protocols::normalmode::NormalModeMinimizer
• NormalModeMultifunc() : protocols::normalmode::NormalModeMultifunc
• NormalModeRelaxMover() : protocols::normalmode::NormalModeRelaxMover
• not_end() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized
• not_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• note_all_jobs_finished() : protocols::jd2::JobDistributor
• note_bbjump_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_designed_residues() : protocols::dna::PDBOutput
• note_filter_fail() : protocols::match::output::MatchProcessor
• note_fixedbb_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• 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
• note_long_range_interactions_exist_for_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• 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_state_substitution_accepted() : protocols::flexpack::interaction_graph::FlexbbEdge
• notify_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• nparams() : protocols::mpi_refinement::Scheduler
• npd_properties() : protocols::pack_daemon::MultistateFitnessFunction
• npd_variable_indices_for_state_begin() : protocols::pack_daemon::DynamicAggregateFunction
• npd_variable_indices_for_state_end() : protocols::pack_daemon::DynamicAggregateFunction
• NPDPropCalculator() : protocols::pack_daemon::NPDPropCalculator
• NPDPropCalculatorCreator() : protocols::pack_daemon::NPDPropCalculatorCreator
• npick_per_iter() : protocols::mpi_refinement::Scheduler
• nposes() : protocols::cluster::GatherPosesMover
• nr_batches() : protocols::jd2::JobDistributor
• nr_fragments() : protocols::loops::loop_closure::ccd::LoopClosure
• nr_models() : protocols::abinitio::PairingStatistics
• nr_moves() : protocols::moves::MoverContainer
• nr_open_slaves() : protocols::jd2::SingleFileBuffer
• nr_recepients() : protocols::topology_broker::ClaimerMessage
• nr_residues() : protocols::loops::Loops
• nrchi_prob_minimum_for_extra_samples() : protocols::match::upstream::SampleStrategyData
• nres() : protocols::helical_bundle::BackboneGridSampler , protocols::toolbox::AllowInsert
• nrotamer_offset_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_moltenres() : 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
• nrows() : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• nsol() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• nspans() : protocols::membrane::geometry::Embedding
• nstep() : protocols::md::MDBase
• nstep_per_update() : protocols::md::Thermostat
• nstruct() : protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::Batch , protocols::jobdist::BasicJob
• nstruct_centroid() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• nstruct_index() : protocols::jd2::Job
• nstruct_max() : protocols::jd2::InnerJob , protocols::jd2::Job
• nstruct_mode() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• nstruct_repeats() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• nsub_bblock() : protocols::matdes::ClashCheckFilter
• Nter_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• Nter_loop_end() : protocols::grafting::AnchoredGraftMover
• Nter_loop_start() : protocols::grafting::AnchoredGraftMover
• Nter_overhang_length() : protocols::grafting::GraftMoverBase
• Nter_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• nth_dna_base() : protocols::dna::DNAParameters
• NtoC_RCG() : protocols::forge::constraints::NtoC_RCG
• ntor() : protocols::normalmode::NormalMode
• ntrials() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ntries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• nudge_distance_bound() : protocols::noesy_assign::CrossPeak
• NullMover() : protocols::moves::NullMover
• num_aa_types() : protocols::flexpack::interaction_graph::FlexbbNode
• num_accepted() : protocols::moves::MoverStatistics
• num_accepts() : protocols::moves::TrialMover
• num_atoms() : protocols::kinematic_closure::ClosureProblem
• num_bb() : protocols::flexpack::interaction_graph::FlexbbEdge
• num_bbconfs() : protocols::flexpack::interaction_graph::FlexbbNode
• num_bins() : protocols::simple_moves::DOFHistogramRecorder
• num_chains() : protocols::frags::VallData
• num_chi_samples_total() : protocols::match::upstream::FullChiSampleSet
• num_chunk_sets() : protocols::farna::RNA_ChunkLibrary
• num_chunks() : protocols::farna::ChunkSet , protocols::farna::RNA_ChunkLibrary
• num_claimers() : protocols::topology_broker::TopologyBroker
• num_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_coef2() : protocols::branch_angle::BranchAngleOptimizer
• num_components() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_designable() : protocols::simple_moves::GenericMonteCarloMover
• num_domains() : protocols::farna::MultipleDomainMover
• num_entities() : protocols::pack_daemon::EntityCorrespondence
• num_enz_cst_template_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• num_fragpick() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• num_geom_cst() : protocols::match::output::PDBWriter
• num_inner_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_interactions() : protocols::toolbox::match_enzdes_util::ResInteractions
• num_iterations() : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_jump() : protocols::scoring::InterfaceInfo
• num_loop() : protocols::loops::Loops
• num_loops() : protocols::anchored_design::AnchorMoversData , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• 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_moving_chunks() : protocols::farna::RNA_ChunkLibrary
• num_negative_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_npd_properties() : protocols::pack_daemon::DynamicAggregateFunction
• num_npd_properties_for_state() : protocols::pack_daemon::DynamicAggregateFunction
• num_origins() : protocols::pockets::FingerprintBase
• num_outer_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_pose_minimize() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• num_positions() : protocols::optimize_weights::OptEData
• num_positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_pts() : protocols::cluster::APCluster
• num_random_samples() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::StepWiseSampleAndScreen
• num_residues() : protocols::kinematic_closure::ClosureProblem , protocols::pack_daemon::EntityCorrespondence
• num_rotamers() : protocols::optimize_weights::OptEData
• num_screeners() : protocols::stepwise::StepWiseSampleAndScreen
• num_segments() : protocols::backrub::BackrubMover
• num_seqpos_lists() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• num_sets() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_sheets() : protocols::fldsgn::topology::SheetSet
• num_states() : protocols::multistate_design::MultiStateFitnessFunction , protocols::pack_daemon::DynamicAggregateFunction
• num_states_for_aa_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_per_backbone_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• num_steps() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• num_strands() : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairingSet
• num_strings() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• num_successes() : protocols::stepwise::StepWiseSampleAndScreen
• num_target_states() : protocols::toolbox::match_enzdes_util::InvrotTree
• num_templates() : protocols::comparative_modeling::ThreadingJobInputter
• num_trials() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• num_tries() : protocols::stepwise::StepWiseSampleAndScreen
• num_triggers() : protocols::simple_moves::GenericMonteCarloMover
• num_try_div() : protocols::loophash::LoopHashDiversifier
• num_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• number_of_basepairs() : protocols::dna::DNAParameters
• number_of_bases() : protocols::dna::DNAParameters
• number_of_basesteps() : protocols::dna::DNAParameters
• number_of_high_resolution_cycles() : protocols::antibody::SnugDock
• 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_to_propagate() : protocols::genetic_algorithm::GeneticAlgorithmBase
• NumberHBondsCalculator() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• numbering_scheme() : protocols::antibody::PDBLandmark
• numbering_scheme_enum_to_string() : protocols::antibody::AntibodyEnumManager
• numbering_scheme_is_present() : protocols::antibody::AntibodyEnumManager
• numbering_scheme_string_to_enum() : protocols::antibody::AntibodyEnumManager
• numbering_scheme_transform_present() : protocols::antibody::AntibodyInfo
• numberOfAtoms() : protocols::pockets::SmallMol
• NumNeighborsMPM() : protocols::match::NumNeighborsMPM
• nvar() : protocols::normalmode::NormalModeMultifunc
• NWDP_TM() : protocols::hybridization::TMalign