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

- n -

• N() : protocols::fldsgn::topology::BB_Pos
• N1_NODE_H : protocols::sparta::ANN
• N1_NODE_I : protocols::sparta::ANN
• N1_NODE_O : protocols::sparta::ANN
• N2_NODE_H : protocols::sparta::ANN
• N2_NODE_I : protocols::sparta::ANN
• N2_NODE_O : protocols::sparta::ANN
• N_ : protocols::fldsgn::topology::BB_Pos
• n_ : protocols::pose_selectors::TopNByProperty
• n_accept_cummul_ : protocols::mpi_refinement::MPI_Refine_Emperor
• n_addcall_ : protocols::mpi_refinement::MPI_Refine_Emperor
• n_addcall_emperor_report_ : protocols::mpi_refinement::MPI_Refine_Emperor
• n_ali8_ : protocols::hybridization::TMalign
• 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_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• n_atoms() : protocols::toolbox::DecoySetEvaluation , protocols::toolbox::InteratomicVarianceMatrix
• n_atoms_ : protocols::frag_picker::scores::FragmentChunkCrms , 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_auto_all : protocols::simple_moves::BBGaussianMover
• N_auto_small : protocols::simple_moves::BBGaussianMover
• n_batchrelax_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• n_bb_ : protocols::make_rot_lib::MakeRotLibOptionsData
• n_best_ : protocols::enzdes::PackRotamersMoverPartGreedy
• n_build_sets() : protocols::match::upstream::ProteinUpstreamBuilder
• n_ca() : protocols::kinematic_closure::ClosureProblem
• n_ca_atom_ : protocols::toolbox::KClusterData
• n_ca_c() : protocols::kinematic_closure::ClosureProblem
• n_candidates_ : protocols::frag_picker::FragmentPicker
• n_centroids_ : protocols::make_rot_lib::MakeRotLibOptionsData
• n_change_emperor_report_ : protocols::mpi_refinement::MPI_Refine_Emperor
• n_chi_ : protocols::make_rot_lib::MakeRotLibOptionsData
• n_classes_ : protocols::frag_picker::scores::ABEGO_SS_Score
• n_closure_attempts_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• n_closure_attempts_is_a_maximum() : protocols::generalized_kinematic_closure::GeneralizedKIC
• n_closure_attempts_is_a_maximum_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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_cycles_ : protocols::docking::TemperedDocking , protocols::enzdes::EnzRepackMinimize
• 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::LazySortedVector1< T, StrictWeakOrdering >
• 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_dof_ : protocols::md::MDBase
• n_dof_angle_ : protocols::simple_moves::BBGaussianMover
• n_dof_temp_ : protocols::md::MDBase
• n_doublebins_per_supervoxel : protocols::match::Bool3DGrid
• n_downstream_to_output_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• n_dump_ : protocols::mpi_refinement::MPI_Refine_Emperor
• n_end_atom_ : protocols::simple_moves::BBGaussianMover
• 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_frags_ : protocols::frag_picker::FragmentPicker
• n_geom_csts_ : protocols::match::MatchCounter
• n_geometric_constraints() : protocols::match::Matcher
• n_geometric_constraints_ : protocols::match::Matcher , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::UpstreamHitCacher
• n_geometric_constraints_per_match_ : protocols::match::HitHasher
• N_HASH_MAPS : protocols::match::HitHasher
• n_helices() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::parameters::BundleParametersSet
• n_helices_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParametersSet
• n_high_entropy_decoys_ : protocols::optimize_weights::PNatStructureOptEData
• N_index_ : protocols::fldsgn::topology::BB_Pos
• n_inserts_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• n_kept_matches() : protocols::match::output::BestMatchesCollection
• n_lanthanides_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• n_lib_modified_ : protocols::mpi_refinement::MPI_Refine_Master
• n_ligands_ : protocols::metal_interface::ZincSiteFinder
• n_loophash_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• n_loops() : protocols::loophash::LoopHashMap
• n_max_cluster_ : protocols::toolbox::ClusterPhilStyle
• n_mutants() : protocols::pmut_scan::PointMutScanDriver
• n_mutations() : protocols::pmut_scan::Mutant
• n_nested_ : protocols::hybridization::BackboneTorsionSampler
• n_nodes_left_to_spin_down_ : protocols::jd2::MPIFileBufJobDistributor
• n_nonchitip_atoms_for_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• n_npd_properties() : protocols::pack_daemon::DaemonSet
• n_npd_properties_ : protocols::pack_daemon::DaemonSet
• n_output_so_far_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• n_pcs_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• n_pcs_spin_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• n_pert_res_ : protocols::simple_moves::BBGaussianMover
• N_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• N_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• n_poses_ : protocols::contact_map::ContactMap , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper
• 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_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_req_res_in_seq() : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• n_rerelaxed() : protocols::mpi_refinement::Scheduler
• n_rerelaxed_ : protocols::mpi_refinement::Scheduler
• n_res_ : protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::PCS_FragDistance
• n_resi_ : protocols::protein_interface_design::movers::BestHotspotCstMover
• 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_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::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• n_sample_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_small_moves_ : protocols::antibody::H3RefineCCD
• 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_temp_levels() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• n_tied_for_worst_ : protocols::pack_daemon::TopEntitySet
• n_to_buffer_ : protocols::jd2::SilentFileJobOutputter
• n_to_gen() : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Scheduler
• n_to_output_per_group() : protocols::match::MatcherTask
• n_to_output_per_group_ : protocols::match::MatcherTask , protocols::match::output::MatchConsolidator
• n_to_rerelax() : protocols::mpi_refinement::Scheduler
• n_to_rerelax_ : protocols::mpi_refinement::Scheduler
• 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_torsion_sets() : protocols::simple_moves::SetTorsion
• 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_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_calculate() : protocols::scoring::Interface
• naccepted_ : protocols::dna::RotamerDNAHBondFilter
• nali() : protocols::frag_picker::VallResidue
• 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::TaskOperationFeatures::Taskop_id_name_factory_ , 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::mpi_refinement::MethodParams , 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::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::modeler::rna::Residue_info , 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::NativeRMSD_Screener , 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
• name2foldtype_ : protocols::fldsgn::topology::SheetFoldTypeManager
• name3 : protocols::dna::DnaDesignDef , protocols::simple_moves::IonizableResidue
• name_ : protocols::abinitio::Template , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::StrandPairing , protocols::flxbb::FilterStructs , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MakeFragmentScoringMethod , protocols::frag_picker::scores::TorsionBinSimilarity , protocols::jd2::archive::AbstractArchiveBase , protocols::ligand_docking::rdf::RDFBase , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::moves::PDBDumpMover , protocols::pack_daemon::VectorExpression , protocols::rigid::UniformRigidBodyCM , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::viewer::ConformationViewer , protocols::wum2::WorkUnit_ElScripts
• 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_hbond_calc_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• 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_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
• NamedAtomPairConstraintCreator() : protocols::constraints_additional::NamedAtomPairConstraintCreator
• NamedAtomPairConstraintList : protocols::abinitio::Template
• NamedDistanceMap : protocols::noesy_assign::FragsToAtomDist
• NamedInnerMap : protocols::noesy_assign::FragsToAtomDist
• NamedStubID : protocols::forge::build::ConnectRight
• names_for_water_ : protocols::features::WaterFeatures
• 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
• 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
• NatbiasStrandPairPotential() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• NatbiasStrandPairPotentialOP : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• native_ : protocols::abinitio::Templates , protocols::docking::membrane::MPDockingMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDockMain , protocols::md::CartesianMD , protocols::rbsegment_relax::OptimizeThreadingMover , 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::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• native_alignment_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• 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_cst_set : protocols::forge::remodel::RemodelGlobalFrame
• native_distance_viol() : protocols::noesy_assign::PeakAssignment
• native_distance_viol_ : protocols::noesy_assign::PeakAssignment
• native_down_ : protocols::simple_filters::JumpEvaluator
• native_edensity_score_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• native_edensity_score_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• native_edensity_score_cutoff_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• native_filename_ : protocols::antibody_legacy::AntibodyModeler
• native_fragment_bb_energies_ : protocols::enzdes::EnzdesFlexBBProtocol
• native_given_ : protocols::md::CartesianMD , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• native_id_ : protocols::jobdist::BasicJob
• native_pdbs_ : protocols::optimize_weights::IterativeOptEDriver
• native_pose() : protocols::evaluation::AlignEvaluator
• native_pose_ : protocols::abinitio::AbrelaxApplication , protocols::antibody_legacy::AntibodyModeler , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::forge::remodel::RemodelMover , protocols::jumping::JumpSelector , protocols::moves::Mover , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine , protocols::relax::WorkUnit_BatchRelax , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::screener::NativeRMSD_Screener
• 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_legacy::AntibodyModeler
• native_residue_bonus_ : protocols::protein_interface_design::FavorNativeResidue
• native_resmap_ : protocols::md::CartesianMD
• native_rmsd_screener_ : protocols::stepwise::screener::IntegrationTestBreaker
• native_rotamer_index_ : protocols::optimize_weights::PNatRotOptEPositionData
• 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_topology_ : protocols::abinitio::PairingStatistics
• native_up_ : protocols::simple_filters::JumpEvaluator
• native_virtual_res_list_ : protocols::stepwise::legacy::modeler::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
• NativeRMSD_Screener() : protocols::stepwise::screener::NativeRMSD_Screener
• natives_ : protocols::ddg::ddGMover , protocols::optimize_weights::PNatStructureOptEData
• natm() : protocols::normalmode::NormalMode
• natom() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• natom_ : protocols::toolbox::KClusterData
• 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
• natro_movemap_ : protocols::forge::remodel::RemodelData
• nb_list : protocols::relax::ClassicRelax , protocols::simple_moves::MinMover
• nb_list_ : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::ub_e2c::ubi_e2c_modeler
• nbackbone_conformations() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nbb() : 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
• nbins_ : protocols::features::AtomAtomPairFeatures
• nbonds_from_bb_atom() : protocols::match::upstream::BuildSet
• nbonds_from_bb_atom_ : protocols::match::upstream::BuildSet
• nbr_cutoff_ : protocols::ddg::ddGMover
• nbr_radius_to_atoms_ : protocols::toolbox::task_operations::CrystalContactsOperation
• nbr_radius_to_nbr_radius_ : protocols::toolbox::task_operations::CrystalContactsOperation
• nc_allatm_ : protocols::fldsgn::NcontactsCalculator
• nc_hpatm_ : protocols::fldsgn::NcontactsCalculator
• nc_hpres_ : protocols::fldsgn::NcontactsCalculator
• ncap_model_ : protocols::helix_capper::HelixNCapperMover
• ncap_prob_from_svm() : protocols::helix_capper::HelixNCapperMover
• ncap_scores_ : protocols::helix_capper::HelixNCapperMover
• ncbb_design_first_ : protocols::ncbb::NcbbDockDesignProtocol
• NcbbDockDesignProtocol() : protocols::ncbb::NcbbDockDesignProtocol
• ncentroid_ : protocols::loophash::LoopHashMoverWrapper
• nchange_emperor_call_ : protocols::mpi_refinement::MPI_Refine_Master
• nchi() : protocols::match::upstream::UpstreamResTypeGeometry
• nchi_max_ : protocols::simple_filters::ChiWellRmsdEvaluator
• ncluster() : protocols::toolbox::KClusterElement
• ncol() : protocols::noesy_assign::PeakFileFormat
• nconformers_ : protocols::pockets::FingerprintMultifunc
• 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
• ncyc_postmin_ : protocols::md::MDBase
• ncyc_premin_ : protocols::md::MDBase
• 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
• ndisAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ndof_ : protocols::md::Thermostat
• nDoFs() : protocols::helical_bundle::BundleGridSamplerHelper
• nDoFs_ : protocols::helical_bundle::BundleGridSamplerHelper
• ndruns_ : protocols::simple_moves::SetReturningPackRotamersMover
• near_interface : protocols::ligand_docking::ligand_options::InterfaceInfo
• Near_Native_StepWiseSampler_Count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• nearby_atom_cut() : protocols::simple_filters::DomainInterfaceFilter
• nearby_atom_cut_ : protocols::simple_filters::DomainInterfaceFilter
• 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_KNOW : protocols::topology_broker::claims::DofClaim
• negate() : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• negate_ : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• negative_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• negmask_from_offsets() : protocols::match::Bool3DGrid
• neighbor_addresses_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• neighbor_copy_dofs_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• neighbor_count() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::qsar::scoring_grid::ChargeAtom
• 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() : protocols::ddg::ddGMover , protocols::simple_filters::NonSequentialNeighborsFilter
• neighbor_cutoff_ : protocols::scoring::ImplicitFastClashCheck , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::toolbox::task_operations::ProteinCore
• neighbor_cutoff_sq_ : protocols::scoring::ImplicitFastClashCheck
• neighbor_design_ : protocols::forge::remodel::RemodelMover::instruction_flags
• 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_dis_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::grafting::AnchoredGraftMover
• neighbor_dist_ : protocols::antibody::H3RefineCCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• neighbor_distance() : protocols::simple_filters::StemFinder
• neighbor_distance_ : protocols::simple_filters::StemFinder
• neighbor_distance_cutoff_ : protocols::features::UnrecognizedAtomFeatures
• neighbor_hits() : protocols::match::HitNeighborFinder
• neighbor_min() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_min_ : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_min_add() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_min_clear() : protocols::antibody::design::CDRGraftDesignOptions
• neighbor_repack_ : protocols::forge::remodel::RemodelMover::instruction_flags
• neighbor_separation() : protocols::simple_filters::StemFinder
• neighbor_separation_ : protocols::simple_filters::StemFinder
• neighbor_strands() : protocols::fldsgn::topology::StrandPairingSet
• 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_ : 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 : protocols::sparta::PDB
• neighbors() : protocols::simple_filters::ResidueBurialFilter , protocols::toolbox::Node
• 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
• 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
• net_charge_max_ : protocols::simple_filters::NetChargeFilter
• net_charge_min_ : protocols::simple_filters::NetChargeFilter
• NetChargeFilter() : protocols::simple_filters::NetChargeFilter
• 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_restype_ : protocols::simple_moves::IonizableResidue
• neutral_restypes() : protocols::simple_moves::IonizableResidue
• never_switched_noe_filter_ : protocols::abinitio::IterativeBase
• new_calculator() : protocols::pack_daemon::NPDPropCalculatorCreator
• new_center_ : protocols::membrane::TranslationRotationMover
• new_chain() : protocols::simple_moves::AddChainMover
• new_chain_ : protocols::simple_moves::AddChainMover
• new_conformation_ : protocols::viewer::ConformationViewer
• 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_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::GeneticAlgorithmBase , protocols::multistate_design::PosTypeCreator
• new_grid() : protocols::qsar::scoring_grid::GridFactory
• new_kinematics() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::LoopJumpFoldCst
• new_level_begins_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• new_normal_ : protocols::membrane::RotationMover , protocols::membrane::TranslationRotationMover
• new_nr_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• new_phi() : protocols::simple_moves::BackboneMover
• new_phi_ : protocols::simple_moves::BackboneMover
• new_position_ : protocols::simple_moves::UniformTranslationMover
• 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_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_tasks() : protocols::matdes::MatDesPointMutationCalculator
• new_tasks_ : protocols::matdes::MatDesPointMutationCalculator
• new_terminal_pos() : protocols::fldsgn::CircularPermutation
• new_terminal_pos_ : protocols::fldsgn::CircularPermutation
• new_vrts : protocols::environment::EnvClaimBroker::BrokerResult
• 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_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_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_suite_atoms_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• NEXT_Tab : protocols::sparta::Sparta::SpartaLib
• next_to_return_ : 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
• next_torsion_string() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• next_trigger_id_ : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• nextFileName : protocols::sparta::Sparta::SpartaLib
• 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::hybridization::CartesianSampler , protocols::jd2::parser::FragmentReader , protocols::seeded_abinitio::SegmentHybridizer
• nfullatom_ : protocols::loophash::LoopHashMoverWrapper
• ngb_mask : protocols::neighbor::Neighborhood
• ngbs : protocols::neighbor::Neighborhood
• ngen_serial_per_structure_ : protocols::mpi_refinement::MPI_Refine_Master
• ngrid_cells_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• ngroups() : protocols::simple_moves::symmetry::NCSResMapping
• ngroups_ : protocols::simple_moves::symmetry::NCSResMapping
• nhashlookups() : protocols::sic_dock::scores::MotifHashRigidScore
• nhashlookups_ : protocols::sic_dock::scores::MotifHashRigidScore
• ninner_cycles_ : protocols::rbsegment_relax::AutoRBMover
• nirotamers() : protocols::motifs::IRCollection
• niter_ : protocols::mpi_refinement::Scheduler , protocols::mpi_refinement::StructAvrgMover
• njobs : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• njump_ : protocols::jumping::JumpSample
• njumps_ : protocols::topology_broker::TMHTopologySamplerClaimer
• nkins_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• nlcontacts_graph_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• nlevels() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• nlevels_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::PoolData
• nlevels_per_dim() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::TemperatureController
• nloop() : protocols::simple_moves::PackRotamersMover
• nloop_ : protocols::simple_moves::PackRotamersMover
• NM() : protocols::normalmode::NormalModeRelaxMover
• NM_ : protocols::normalmode::NormalModeMultifunc , protocols::normalmode::NormalModeRelaxMover
• nmax_ : protocols::noesy_assign::PeakAssignmentParameters
• nmer_seq : protocols::simple_filters::nmer_svm_res_data
• NMerPSSMEnergyFilter() : protocols::simple_filters::NMerPSSMEnergyFilter
• NMerSVMEnergyFilter() : protocols::simple_filters::NMerSVMEnergyFilter
• nmethods_enrich_max_ : protocols::mpi_refinement::Scheduler
• nminsteps_ : protocols::hybridization::CartesianSampler
• nmode() : protocols::normalmode::NormalMode
• nmodes() : protocols::normalmode::NormalModeMultifunc
• nmolten_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmoltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmoltenres_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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::RepeatMover , protocols::moves::WhileMover , protocols::relax::ClassicRelax , protocols::simple_moves::BackboneMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• nmr2rosetta() : protocols::noesy_assign::MethylNames
• nmr2rosetta_ : protocols::noesy_assign::MethylNames
• NmrConstraint : protocols::noesy_assign::PeakAssignment
• NmrConstraintOP : protocols::noesy_assign::PeakAssignment
• NO_CONTACT : protocols::noesy_assign::FragsToAtomDist
• no_data_cdrs_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• no_design() : protocols::flxbb::FlxbbDesign
• NO_DESIGN : protocols::flxbb::LayerDesignOperation
• no_design_ : protocols::flxbb::FlxbbDesign , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• no_design_cys_ : protocols::enzdes::DetectProteinLigandInterface
• no_filters_ : protocols::docking::DockingProtocol
• no_frags_ : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchorMoversData , protocols::forge::remodel::RemodelMover::instruction_flags
• no_global_frame_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• no_helix_in_pdb_ : protocols::features::strand_assembly::SandwichFeatures
• no_lr_ : protocols::rbsegment_relax::RBSegmentRelax
• no_modified_ddG_ : protocols::simple_filters::RotamerBoltzmannWeight
• no_network_ : protocols::noesy_assign::PeakAssignmentParameters
• no_nstruct_label_ : protocols::jd2::JobOutputter
• 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
• nobjs() : protocols::mpi_refinement::MultiObjective
• nocst_scorefxn_ : protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• Node() : protocols::toolbox::Node
• node_considering_alt_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• node_considering_alt_state_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• node_name() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• nodes() : protocols::toolbox::ResidueNetwork
• nodes_ : protocols::toolbox::ResidueNetwork
• nodes_alt_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_info_ : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• nodes_alt_state_ : protocols::flexpack::interaction_graph::FlexbbEdge
• 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_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• nodes_from_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• 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
• 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
• nofragbias_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• nojumps_ : protocols::forge::remodel::RemodelMover::instruction_flags
• nominal_depth() : protocols::qsar::scoring_grid::ChargeGrid
• non_clash_sugar : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• non_collision_detection_atoms_reqd_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• 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_ideal() : protocols::loophash::FastGapMover
• non_ideal_ : protocols::loophash::FastGapMover
• non_interface : protocols::ligand_docking::ligand_options::InterfaceInfo
• non_main_chain_sugar_coords() : protocols::farna::FullAtomRNA_Fragments , protocols::farna::TorsionSet
• non_main_chain_sugar_coords_defined() : protocols::farna::FullAtomRNA_Fragments , protocols::farna::TorsionSet
• non_native_residue_bonus_ : protocols::protein_interface_design::FavorNonNativeResidue
• non_standard_residues_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• 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_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
• None : protocols::hotspot_hashing::movers::PlaceProbeMover
• nonideal_ : protocols::loophash::LoopHashSampler , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::RotamerTrialsMinMover
• 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
• nonpivot_res_to_sweep_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• nonpivot_residues() : protocols::kinematic_closure::ClosureProblem
• nonpivot_torsion_sampling_ : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• NonPlaidFingerprint : protocols::pockets::EggshellGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::NonPlaidFingerprint , protocols::pockets::PocketGrid
• 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
• nooutput_ : protocols::jobdist::BaseJobDistributor
• NoOutputJobOutputter() : protocols::jd2::NoOutputJobOutputter
• NoPoseXYX_Func() : protocols::sic_dock::NoPoseXYX_Func
• norepack1_ : protocols::docking::DockMCMCycle , protocols::docking::DockTaskFactory
• norepack2_ : protocols::docking::DockMCMCycle , protocols::docking::DockTaskFactory
• norepack_res_ : protocols::seeded_abinitio::SeedSetupMover
• norm : protocols::sparta::RingData
• norm_ : protocols::scoring::methods::saxs::PDDFEnergy
• norm_function_ : protocols::qsar::scoring_grid::GridManager
• 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
• normal() : protocols::membrane::geometry::EmbeddingDef
• Normal : protocols::nonlocal::Chunk
• normal_ : protocols::docking::membrane::MPDockingMover , protocols::membrane::AddMembraneMover , protocols::membrane::geometry::EmbeddingDef , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover
• normal_to_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• normal_to_plane_ : protocols::docking::EllipsoidalRandomizationMover
• normalization_1_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• normalization_2_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• normalization_3_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• normalization_factor_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• normalization_factor_inversed_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• normalization_function_ : protocols::ligand_docking::InterfaceScoreCalculator
• normalize_by_carbon_count_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• normalize_by_sasa_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• normalize_decoy_stddev_ : protocols::optimize_weights::PNatStructureOptEData
• normalize_isc() : protocols::analysis::PeptideDeriverFilter
• normalize_template_wts() : protocols::hybridization::FoldTreeHybridize
• normalized_distance_ : protocols::antibody::clusters::CDRCluster
• 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
• normals_ : protocols::viewer::triangle
• norme_vector_ : 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
• north_pucker_dof_key_values_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• north_pucker_dofs_have_not_been_initialized_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• NOT_ELIMINATED : protocols::noesy_assign::CrossPeak
• 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
• 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
• nouter_cycles_ : protocols::rbsegment_relax::AutoRBMover
• nparams() : protocols::mpi_refinement::Scheduler , 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_state_begin() : protocols::pack_daemon::DynamicAggregateFunction
• npd_variable_indices_for_state_end() : 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
• nperrun : protocols::mpi_refinement::MethodParams
• npes_ : 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 , protocols::jd2::MPIWorkPoolJobDistributor
• npick_per_iter() : protocols::mpi_refinement::Scheduler
• npick_per_iter_ : protocols::mpi_refinement::Scheduler
• nprefilter_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• nproc_ : protocols::jobdist::BaseJobDistributor
• 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_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• nr_jobs_ : protocols::jd2::archive::MPIArchiveJobDistributor
• 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_residues() : protocols::loops::Loops
• nr_scored_fragments_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• nr_scored_sampling_passes_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• nrchi_prob_minimum_for_extra_samples() : protocols::match::upstream::SampleStrategyData
• nrchi_prob_minimum_for_extra_samples_ : protocols::match::upstream::SampleStrategyData
• nreplica_frequency_ : protocols::moves::ReplicaExchangeMC
• nres() : protocols::toolbox::AllowInsert
• nres_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::electron_density::DensityMorphingMover , protocols::simple_filters::TruncatedScoreEvaluator , protocols::simple_moves::symmetry::NCSResMapping , protocols::toolbox::AllowInsert , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker
• nres_peptide_ : protocols::flexpep_docking::FlexPepDockingProtocol
• nres_protein_asu() : protocols::hybridization::HybridizeSetup
• nres_protein_tgt_ : protocols::hybridization::HybridizeSetup
• nres_receptor_ : protocols::flexpep_docking::FlexPepDockingProtocol
• nres_req_per_secstruct_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• nres_template_ : protocols::comparative_modeling::ThreadingJob
• nres_tgt_ : protocols::hybridization::HybridizeSetup
• nres_tgt_asu() : protocols::hybridization::HybridizeSetup
• nresbins_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• nresidues_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• nrmlQueue : protocols::viewer::triangleIterator
• nrotamer_offset_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_moltenres() : 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
• 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::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• nrun : protocols::mpi_refinement::MethodParams
• nsegs_ : protocols::simple_filters::SymmetricMotifFilter
• nseq_ : protocols::hybridization::DDomainParse
• nsequence_ : protocols::seeded_abinitio::GrowPeptides
• nsol() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• nsol_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• nspans() : protocols::membrane::geometry::Embedding
• nstep() : protocols::md::MDBase , protocols::md::MDscheduleData
• nstep_ : protocols::md::MDBase
• nstep_per_update() : protocols::md::Thermostat
• nstep_per_update_ : protocols::md::Thermostat
• nsteps_ : protocols::rbsegment_relax::OptimizeThreadingMover
• nstruct() : protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::Batch , protocols::jobdist::BasicJob
• nstruct_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::Batch , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jobdist::BasicJob , protocols::stepwise::setup::StepWiseJobDistributor
• nstruct_centroid() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• nstruct_centroid_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• nstruct_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• nstruct_index() : protocols::jd2::Job
• nstruct_index_ : protocols::jd2::Job
• nstruct_iter_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• nstruct_max() : protocols::jd2::InnerJob , protocols::jd2::Job
• nstruct_max_ : protocols::jd2::InnerJob
• nstruct_mode() : protocols::helical_bundle::BundleGridSampler
• nstruct_mode_ : protocols::helical_bundle::BundleGridSampler
• nstruct_mode_repeats_ : protocols::helical_bundle::BundleGridSampler
• nstruct_repeats() : protocols::helical_bundle::BundleGridSampler
• nsub_bblock() : protocols::matdes::ClashCheckFilter
• nsub_bblock_ : protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter
• Nter_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• Nter_insert_flexibility_ : protocols::grafting::AnchoredGraftMover
• Nter_loop_end() : protocols::grafting::AnchoredGraftMover
• Nter_loop_end_ : protocols::grafting::AnchoredGraftMover
• Nter_loop_start() : protocols::grafting::AnchoredGraftMover
• Nter_loop_start_ : protocols::grafting::AnchoredGraftMover
• nter_overhang_ : protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover
• Nter_overhang_length() : protocols::grafting::GraftMoverBase
• Nter_overhang_length_ : protocols::grafting::GraftMoverBase
• Nter_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• Nter_scaffold_flexibility_ : protocols::grafting::AnchoredGraftMover
• nTerm_cap_size_ : protocols::simple_moves::RepeatPropagationMover
• nterm_length_ : protocols::match::RemoveNorCTermMPM
• nterm_rsd_num_ : protocols::simple_moves::CyclizationMover
• nth_dna_base() : protocols::dna::DNAParameters
• NtoC_RCG() : protocols::forge::constraints::NtoC_RCG
• ntor() : protocols::normalmode::NormalMode
• ntorsionA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntorsionAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntorsionB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ntrial_ : protocols::flxbb::FilterStructs
• ntrials() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ntrials_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::moves::ReplicaExchangeMC , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ntries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• ntries_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• ntries_before_giving_up_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• nucleoside_num_ : protocols::stepwise::monte_carlo::mover::AddMover
• nudge_distance_bound() : protocols::noesy_assign::CrossPeak
• NullMover() : protocols::moves::NullMover
• num_ : protocols::moves::PDBDumpMover , protocols::simple_moves::BackboneMover
• num_aa_types() : protocols::flexpack::interaction_graph::FlexbbNode
• num_aa_types_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode
• 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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• num_atoms() : protocols::kinematic_closure::ClosureProblem
• 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_bbconfs() : protocols::flexpack::interaction_graph::FlexbbNode
• num_bbs_ : protocols::make_rot_lib::RotData
• num_bins() : protocols::simple_moves::DOFHistogramRecorder
• num_bins_ : protocols::simple_moves::DOFHistogramRecorder
• num_chains() : protocols::frags::VallData
• num_chi_ : protocols::make_rot_lib::RotData
• num_chi_samples_total() : protocols::match::upstream::FullChiSampleSet
• 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_clash_atom_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• num_clash_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• num_clusters_ : protocols::make_rot_lib::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_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_components() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_cons_ : protocols::simple_filters::RegionalConnections
• num_considered_muliple_origins : protocols::match::MatcherOutputStats
• num_contact_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• num_cycles1_ : protocols::antibody::H3PerturbCCD
• num_cycles_ : protocols::ligand_docking::HighResDocker , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• num_decoys_used_in_calculations_ : protocols::ddg::ddGMover
• num_designable() : protocols::simple_moves::GenericMonteCarloMover
• num_domains() : protocols::farna::MultipleDomainMover
• num_domains_ : protocols::farna::MultipleDomainMover
• num_ds_hit_incompatible : protocols::match::MatcherOutputStats
• NUM_EDGES_TO_RESERVE : protocols::toolbox::pose_metric_calculators::EmptyVertexData
• num_empty_uplist : protocols::match::MatcherOutputStats
• num_energy_dofs_ : protocols::optimize_weights::OptEMultifunc
• 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_filter_tries_ : protocols::antibody::RefineOneCDRLoop
• num_find_fragment_tries_ : protocols::farna::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
• num_fragpick_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• num_geom_cst() : protocols::match::output::PDBWriter
• num_geom_cst_ : protocols::match::output::PDBWriter
• num_helices_ : protocols::fldsgn::topology::HelixPairingSet
• num_helix_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_helix_pose_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_helix_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_inner_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_insertable_residues_ : protocols::farna::RNA_FragmentMover
• num_interactions() : protocols::toolbox::match_enzdes_util::ResInteractions
• num_interactions_ : protocols::toolbox::match_enzdes_util::ResInteractions
• num_iterations() : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_iterations_ : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_jump() : protocols::scoring::InterfaceInfo
• num_jump_ : protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::scoring::InterfaceInfo , protocols::topology_broker::RigidBodyRandomTMHMover
• num_loop() : protocols::loops::Loops
• num_loop_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_loop_pose_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_loops() : protocols::anchored_design::AnchorMoversData , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• 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_moves_ : protocols::simple_moves::RandomTorsionMover
• num_moving_chunks() : protocols::farna::RNA_ChunkLibrary
• num_negative_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_neighbors_ : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• num_neighbors_map_ : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• num_new_neighbors_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• num_nodes_changing_state_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_non_up_only_incompatible : protocols::match::MatcherOutputStats
• num_nonvirt_residues_ : protocols::hybridization::HybridizeFoldtreeDynamic
• num_npd_properties() : protocols::pack_daemon::DynamicAggregateFunction
• num_npd_properties_for_state() : protocols::pack_daemon::DynamicAggregateFunction
• num_of_first_cycle_ : protocols::docking::DockMCMProtocol
• num_of_pairings_ : protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary
• num_of_second_cycle_ : protocols::docking::DockMCMProtocol
• num_origins() : protocols::pockets::FingerprintBase
• num_origins_ : protocols::pockets::FingerprintBase
• num_outer_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_packs_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::MultiStatePacker , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• num_partitions_ : protocols::loophash::LoopHashLibrary
• num_perturb_steps_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• num_pose_in_cluster_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• num_pose_kept_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• num_pose_minimize() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• num_pose_minimize_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• 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_random_samples() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::StepWiseSampleAndScreen
• num_random_samples_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::StepWiseSampleAndScreen
• num_ref_dofs_ : protocols::optimize_weights::OptEMultifunc
• num_rejections_ : protocols::simple_moves::GenericMonteCarloMover
• num_repacks_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• num_repeats_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy
• num_report : protocols::forge::remodel::RemodelMover::instruction_flags
• num_residues() : protocols::kinematic_closure::ClosureProblem , protocols::pack_daemon::EntityCorrespondence
• num_rotamers() : protocols::optimize_weights::OptEData
• NUM_ROUNDS_ : protocols::farna::RNA_LoopCloser
• num_sa_ : protocols::pack_daemon::FASTER_IG_Repacker
• num_screeners() : protocols::stepwise::StepWiseSampleAndScreen
• num_segments() : protocols::backrub::BackrubMover
• num_sent_to_proc : protocols::match::MatcherOutputStats
• num_seqpos_lists() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• num_sets() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• num_sheet_pose_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• 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_aa_for_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• num_states_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_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::BaseTabooPerturber
• num_strings_ : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• num_structures_added_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• num_successes() : protocols::stepwise::StepWiseSampleAndScreen
• num_target_states() : protocols::toolbox::match_enzdes_util::InvrotTree
• num_templates() : protocols::comparative_modeling::ThreadingJobInputter
• num_top_designs_ : protocols::antibody::design::AntibodyGraftDesignMover
• num_total_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• num_total_dofs_ : protocols::optimize_weights::OptEMultifunc
• num_total_rbconfs_ : protocols::enzdes::GenerateStoredRBConfs
• num_trajectory : protocols::forge::remodel::RemodelMover::instruction_flags
• num_trials() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• num_trials_ : protocols::ligand_docking::RigidSearchMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• num_tries() : protocols::stepwise::StepWiseSampleAndScreen
• 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_up_only_incompatible : protocols::match::MatcherOutputStats
• num_written_ : protocols::match::output::PDBWriter
• numb_repeats_ : protocols::simple_filters::RepeatParameterFilter , protocols::simple_moves::RepeatPropagationMover
• number_cavities : protocols::vip::VIP_Mover
• number_designable_ : protocols::simple_moves::GenericMonteCarloMover
• number_failed_jobs_ : protocols::jd2::JobDistributor
• 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_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_score_calls_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• number_to_propagate() : protocols::genetic_algorithm::GeneticAlgorithmBase
• number_to_propagate_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• NumberHBonds_ : protocols::analysis::InterfaceAnalyzerMover
• NumberHBondsCalculator() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• numbering_database_directory_ : protocols::antibody::AntibodyNumberingParser
• numbering_info_ : protocols::antibody::AntibodyInfo
• numbering_parser_ : protocols::antibody::AntibodyInfo
• numbering_scheme : protocols::antibody::AntibodyNumbering , protocols::antibody::PDBLandmark
• numbering_scheme_ : protocols::antibody::clusters::CDRClusterFeatures , 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_to_enum_ : protocols::antibody::AntibodyEnumManager
• numbering_scheme_to_string_ : protocols::antibody::AntibodyEnumManager
• numbering_scheme_transform : protocols::antibody::AntibodyNumbering
• numbering_scheme_transform_present() : protocols::antibody::AntibodyInfo
• numberOfAtoms() : protocols::pockets::SmallMol
• numbRepeats_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• NumNeighborsMPM() : protocols::match::NumNeighborsMPM
• numresults_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• numTargets_ : protocols::pockets::PocketGrid
• nv_score_ : protocols::features::ResidueBurialFeatures
• nvar() : protocols::normalmode::NormalModeMultifunc
• nvar_ : protocols::normalmode::NormalModeMultifunc
• nvec_ : protocols::evaluation::PCA
• NWDP_TM() : protocols::hybridization::TMalign