- n -

• N() : core::scoring::BB_Pos
• n() : core::scoring::elec::FAElecContextData
• N() : protocols::fldsgn::topology::BB_Pos
• n_active_score_types() : core::scoring::EnergyGraph
• n_alt_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• n_alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_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() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• N_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• n_atoms() : protocols::toolbox::DecoySetEvaluation , protocols::toolbox::InteratomicVarianceMatrix
• n_atoms_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_atomtypes() : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::scoring::etable::Etable
• n_attached_waters() : core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::lkbtrie::LKBAtom
• n_bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• n_bins_i() : core::scoring::bin_transitions::BinTransitionData
• n_bins_iplus1() : core::scoring::bin_transitions::BinTransitionData
• n_bonded_neighbor_all_res() : core::conformation::Residue
• n_branches() : core::chemical::carbohydrates::CarbohydrateInfo
• n_build_sets() : protocols::match::upstream::ProteinUpstreamBuilder
• n_ca() : protocols::kinematic_closure::ClosureProblem
• n_ca_bond() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• n_ca_c() : protocols::kinematic_closure::ClosureProblem
• n_ca_c_angle() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• n_carbons() : core::chemical::carbohydrates::CarbohydrateInfo
• n_chi() : core::io::silent::ProteinSilentStruct_Template< T >
• n_chi_bins() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_clusters_from_last_run() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• n_collision_check_atoms() : protocols::toolbox::match_enzdes_util::LigandConformer
• n_columns() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_connected_residues() : core::scoring::etable::etrie::CountPairDataGeneric
• n_connection_pairs() : core::scoring::mm::MMBondAngleResidueTypeParam
• n_connpoints_for_entry() : core::scoring::trie::CPDataCorrespondence
• n_curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• n_curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• n_current_residue_connections() : core::conformation::Residue
• n_cycle() : protocols::recces::options::RECCES_Options
• n_cycles() : protocols::stepwise::options::StepWiseBasicOptions
• n_decoys() : protocols::toolbox::DecoySetEvaluation
• n_decoys_max() : protocols::toolbox::DecoySetEvaluation
• n_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• n_deriv_check_results() : core::optimization::NumericalDerivCheckResult
• n_derivs() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• n_designed() : protocols::mean_field::RotMatrix
• n_dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• n_dof() : protocols::md::MDBase
• n_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• n_dof_temp() : protocols::md::MDBase
• n_dump() : protocols::recces::options::RECCES_Options
• n_elements() : core::chemical::ElementSet
• n_entries() : core::scoring::trie::CPDataCorrespondence
• n_external_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• n_filters_passed_in_previous_run() : protocols::rosetta_scripts::ParsedProtocol
• n_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• n_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• n_geometric_constraints() : protocols::match::Matcher
• n_hbond_acceptors() : core::chemical::ResidueType , core::conformation::Residue
• n_hbond_donors() : core::chemical::ResidueType , core::conformation::Residue
• n_hbonds() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge
• n_helices() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle
• n_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• n_input_sources() : protocols::jd3::InnerLarvalJob
• n_kept_matches() : protocols::match::output::BestMatchesCollection
• n_ligand_rots() : protocols::simple_moves::WaterRotsDB
• n_loops() : protocols::loophash::LoopHashMap
• n_mainchain_atoms() : core::conformation::Residue
• n_mainchain_torsions_i() : core::scoring::bin_transitions::BinTransitionData
• n_mainchain_torsions_iplus1() : core::scoring::bin_transitions::BinTransitionData
• n_mutants() : protocols::pmut_scan::PointMutScanDriver
• n_mutations() : protocols::pmut_scan::Mutant
• n_non_polymeric_residue_connections() : core::chemical::ResidueType , core::conformation::Residue
• n_nonchitip_atoms_for_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• n_nonjump_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• n_npd_properties() : protocols::pack_daemon::DaemonSet
• n_nucleotide_mut_trials_corrected() : protocols::evolution::EvolutionaryDynamicsMover
• n_nus() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• n_omega() : core::chemical::carbohydrates::LinkageConformerData
• n_orbitals() : core::chemical::ResidueTypeBase , core::conformation::Residue
• n_packed_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_parameters() : core::conformation::parametric::ParametersSet
• n_parameters_sets() : core::conformation::Conformation
• n_phi_bins() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_phore_match() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• n_polymeric_residue_connections() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• 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_possible_residue_connections() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue , core::scoring::mm::MMBondAngleResidueTypeParam
• n_possible_rots() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_predecessors_w_outstanding_jobs() : protocols::jd3::JobDirectedNode
• n_property_sets() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• n_protein_rots() : protocols::simple_moves::WaterRotsDB
• n_proton_chi() : core::chemical::MutableResidueType , core::chemical::ResidueType
• n_protons() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• n_psi_bins() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• n_pssms() : core::scoring::methods::NMerPSSMEnergy
• n_rank() : protocols::jd2::MPIFileBufJobDistributor
• n_real_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• n_rebuild_tries() : protocols::comparative_modeling::LoopRelaxMover
• n_reference_pose() : core::pose::reference_pose::ReferencePoseSet
• n_req_res_in_seq() : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• n_rerelaxed() : protocols::mpi_refinement::Scheduler
• n_residue() : core::conformation::parametric::Parameters , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• n_residue_connections_for_atom() : core::chemical::MutableResidueType , core::chemical::ResidueType
• n_residues() : core::fragment::picking_old::vall::VallLibrary
• n_residues_after_cutpoint() : protocols::denovo_design::components::Segment
• n_residues_before_cutpoint() : protocols::denovo_design::components::Segment
• 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_ring_carbons() : core::chemical::carbohydrates::CarbohydrateInfo
• n_ring_conformer_sets() : core::chemical::ResidueType
• n_rings() : core::chemical::MutableResidueType , core::chemical::ResidueType
• n_rotamer_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamer_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamer_bins_for_aa_02() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotameric_bins_for_aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• n_rotamers_for_restype() : protocols::match::downstream::TargetRotamerCoords
• n_rots_total() : protocols::match::downstream::TargetRotamerCoords
• n_rounds() : protocols::rna::movers::ERRASER2Protocol
• n_rows() : protocols::frag_picker::quota::ABEGO_SS_Config
• n_sample() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• n_sample_rotamers() : core::pack::rotamer_set::ContinuousRotamerSets
• 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_scores() : core::fragment::picking_old::vall::VallLibrarian
• n_segment() : protocols::legacy_sewing::SegmentGraph
• n_seqs() : core::sequence::CompositeSequence
• n_sequence_constraints() : core::scoring::constraints::ConstraintSet
• n_svms() : core::scoring::methods::NMerSVMEnergy
• n_tables() : core::scoring::methods::NMerRefEnergy
• n_temp_levels() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• n_terminal_constraint_strength() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• N_terminal_count() : protocols::splice::AlignEndsMover
• n_terminus_size() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• 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() : core::chemical::carbohydrates::LinkageConformerData , protocols::helical_bundle::BackboneGridSamplerHelper
• n_torsions_total() : protocols::helical_bundle::BackboneGridSamplerHelper
• n_trees() : core::conformation::carbohydrates::GlycanTreeSet
• n_types() : core::chemical::gasteiger::GasteigerAtomTypeSet
• n_unassigned() : core::pack::scmin::SidechainStateAssignment
• n_virtual_atoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::Residue
• n_Vmin_assignments() : protocols::noesy_assign::CrossPeak
• n_waters() : core::scoring::lkball::WaterBuilderForRestype
• n_waters_for_atom() : core::scoring::lkball::WaterBuilderForRestype
• n_worker() : protocols::jd2::MPIFileBufJobDistributor
• n_xyz() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• na_analogue() : core::chemical::ResidueTypeBase , core::conformation::Residue
• na_analogue_raw() : core::chemical::ResidueTypeBase
• NA_calculate() : protocols::scoring::Interface
• na_set() : core::io::NomenclatureManager
• nactive_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• nali() : protocols::frag_picker::VallResidue
• name() : core::chemical::AddAtom , core::chemical::AddAtomAlias , core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddConnect , core::chemical::AddConnectAndTrackingVirt , core::chemical::AddConnectDeleteChildProton , core::chemical::AddProperty , core::chemical::AddProtonChi , core::chemical::AppendMainchainAtom , core::chemical::Atom , core::chemical::AtomType , core::chemical::AtomTypeSet , core::chemical::ChangeAncestory , core::chemical::ChangeBondType , core::chemical::ChiralFlipAtoms , core::chemical::ChiralFlipNaming , core::chemical::ClearChiRotamers , core::chemical::ConnectSulfurAndMakeVirtualProton , core::chemical::DeleteActCoordAtom , core::chemical::DeleteAtom , core::chemical::DeleteChildProton , core::chemical::DeleteMetalbindingAtom , core::chemical::DeleteProperty , core::chemical::DeleteTerminalChi , core::chemical::DeleteVariantType , core::chemical::ElementSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::GlobalResidueTypeSet , core::chemical::ICoorAtomID , core::chemical::Metapatch , core::chemical::MMAtomType , core::chemical::MMAtomTypeSet , core::chemical::NCAARotLibBBTorsions , core::chemical::NCAARotLibNumRotamerBins , core::chemical::NCAARotLibPath , core::chemical::Orbital , core::chemical::orbitals::OrbitalType , core::chemical::orbitals::OrbitalTypeSet , core::chemical::Patch , core::chemical::PatchOperation , core::chemical::PrependMainchainAtom , core::chemical::RamaPreproFilename , core::chemical::RamaPreproResname , core::chemical::RedefineChi , core::chemical::RemoveRotamerSpecifications , core::chemical::RenameAtom , core::chemical::ReplaceMainchainAtom , core::chemical::ReplaceProtonWithBromine , core::chemical::ReplaceProtonWithChlorine , core::chemical::ReplaceProtonWithEthyl , core::chemical::ReplaceProtonWithFluorine , core::chemical::ReplaceProtonWithHydroxyl , core::chemical::ReplaceProtonWithIodine , core::chemical::ReplaceProtonWithMethoxy , core::chemical::ReplaceProtonWithMethyl , core::chemical::ReplaceProtonWithTrifluoromethyl , core::chemical::ResetBondLength , core::chemical::ResidueTypeBase , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOMolecule , core::chemical::Set_AA , core::chemical::SetAllAtomsRepulsive , core::chemical::SetAtomicCharge , core::chemical::SetAtomType , core::chemical::SetBackboneHeavyatom , core::chemical::SetDisulfideAtomName , core::chemical::SetFormalCharge , core::chemical::SetICoor , core::chemical::SetInterchangeabilityGroup_String , core::chemical::SetIO_String , core::chemical::SetMMAtomType , core::chemical::SetNbrAtom , core::chemical::SetNbrRadius , core::chemical::SetNetFormalCharge , core::chemical::SetOrientAtom , core::chemical::SetPolymerConnectAtom , core::chemical::SetVirtualShadow , core::chemical::VirtualizeAll , core::chemical::VirtualizeSidechain , core::conformation::Residue , core::environment::EnvCore , core::fragment::rna::FullAtomRNA_Fragments , core::io::rna::RDAT , core::io::silent::SilentEnergy , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NoDesignPackerPalette , core::pack::palette::PackerPalette , core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AROMATIC , core::pack::task::AUTO , core::pack::task::CHARGED , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::POLAR , core::pack::task::PROPERTY , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC , core::pose::PDBInfo , core::scoring::methods::GoapRsdType , core::scoring::saxs::FormFactor , core::scoring::ScoreFunction , core::sequence::ABEGO , core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::PerResidueClashMetric , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::SimpleMetric , core::simple_metrics::StringMetric , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeStringMetric , core::simple_metrics::TestPerResidueRealMetric , core::simple_metrics::TestPerResidueStringMetric , core::simple_metrics::TestRealMetric , core::simple_metrics::TestStringMetric , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::abinitio::Template , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::Sigmoid , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::cryst::Spacegroup , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::evaluation::MetaPoseEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::FilterValueMetric , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::FilterStructs , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::frag_picker::FragmentScoreFilter , protocols::genetic_algorithm::EntityElement , protocols::hbnet::HBNetScore , protocols::helical_bundle::BundleReporterFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jd2::archive::AbstractArchiveBase , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::loops::filters::LoopAnalyzerFilter , 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::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::moves::Mover , protocols::moves::PDBDumpMover , protocols::multistate_design::PosType , protocols::noesy_assign::Resonance , protocols::pack_daemon::VectorExpression , protocols::peptide_deriver::PeptideDeriverFilter , protocols::pose_creation::MergePDBMover::Overlap , 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::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::quantum_annealing::InteractionGraphSummaryMetric , protocols::rigid::UniformRigidBodyCM , protocols::rosetta_scripts::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , protocols::simple_ddg::AlaScan , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_ddg::InterfaceBindingEnergyDensityFilter , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BatchEvaluator , protocols::simple_filters::BuriedSurfaceAreaFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HelixHelixAngleFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::LongestContinuousApolarSegmentFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MPSpanAngleFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDepthFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::ResidueSelectionDistanceFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TMsAACompFilter , protocols::simple_filters::TMsSpanMembraneFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::bb_sampler::SugarBBSampler , 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
• name1() : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::conformation::Residue
• name2enum_() : core::pose::datacache::CacheableDataType
• name2suite() : core::pose::rna::RNA_SuiteName
• name3() : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::conformation::Residue , core::pack::interaction_graph::RotamerDots , protocols::simple_moves::IonizableResidue
• name3_generated_by_base_residue_name() : core::chemical::ResidueTypeSetCache
• name_for_filter() : protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail
• name_from_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
• name_from_deriv_type() : core::scoring::hbonds::HBondTypeManager
• name_from_don_chem_type() : core::scoring::hbonds::HBondTypeManager
• name_from_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• name_from_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
• name_from_hybridization_type() : core::scoring::hbonds::HBondTypeManager
• name_from_loop_configuration() : protocols::loops::JSONFormattedLoopsFileReader
• name_from_residue_identifier() : protocols::loops::JSONFormattedLoopsFileReader
• name_from_score_type() : core::scoring::ScoreTypeManager
• name_from_seq_sep_type() : core::scoring::hbonds::HBondTypeManager
• name_from_weight_type() : core::scoring::hbonds::HBondTypeManager
• name_map() : core::chemical::ResidueTypeSet , core::chemical::ResidueTypeSetCache
• name_map_or_null() : core::chemical::ResidueTypeSetCache
• name_mapOP() : core::chemical::ResidueTypeSet
• name_mapOP_write_locked() : core::chemical::ResidueTypeSet
• name_of_hbond_calc() : protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• name_of_sasa_calc() : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• name_static() : core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::PerResidueClashMetric , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeStringMetric , core::simple_metrics::TestPerResidueRealMetric , core::simple_metrics::TestPerResidueStringMetric , core::simple_metrics::TestRealMetric , core::simple_metrics::TestStringMetric , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::filters::FilterValueMetric , protocols::quantum_annealing::InteractionGraphSummaryMetric
• name_wo_rgstr() : protocols::fldsgn::topology::StrandPairingSet
• NamedAngleConstraint() : core::scoring::constraints::NamedAngleConstraint
• NamedAngleConstraintCreator() : core::scoring::constraints::NamedAngleConstraintCreator
• NamedAtomID() : core::id::NamedAtomID
• NamedAtomID_Map() : core::id::NamedAtomID_Map< T >
• NamedAtomPairConstraint() : core::scoring::constraints::NamedAtomPairConstraint
• NamedAtomPairConstraintCreator() : core::scoring::constraints::NamedAtomPairConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator
• NamedDihedralConstraint() : core::scoring::constraints::NamedDihedralConstraint
• NamedSegmentSelector() : protocols::denovo_design::residue_selectors::NamedSegmentSelector
• NamedSolution() : protocols::denovo_design::components::NamedSolution
• NamedSolutions() : protocols::denovo_design::components::NamedSolutions
• NamedStubID() : core::id::NamedStubID
• names_vector() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• nangles() : core::fragment::BBTorsionAndAnglesSRFD , core::optimization::MinimizerMap , core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::SymMinimizerMap
• nat_ro_map() : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• 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_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• native_ensemble_best() : protocols::ligand_docking::InterfaceScoreCalculator
• native_file() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• native_pose() : core::import_pose::RNA_DeNovoSetup , protocols::evaluation::AlignEvaluator , protocols::jd3::chunk_library::ChunkLibraryJobResult
• native_positions() : protocols::legacy_sewing::Assembly
• native_rotamers_map() : protocols::legacy_sewing::LegacyReadNativeRotamersFile
• native_secstruct() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• native_tag() : protocols::jobdist::BasicJob
• NativeAntibodySeq() : protocols::antibody::design::NativeAntibodySeq
• NativeEvaluatorCreator() : protocols::simple_filters::NativeEvaluatorCreator
• nativeness() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_high() : protocols::optimize_weights::PNatStructureOptEData
• nativeness_low() : protocols::optimize_weights::PNatStructureOptEData
• natives_select() : protocols::legacy_sewing::Assembly
• NativeSelector() : protocols::residue_selectors::NativeSelector
• natm() : protocols::normalmode::NormalMode
• natom() : core::scoring::methods::GoapRsdType , core::scoring::packstat::SimplePDB , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• natoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::Residue , core::conformation::UltraLightResidue , core::optimization::CartesianMinimizerMap , core::optimization::DOF_DataPoint , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pose::PDBInfo , core::scoring::aa_composition_energy::SequenceConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BasePairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MembraneSpanConstraint , core::scoring::constraints::MembraneSpanTermZConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueCouplingConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::RTConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::FACTSResidueInfo , core::scoring::FACTSRsdTypeInfo , core::scoring::hbonds::HBondResidueMinData , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo , 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::minimization_packing::MinMover
• nb_weight() : core::scoring::packing::HolesParams
• nbackbone_conformations() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nballs() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• nbb() : core::fragment::BBTorsionSRFD , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , 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
• nbhist() : core::scoring::packing::PoseBalls
• nblist() : core::scoring::Energies , core::scoring::methods::NeighborListData
• nblist_auto_update() : core::import_pose::options::RNA_MinimizerOptions , core::optimization::MinimizerOptions
• nblist_dis2_cutoff_HH() : core::scoring::etable::Etable , core::scoring::mm::MMLJLibrary
• nblist_dis2_cutoff_XH() : core::scoring::etable::Etable , core::scoring::mm::MMLJLibrary
• nblist_dis2_cutoff_XX() : core::scoring::etable::Etable , core::scoring::mm::MMLJLibrary
• nblist_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• nbonds() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::PseudoBond
• nbonds_from_bb_atom() : protocols::match::upstream::BuildSet
• nbr_atom() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue , protocols::ligand_docking::ga_ligand_dock::atmInfo , protocols::ligand_docking::ga_ligand_dock::hbAcc , protocols::ligand_docking::ga_ligand_dock::hbDon
• nbr_atom_xyz() : core::conformation::Residue
• nbr_dis2_threshold() : core::scoring::dna::DNA_EnvPairPotential
• nbr_e_threshold() : protocols::evolution::AlignmentGapInserter
• nbr_radius() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• nbr_vertex() : core::chemical::MutableResidueType
• nbrs() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::HBondSet
• nbrs1() : core::scoring::motif::ResPairMotif
• nbrs2() : core::scoring::motif::ResPairMotif
• nc_begin() : core::kinematics::FoldTree
• NC_distance_filter() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• nc_end() : core::kinematics::FoldTree
• ncaa_rotlib_n_bin_per_rot() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• ncaa_rotlib_n_rotameric_bins() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• ncaa_rotlib_path() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• NCAADefaultPackerPalette() : core::pack::palette::NCAADefaultPackerPalette
• NCAARotamerLibrarySpecification() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• NCAARotLibBBTorsions() : core::chemical::NCAARotLibBBTorsions
• NCAARotLibNumRotamerBins() : core::chemical::NCAARotLibNumRotamerBins
• NCAARotLibPath() : core::chemical::NCAARotLibPath
• NCaCaC_Dihedral_Func() : core::scoring::disulfides::NCaCaC_Dihedral_Func
• ncap_prob_from_svm() : protocols::helix_capper::HelixNCapperMover
• NcbbDockDesignProtocol() : protocols::ncbb::NcbbDockDesignProtocol
• nchi() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue , core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , 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::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
• ndaemons() : protocols::pack_daemon::DaemonSet
• ndihe() : core::chemical::ResidueType
• ndofs() : core::optimization::CartesianMinimizerMap
• nDoFs() : protocols::helical_bundle::BundleGridSamplerHelper
• ndots() : protocols::vardist_solaccess::VarSolDRotamerDots
• near_wat() : core::scoring::hbonds::hbtrie::HBAtom
• nearby_atom_cut() : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• nearby_atom_cutoff() : protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperation
• NearNativeLoopCloser() : protocols::pose_length_moves::NearNativeLoopCloser
• needs_update() : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::StrandArchitect
• neg_Tds() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• negate() : protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::Sigmoid
• negative_better() : core::sequence::SequenceProfile
• negln_rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• 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() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::ddg::ddGMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::simple_filters::NonSequentialNeighborsFilter
• neighbor_detection_dis() : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::design::GeneralAntibodyModeler
• neighbor_dis() : protocols::grafting::AnchoredGraftMover
• neighbor_distance() : protocols::simple_filters::StemFinder
• neighbor_hits() : protocols::match::HitNeighborFinder
• neighbor_id() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• neighbor_mass() : core::scoring::TenANeighborNode
• 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
• neighbor_weight() : core::scoring::nv::NVscore
• 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_lookup() : protocols::legacy_sewing::Hasher
• neighborhood_lookup_125() : protocols::legacy_sewing::Hasher
• neighborhood_of_mutations() : protocols::ddg::ddGMover
• NeighborhoodByDistanceCalculator() : protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator
• NeighborhoodResidueSelector() : core::select::residue_selector::NeighborhoodResidueSelector
• neighboring_atoms() : core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy
• NeighborList() : core::scoring::NeighborList
• NeighborListData() : core::scoring::methods::NeighborListData
• neighbors() : protocols::simple_filters::ResidueBurialFilter , protocols::splice::AlignEndsMover , protocols::splice::FindEndpointsOperation , protocols::toolbox::CalcInterNeighborGroup
• NeighborsByDistanceCalculator() : protocols::pose_metric_calculators::NeighborsByDistanceCalculator
• NeighborTypeFilter() : protocols::simple_filters::NeighborTypeFilter
• NeighTeller() : protocols::constel::NeighTeller
• NelderMeadSimplex() : core::optimization::NelderMeadSimplex
• Nend_orient() : protocols::fldsgn::topology::SS_Base
• Nend_pos() : protocols::fldsgn::topology::SS_Base
• NestedEnergyTermDDGMutationOptEData() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• NestedEnergyTermPNatAAOptEPositionData() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• net_clash() : protocols::hbnet::HBNet
• net_formal_charge() : core::chemical::ResidueTypeBase
• netcharge_energy_setup() : core::scoring::netcharge_energy::NetChargeConstraint
• netcharge_setup_file() : core::scoring::methods::EnergyMethodOptions
• netcharge_setup_file_count() : core::scoring::methods::EnergyMethodOptions
• NetChargeConstraint() : core::scoring::netcharge_energy::NetChargeConstraint
• NetChargeEnergy() : core::scoring::netcharge_energy::NetChargeEnergy
• NetChargeEnergySetup() : core::scoring::netcharge_energy::NetChargeEnergySetup
• NetChargeFilter() : protocols::simple_filters::NetChargeFilter
• netTargetPocketVolume() : protocols::pockets::PocketGrid
• network_already_stored() : protocols::hbnet::HBNet
• 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
• network_meets_final_criteria() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• network_meets_initial_criteria() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• network_spans_all_helices() : protocols::hbnet::HBNetStapleInterface
• network_state_is_done_growing() : protocols::hbnet::HBNet
• network_state_is_satisfied() : protocols::hbnet::HBNet
• NetworkQueue() : protocols::network::NetworkQueue
• networks_identical_aa_sequence() : protocols::hbnet::HBNet
• networks_unique() : protocols::hbnet::HBNet
• NetworkState() : protocols::hbnet::NetworkState
• neutral_restypes() : protocols::simple_moves::IonizableResidue
• new_calculator() : protocols::pack_daemon::NPDPropCalculatorCreator
• new_calculator_id() : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• new_chain() : protocols::simple_moves::AddChainMover
• new_chain_order() : core::io::StructFileReaderOptions
• new_checkpoint_file() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• new_chemical_bond() : core::kinematics::FoldTree
• new_chunk_library_inputter() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• new_cluster_metric() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• new_constraint_generator() : protocols::constraint_generator::ConstraintGeneratorFactory
• 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_fold_tree_initializer() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::RNA_DeNovoPoseInitializer
• new_full_model_inputter() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• new_func() : core::scoring::func::FuncFactory
• new_grid() : protocols::qsar::scoring_grid::GridFactory
• new_icoor() : core::chemical::Orbital
• new_jump() : core::kinematics::FoldTree
• new_jump_selector() : core::select::jump_selector::JumpSelectorFactory
• new_kinematics() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::LoopJumpFoldCst
• new_move_selector() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• new_orbital_icoor_data() : core::chemical::ResidueType
• new_pose_inputter() : protocols::jd3::pose_inputters::PoseInputterFactory
• new_pose_outputter() : protocols::jd3::pose_outputters::PoseOutputterFactory
• 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_residue_group() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_residue_selector() : core::select::residue_selector::ResidueSelectorFactory
• new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• new_secondary_outputter() : protocols::jd3::pose_outputters::PoseOutputterFactory
• new_secondary_structure_override() : protocols::forge::components::VarLengthBuild
• new_segment_name() : protocols::denovo_design::components::SegmentCounts
• new_sequence_override() : protocols::forge::components::VarLengthBuild
• new_sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• new_simple_metric() : core::simple_metrics::SimpleMetricFactory
• new_sym_min() : core::optimization::symmetry::SymMinimizerMap
• new_tasks() : protocols::matdes::MatDesPointMutationCalculator
• new_terminal_pos() : protocols::fldsgn::CircularPermutation
• newConstraint() : core::scoring::constraints::ConstraintFactory
• newDataLoader() : protocols::parser::DataLoaderFactory
• newFilter() : protocols::filters::FilterFactory
• newick_tree() : protocols::jd3::JobGenealogist
• newMover() : protocols::moves::MoverFactory
• newNode() : core::environment::FoldTreeSketch::Node
• newPackerPalette() : core::pack::palette::PackerPaletteFactory
• newPackerPalettes() : core::pack::palette::PackerPaletteFactory
• newPosePropertyReporter() : protocols::rosetta_scripts::PosePropertyReporterFactory
• newPoseSelector() : protocols::rosetta_scripts::PoseSelectorFactory
• newResFilter() : core::pack::task::operation::ResFilterFactory
• newRLTO() : core::pack::task::operation::ResLvlTaskOperationFactory
• newSearch() : protocols::pockets::PocketGrid
• newTaskOperation() : core::pack::task::operation::TaskOperationFactory
• newTaskOperations() : core::pack::task::operation::TaskOperationFactory
• newTopologyClaimer() : protocols::topology_broker::TopologyClaimerFactory
• next() : core::chemical::AutomorphismIterator , core::sequence::Cell , protocols::legacy_sewing::SegmentGraph , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , 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_batch_of_larval_jobs_for_job_node() : protocols::jd3::standard::StandardJobQueen
• next_batch_of_larval_jobs_from_prelim() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• next_center() : 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_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• next_circle() : core::scoring::packstat::trace
• 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_generation() : protocols::ligand_docking::ga_ligand_dock::GAOptimizer
• next_job() : protocols::jobdist::BaseJobDistributor
• next_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• next_ligand_orientation() : protocols::nmr::pcs::PCSLigandTransformMover
• next_ligand_position() : protocols::nmr::pcs::PCSLigandTransformMover
• next_random_job() : protocols::jd2::ShuffleFileSystemJobDistributor
• next_residue_skipping_merges() : core::io::pose_from_sfr::PoseFromSFRBuilder
• next_residue_skipping_null_residue_types() : core::io::pose_from_sfr::PoseFromSFRBuilder
• next_resnum() : protocols::simple_moves::sidechain_moves::SidechainMover
• next_segment_id() : protocols::backrub::BackrubMover
• next_struct() : core::import_pose::pose_stream::SilentFilePoseInputStream
• next_torsion_string() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• nextsym() : core::scoring::BondOrderParser
• nflexible_segments() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• ngaussians() : core::scoring::SmoothScoreTermCoeffs
• ngroups() : protocols::symmetry::NCSResMapping
• nhashlookups() : protocols::sic_dock::scores::MotifHashRigidScore
• nhbonds() : core::scoring::hbonds::HBondSet
• nheavyatoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::Residue
• nirotamers() : protocols::motifs::IRCollection
• niter() : protocols::simple_filters::ResidueDepthCalculator
• njumps() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• nlevels() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• nlevels_per_dim() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::TemperatureController
• nloop() : protocols::minimization_packing::PackRotamersMover
• nlr_gaussians() : core::scoring::CenHBPotential
• NM() : protocols::normalmode::NormalModeRelaxMover
• nmer_length() : core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
• nmer_pssm_scorecut() : core::scoring::methods::NMerPSSMEnergy
• nmer_ref_seq_length() : core::scoring::methods::EnergyMethodOptions
• nmer_svm() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_aa_matrix() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_aa_matrix_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_avg_rank_as_energy() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_list() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_list_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_pssm_feat() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_rank() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_rank_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_rank_list() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_rank_list_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_scorecut() : core::scoring::methods::EnergyMethodOptions , core::scoring::methods::NMerSVMEnergy
• nmer_svm_scorecut_defined() : core::scoring::methods::EnergyMethodOptions
• nmer_svm_term_length() : core::scoring::methods::EnergyMethodOptions
• NMerPSSMEnergy() : core::scoring::methods::NMerPSSMEnergy
• NMerPSSMEnergyFilter() : protocols::simple_filters::NMerPSSMEnergyFilter
• NMerRefEnergy() : core::scoring::methods::NMerRefEnergy
• NMerSVMEnergy() : core::scoring::methods::NMerSVMEnergy
• NMerSVMEnergyFilter() : protocols::simple_filters::NMerSVMEnergyFilter
• nmissing() : core::scoring::loop_graph::LoopGraph
• nmode() : protocols::normalmode::NormalMode
• nmodes() : protocols::normalmode::NormalModeMultifunc
• nmolten_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmoltenres() : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::scmin::SidechainStateAssignment , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nmotifs() : protocols::motifs::MotifLibrary
• nmoves() : protocols::simple_moves::BackboneMover
• nmr2rosetta() : protocols::noesy_assign::MethylNames
• NMRDataFactory() : core::scoring::nmr::NMRDataFactory
• NMRDummySpinlabelAtom() : core::scoring::nmr::NMRDummySpinlabelAtom
• NMRDummySpinlabelConformer() : core::scoring::nmr::NMRDummySpinlabelConformer
• NMRDummySpinlabelEnsemble() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• NMRDummySpinlabelVoxelGrid() : core::scoring::nmr::NMRDummySpinlabelVoxelGrid
• NMRGridSearch() : core::scoring::nmr::NMRGridSearch
• NMRSpinlabel() : core::scoring::nmr::NMRSpinlabel
• NMRTensor() : core::scoring::nmr::NMRTensor
• nmtr() : core::scoring::FACTSResidueInfo
• nneighbors() : core::scoring::hbonds::HBondResidueMinData
• no_chainend_ter() : core::io::StructFileRepOptions
• no_design() : protocols::flxbb::FlxbbDesign
• no_detect_pseudobonds() : core::io::StructFileRepOptions
• no_dis_dep_die() : core::scoring::etable::coulomb::Coulomb
• no_metapatches() : core::chemical::ResidueTypeFinder
• no_modified_ddG() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• no_optH() : core::import_pose::ImportPoseOptions
• no_output_cen() : core::io::StructFileRepOptions
• no_ranked_frags() : protocols::enzdes::EnzdesFlexibleRegion
• no_relax() : protocols::flxbb::FlxbbDesign
• no_residues_with_nonzero_change_id() : core::kinematics::ResidueCoordinateChangeList
• nobjs() : protocols::mpi_refinement::MultiObjective
• nobu_register_shift() : protocols::denovo_design::components::StrandPairing
• Node() : core::environment::FoldTreeSketch::Node , core::kinematics::Node
• node() : protocols::jd3::JGJobNode
• Node() : protocols::toolbox::Node
• node_considering_alt_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• node_is_compatible() : protocols::hbnet::HBNet
• node_name() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• NodeBase() : core::pack::interaction_graph::NodeBase
• nodeidx() : protocols::denovo_design::components::FoldGraph
• nodeindex_to_residue_memory_address() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• NodeManager() : protocols::jd3::dag_node_managers::NodeManager
• NodeManagerStorageMatrix() : protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• nodes() : protocols::hbnet::NetworkState , 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_in_solution() : protocols::denovo_design::components::SolutionSorter
• nodes_part_of_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbEdge
• NoDesignPackerPalette() : core::pack::palette::NoDesignPackerPalette
• NoesyModule() : protocols::noesy_assign::NoesyModule
• NoFailDataMap() : protocols::multistage_rosetta_scripts::NoFailDataMap
• noise() : core::scoring::epr_deer::DEERDecayData
• nomenclature_table() : core::chemical::carbohydrates::CarbohydrateInfoManager
• NomenclatureManager() : core::io::NomenclatureManager
• nominal_depth() : protocols::qsar::scoring_grid::ChargeGrid
• non_const_pose() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• non_hbonding_atom() : core::scoring::hbonds::hbtrie::HBAtom
• non_helix_in_membrane_penalty() : core::scoring::MembranePotential
• non_ideal() : protocols::loophash::FastGapMover
• non_main_chain_sugar_coords() : core::fragment::rna::FullAtomRNA_Fragments
• non_main_chain_sugar_coords_defined() : core::fragment::rna::FullAtomRNA_Fragments
• non_polymer_bond() : protocols::denovo_design::components::StructureData
• non_polymer_bond_exists() : protocols::denovo_design::components::StructureData
• non_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• non_standard_residue_map() : core::pose::full_model_info::FullModelParameters
• non_standard_residue_map_nonconst() : core::pose::full_model_info::FullModelParameters
• non_virtual_score() : core::scoring::constraints::CoordinateConstraint
• noncanonical_disulfide() : protocols::denovo_design::DisulfidizeMover
• nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• nonconst_atom() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• nonconst_atom_numbers_for_mg_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_ScoringInfo
• nonconst_atoms() : core::scoring::power_diagram::PDinter
• nonconst_begin() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet
• nonconst_cenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• nonconst_circle() : core::scoring::power_diagram::PDinter
• nonconst_data() : core::conformation::Residue
• nonconst_data_ptr() : core::conformation::Residue
• nonconst_dcenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• nonconst_dipole() : core::scoring::MultipoleElecResidueInfo
• nonconst_direction() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• nonconst_downstream_algorithms() : protocols::match::Matcher
• nonconst_end() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet
• nonconst_generators() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• nonconst_get_orig_pose() : protocols::hbnet::HBNet
• nonconst_id() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• nonconst_induced_dipole() : core::scoring::MultipoleElecResidueInfo
• nonconst_induced_rf_dipole() : core::scoring::MultipoleElecResidueInfo
• nonconst_inner_job() : protocols::jd3::LarvalJob
• nonconst_interface_from_pose() : protocols::scoring::InterchainPotential
• nonconst_is_buried() : core::scoring::rna::RNA_ScoringInfo
• nonconst_is_interface() : core::scoring::rna::RNA_ScoringInfo
• nonconst_is_magnesium() : core::scoring::rna::RNA_ScoringInfo
• nonconst_long_range_container() : core::scoring::Energies
• nonconst_MembraneEmbed_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_MembraneTopology_from_pose() : protocols::abinitio::MembraneAbinitio
• nonconst_mindata_from_pose() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• nonconst_monopole() : core::scoring::MultipoleElecResidueInfo
• nonconst_monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover
• nonconst_mp_param() : core::scoring::MultipoleElecResidueInfo
• nonconst_other_struct_list() : core::io::silent::SilentStruct
• nonconst_partners() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• nonconst_pose() : protocols::multistate_design::SingleState
• nonconst_power() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• nonconst_quadrupole() : core::scoring::MultipoleElecResidueInfo
• nonconst_rad() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• nonconst_rad2() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• nonconst_res() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• nonconst_resA() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nonconst_resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• nonconst_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• nonconst_rKirkwood() : core::scoring::MultipoleElecResidueInfo
• nonconst_rna_task() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• nonconst_rosetta_res_type() : core::scoring::MultipoleElecResidueInfo
• nonconst_rotamer() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• nonconst_stored_induced_dipole() : core::scoring::MultipoleElecResidueInfo
• nonconst_stored_induced_rf_dipole() : core::scoring::MultipoleElecResidueInfo
• nonconst_vdw_type() : core::scoring::VdWTinkerResidueInfo
• nonconst_xyz() : core::scoring::PDatom , core::scoring::PDvertex , core::scoring::power_diagram::PDsphere , core::scoring::power_diagram::PDvertex
• NonContinuousFrame() : core::fragment::NonContinuousFrame
• nonjump_atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• nonlocal_pairs() : protocols::frag_picker::FragmentPicker
• nonlocal_pairs_at_position() : protocols::frag_picker::FragmentPicker
• NonlocalContactsCalculator() : protocols::pose_metric_calculators::NonlocalContactsCalculator
• NonlocalFrags() : protocols::frag_picker::nonlocal::NonlocalFrags
• NonlocalPair() : protocols::frag_picker::nonlocal::NonlocalPair
• nonmonotone() : core::optimization::LineMinimizationAlgorithm
• nonpivot_residues() : protocols::kinematic_closure::ClosureProblem
• NonPlaidFingerprint() : protocols::pockets::NonPlaidFingerprint
• nonprot_intrares_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• NonResidueTypeConstraint() : core::scoring::constraints::NonResidueTypeConstraint
• NonSequentialNeighborsFilter() : protocols::simple_filters::NonSequentialNeighborsFilter
• NonTerminalStartingSegmentRequirement() : protocols::sewing::requirements::NonTerminalStartingSegmentRequirement
• NonTerminalStartingSegmentRequirementCreator() : protocols::sewing::requirements::NonTerminalStartingSegmentRequirementCreator
• nonzero_deltas() : core::kinematics::Jump
• nonzero_weight_score_types() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• nook_finder() : protocols::vip::VIP_Mover
• nooutput() : protocols::jobdist::BaseJobDistributor
• NoOutputJobOutputter() : protocols::jd2::NoOutputJobOutputter
• NoPoseXYX_Func() : protocols::sic_dock::NoPoseXYX_Func
• NoRepackDisulfides() : core::pack::task::operation::NoRepackDisulfides
• NoResFilter() : core::pack::task::operation::NoResFilter
• norm_factor() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• norm_motif_score() : protocols::legacy_sewing::scoring::LegacyMotifScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::TopNMotifScorer
• norm_neg() : protocols::protein_interface_design::filters::BoltzmannFilter
• norm_squared() : core::scoring::EMapVector
• normal() : core::scoring::MembraneEmbed , protocols::membrane::geometry::EmbeddingDef
• normal_to_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• normalization() : protocols::cryst::ReportGradientsMover
• normalize() : core::chemical::sdf::MolFileIOMolecule , protocols::qsar::scoring_grid::GridSet
• normalize_distribution() : core::scoring::epr_deer::DEERIO , core::scoring::epr_deer::EPRSpinLabel
• normalize_isc() : protocols::peptide_deriver::PeptideDeriverFilter
• normalize_probabilities() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• normalize_template_wts() : protocols::hybridization::FoldTreeHybridize
• normalize_to_thk() : core::io::StructFileRepOptions
• normalized_data() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PRESingleSet
• 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_done() : protocols::jd3::job_distributors::JobExtractor
• not_end() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::StepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized
• not_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• not_using() : core::scoring::FACTSRsdTypeInfo
• not_valid() : core::conformation::membrane::Span
• NOTAA() : core::pack::task::NOTAA
• note_all_jobs_finished() : protocols::jd2::JobDistributor
• note_bbjump_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_chi_controls_atom() : core::chemical::ResidueType
• note_coordinate_change_registered() : core::kinematics::AtomTree
• note_current_network_state() : core::pack::annealer::FASTERAnnealer
• note_designed_residues() : protocols::dna::PDBOutput
• note_dof_change() : core::kinematics::tree::Atom_
• note_filter_fail() : protocols::match::output::MatchProcessor
• note_fixedbb_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_fwd_element_extensions() : protocols::denovo_design::components::IdealAbegoGenerator
• note_has_pseudobonds() : core::scoring::trie::CPDataCorrespondence
• note_hit_geometry() : protocols::match::OccupiedSpaceHash
• note_job_completed() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::dag_node_managers::NodeManager , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobGenealogist , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• note_job_completed_and_track() : protocols::jd3::JobQueen
• note_job_no_longer_running() : protocols::jd3::job_distributors::JobExtractor
• note_job_result_discarded() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::standard::StandardJobQueen
• note_last_considered_substitution_resolved() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• note_long_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• note_long_range_interactions_exist_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , 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::minimization_packing::PackRotamersMover
• note_preliminary_job_node_is_complete() : protocols::jd3::standard::StandardJobQueen , protocols::rosetta_scripts::RosettaScriptsJobQueen
• note_primary_change_to_geom_csts_hitlist() : protocols::match::Matcher
• note_rev_element_extensions() : protocols::denovo_design::components::IdealAbegoGenerator
• note_rpe_calculated() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• note_short_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• note_short_range_interactions_exist_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• note_state_substitution_accepted() : protocols::flexpack::interaction_graph::FlexbbEdge
• note_submatrix_accessed() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• note_submatrix_added() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• note_vertex_reached() : core::pack::interaction_graph::InteractionGraphBase
• note_xyz_uptodate() : core::kinematics::tree::Atom_
• notify_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• notify_conformation_obs() : core::pose::Pose
• notify_connection_obs() : core::conformation::Conformation
• notify_destruction_obs() : core::pose::Pose
• notify_energy_change() : core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator
• notify_energy_obs() : core::pose::Pose
• notify_general_obs() : core::conformation::Conformation , core::pose::Pose
• notify_identity_obs() : core::conformation::Conformation
• notify_length_obs() : core::conformation::Conformation
• notify_structure_change() : core::pose::metrics::PoseMetricCalculator , core::pose::metrics::StructureDependentCalculator
• notify_topological_change() : core::kinematics::AtomTree
• notify_xyz_obs() : core::conformation::Conformation
• NotJumpSelector() : core::select::jump_selector::NotJumpSelector
• NotResidueSelector() : core::select::residue_selector::NotResidueSelector
• nparams() : protocols::mpi_refinement::Scheduler
• npd_hb_weight() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• npd_hbond_set() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• 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
• npdhb_cast() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::NPDHBSimpleNode
• npdhb_owner() : core::pack::interaction_graph::NPDHBSimpleNode
• NPDHBondBackgroundEdge() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >
• NPDHBondBackgroundNode() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >
• NPDHBondEdge() : core::pack::interaction_graph::NPDHBondEdge< V, E, G >
• NPDHBondEnergy() : core::scoring::hbonds::NPDHBondEnergy
• NPDHBondInteractionGraph() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• NPDHBondNode() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• NPDHBondSet() : core::scoring::hbonds::NPDHBondSet
• NPDHBSimpleEdge() : core::pack::interaction_graph::NPDHBSimpleEdge
• NPDHBSimpleInteractionGraph() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• NPDHBSimpleNode() : core::pack::interaction_graph::NPDHBSimpleNode
• NPDPropCalculator() : protocols::pack_daemon::NPDPropCalculator
• NPDPropCalculatorCreator() : protocols::pack_daemon::NPDPropCalculatorCreator
• npick_per_iter() : protocols::mpi_refinement::Scheduler
• npoints() : protocols::ligand_docking::ga_ligand_dock::GridHash3D< T > , protocols::simple_moves::AtomHash
• npos() : core::sequence::SequenceCoupling
• nposes() : protocols::cluster::GatherPosesMover
• npr() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nproc() : protocols::rna::movers::ErraserMinimizerMover
• nr_batches() : protocols::jd2::JobDistributor
• nr_fragments() : protocols::loops::loop_closure::ccd::LoopClosure
• nr_frags() : core::fragment::Frame
• nr_frames() : core::fragment::FragSet
• nr_models() : protocols::abinitio::PairingStatistics
• nr_moves() : protocols::moves::MoverContainer
• nr_open_slaves() : protocols::jd2::SingleFileBuffer
• nr_recepients() : protocols::topology_broker::ClaimerMessage
• nr_res_affected() : core::fragment::Frame
• nr_residues() : protocols::loops::Loops
• nrad() : core::scoring::packstat::PackingScore , core::scoring::packstat::PackingScoreResData
• nrchi_bin_id() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• nrchi_lower_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_prob_minimum_for_extra_samples() : protocols::match::upstream::SampleStrategyData
• nrchi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_sample() : core::pack::dunbrack::DunbrackRotamerSampleData
• nrchi_start_angle() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• nrchi_symmetric() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• nrchi_upper_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• nremain_reset() : protocols::mpi_refinement::MultiObjective
• nres() : core::environment::FoldTreeSketch , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::silent::SilentFileData , core::io::silent::SilentStruct , core::kinematics::FoldTree , core::pose::PDBInfo , core::pose::toolbox::AtomID_Mapper , protocols::helical_bundle::BackboneGridSampler , protocols::simple_filters::ResidueDepthCalculator
• nres_topo() : core::conformation::membrane::SpanningTopology
• nrot() : protocols::mean_field::AAProb
• nrotamer_offset_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• nrotamers_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack_basic::RotamerSetsBase , 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
• nshells_for_atom() : protocols::vardist_solaccess::VarSolDRotamerDots
• nsigmoids() : core::scoring::SmoothScoreTermCoeffs
• nsol() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• nspans() : core::conformation::membrane::SpanningTopology , protocols::membrane::geometry::Embedding
• nsr_gaussians() : core::scoring::CenHBPotential
• nstep() : core::pack::rotamer_set::WaterAnchorInfo , protocols::md::MDBase
• nstep_per_update() : protocols::md::Thermostat
• nsteps() : core::optimization::SimpleDerivCheckResult
• nstrand_values() : protocols::denovo_design::components::SheetDB
• nstruct() : core::import_pose::options::RNA_DeNovoProtocolOptions , protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::Batch , protocols::jobdist::BasicJob , protocols::rna::movers::ErraserMinimizerMover
• nstruct_centroid() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• nstruct_for_job() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• nstruct_index() : protocols::jd2::Job , protocols::jd3::LarvalJob
• nstruct_max() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• 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
• nsymmops() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• 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
• nterm() : core::scoring::BondOrderParser
• nterm_included() : protocols::denovo_design::components::Segment
• Nterm_offset() : protocols::splice::FindEndpointsOperation
• NTerminalAcetyltransferaseMover() : protocols::enzymatic_movers::NTerminalAcetyltransferaseMover
• nth_dna_base() : protocols::dna::DNAParameters
• NtoCConstraintGenerator() : protocols::forge::constraints::NtoCConstraintGenerator
• nton3_hbond_score() : protocols::loop_grower::LoopGrower
• ntor() : protocols::normalmode::NormalMode
• ntorsions() : core::optimization::CartesianMinimizerMap
• ntrials() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ntries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• nu() : core::conformation::Residue
• nu0_components() : core::scoring::dna::DNATorsionPotential
• nu1_components() : core::scoring::dna::DNATorsionPotential
• nu1_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu1_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_components() : core::scoring::dna::DNATorsionPotential
• nu2_north() : core::chemical::rna::RNA_FittedTorsionInfo
• nu2_south() : core::chemical::rna::RNA_FittedTorsionInfo
• nu3_components() : core::scoring::dna::DNATorsionPotential
• nu4_components() : core::scoring::dna::DNATorsionPotential
• nu_atoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• nub() : protocols::fold_from_loops::NubInitioMover
• Nub() : protocols::fold_from_loops::utils::Nub
• NubInitioLoopClosureMover() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• NubInitioMover() : protocols::fold_from_loops::NubInitioMover
• nucleation_prob() : protocols::helical_bundle_predict::HBPHelix
• NucleotideMutation() : protocols::evolution::NucleotideMutation
• nudge_distance_bound() : protocols::noesy_assign::CrossPeak
• NullMover() : protocols::moves::NullMover
• NullPerturber() : protocols::denovo_design::components::NullPerturber
• NullPoseFolder() : protocols::denovo_design::components::NullPoseFolder
• num_aa_types() : protocols::flexpack::interaction_graph::FlexbbNode
• num_accepted() : protocols::moves::MoverStatistics
• num_accepted_scores() : protocols::monte_carlo::GenericSimulatedAnnealer
• num_accepts() : protocols::moves::TrialMover
• num_asymmetric_binstrings() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• num_asymmetric_binstrings_with_mirror_counterpart_represented() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• num_atoms() : protocols::kinematic_closure::ClosureProblem
• num_base_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_bb() : protocols::flexpack::interaction_graph::FlexbbEdge
• num_bb_clones() : core::conformation::symmetry::SymmetryInfo
• num_bbconfs() : protocols::flexpack::interaction_graph::FlexbbNode
• num_bins() : core::scoring::motif::XformScore , protocols::simple_moves::DOFHistogramRecorder
• num_bondangles() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• num_boundary_res() : protocols::hbnet::HBNet
• num_bulge() : core::import_pose::libraries::BasePairStepSequence
• num_chains() : core::conformation::Conformation , core::pose::PDBInfo , core::pose::Pose , protocols::denovo_design::components::StructureData , protocols::frags::VallData
• num_chi_clones() : core::conformation::symmetry::SymmetryInfo
• num_chi_samples_total() : protocols::match::upstream::FullChiSampleSet
• num_chunk_sets() : core::import_pose::libraries::RNA_ChunkLibrary
• num_chunks() : core::import_pose::libraries::ChunkSet , core::import_pose::libraries::RNA_ChunkLibrary
• num_claimers() : protocols::topology_broker::TopologyBroker
• num_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_coef2() : protocols::branch_angle::BranchAngleOptimizer
• num_components() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• num_core_res() : protocols::hbnet::HBNet
• num_current_pose_loops() : core::scoring::loop_graph::LoopGraph
• num_cutpoint() : core::kinematics::FoldTree
• num_cuts() : core::environment::FoldTreeSketch
• num_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• num_designable() : protocols::monte_carlo::GenericMonteCarloMover
• num_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• num_domains() : protocols::rna::denovo::coarse::MultipleDomainMover
• num_donor_acceptor_groups() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• num_entities() : protocols::pack_daemon::EntityCorrespondence
• num_enz_cst_template_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• num_features_proq2() : core::scoring::ProQPotential
• num_features_proqm() : core::scoring::ProQPotential
• num_fragpick() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• num_geom_cst() : protocols::match::output::PDBWriter
• num_heavy_atoms() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_helices_w_hbond() : protocols::hbnet::HBNetStapleInterface
• num_hits() : core::scoring::motif::MotifHits
• num_hits1() : core::scoring::motif::MotifHits
• num_hits2() : core::scoring::motif::MotifHits
• num_independent_residues() : core::conformation::symmetry::SymmetryInfo
• num_inner_iterations() : protocols::optimize_weights::IterativeOptEDriver
• num_input_structs() : protocols::multistage_rosetta_scripts::MRSJobQueen
• num_interactions() : protocols::toolbox::match_enzdes_util::ResInteractions
• num_interfaces() : core::conformation::symmetry::SymmetryInfo
• num_intermolecular_hbonds() : protocols::hbnet::HBNetStapleInterface
• num_iterations() : protocols::ddg::ddGMover , protocols::loophash::LoopHashDiversifier
• num_jobs() : protocols::jd3::dag_node_managers::NodeManager
• num_jobs_completed() : protocols::jd3::dag_node_managers::NodeManager
• num_jobs_submitted() : protocols::jd3::dag_node_managers::NodeManager
• num_jump() : core::kinematics::FoldTree , core::pose::Pose , protocols::scoring::InterfaceInfo
• num_jump_clones() : core::conformation::symmetry::SymmetryInfo
• num_jumps() : core::environment::FoldTreeSketch
• 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_motifs() : core::scoring::motif::MotifHash
• num_moving_chunks() : core::import_pose::libraries::RNA_ChunkLibrary
• num_negative_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_neighbors() : protocols::toolbox::CalcInterNeighborGroup
• num_neighbors_counting_self() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• 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_packed() : protocols::mean_field::MeanField
• num_pairings() : core::scoring::dssp::Dssp
• num_parameters() : core::conformation::parametric::Parameters
• num_partitions() : protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• num_pose_minimize() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• num_poses() : protocols::mean_field::MeanField
• num_positions() : protocols::optimize_weights::OptEData
• num_positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• num_possible_bins() : core::scoring::motif::XformScore
• num_pts() : protocols::cluster::APCluster
• num_random_samples() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::StepWiseSampleAndScreen
• num_rejections() : protocols::monte_carlo::GenericMonteCarloMover
• num_residues() : core::scoring::disulfides::FullatomDisulfideEnergyContainer , protocols::kinematic_closure::ClosureProblem , protocols::pack_daemon::EntityCorrespondence
• num_results_received() : protocols::jd3::dag_node_managers::NodeManager
• num_results_to_keep() : protocols::jd3::dag_node_managers::NodeManager
• num_results_to_keep_for_stage() : protocols::multistage_rosetta_scripts::MRSJobQueen
• num_results_total() : protocols::jd3::dag_node_managers::NodeManager
• num_rings() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• num_rotamers() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , protocols::optimize_weights::OptEData , protocols::recces::sampler::MC_Comb
• num_rotamers_in_subtree() : core::scoring::trie::TrieNode< AT, CPDATA >
• num_rots_to_pack() : core::pack::annealer::SimAnnealerBase
• num_sampling_rotamers_total() : core::pack::rotamer_set::ContinuousRotamerSet
• num_screeners() : protocols::stepwise::StepWiseSampleAndScreen
• num_segments() : protocols::backrub::BackrubMover
• num_selectors() : core::select::jump_selector::AndJumpSelector , core::select::jump_selector::OrJumpSelector , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::OrResidueSelector
• num_seqpos_lists() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• num_sets() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• num_sheets() : protocols::fldsgn::topology::SheetSet
• num_simulated_annealing_rounds_centroid() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• num_slidablejumps() : core::conformation::symmetry::SymmetryInfo
• num_stages() : protocols::multistage_rosetta_scripts::MRSJobQueen
• 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_steps_per_simulated_annealing_round_centroid() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• 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_to_be_packed() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• num_to_dock() : protocols::indel::IndelOptimizationMover
• num_total_residues() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_with_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_total_residues_without_pseudo() : core::conformation::symmetry::SymmetryInfo
• num_trials() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• num_tries() : protocols::stepwise::StepWiseSampleAndScreen
• num_triggers() : protocols::monte_carlo::GenericMonteCarloMover
• num_try_div() : protocols::loophash::LoopHashDiversifier
• num_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• num_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• num_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• num_virtuals() : core::conformation::symmetry::SymmetryInfo
• num_water() : core::scoring::packstat::SimplePDB
• number() : core::pose::PDBInfo
• number_bonded_heavyatoms() : core::chemical::MutableResidueType , core::chemical::ResidueType
• number_bonded_hydrogens() : core::chemical::MutableResidueType , core::chemical::ResidueType
• number_of_atoms() : protocols::backbone_moves::local_backbone_mover::FreePeptide
• 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::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_of_residues() : protocols::backbone_moves::local_backbone_mover::FreePeptide
• number_to_propagate() : protocols::genetic_algorithm::GeneticAlgorithmBase
• NumberHBondsCalculator() : protocols::simple_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
• NumDerivCheckData() : core::optimization::NumDerivCheckData
• numeric_properties() : core::chemical::ResidueProperties
• NumericalDerivCheckResult() : core::optimization::NumericalDerivCheckResult
• numGaussians() : core::scoring::func::USOGFunc
• NumNeighborsMPM() : protocols::match::NumNeighborsMPM
• NumNeighborsSelector() : core::select::residue_selector::NumNeighborsSelector
• nus() : core::conformation::Residue
• nusing() : core::scoring::methods::GoapRsdType
• nvar() : protocols::normalmode::NormalModeMultifunc
• NVlookup() : core::scoring::nv::NVlookup
• NVscore() : core::scoring::nv::NVscore
• NWAligner() : core::sequence::NWAligner
• NWDP_TM() : protocols::hybridization::TMalign