- o -

• O() : protocols::fldsgn::topology::BB_Pos
• O2M_MutateMover() : protocols::simple_moves::O2M_MutateMover
• o2prime_legacy_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• o2prime_trials() : protocols::farna::RNA_Minimizer
• O2PrimePacker() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• O2PrimeScreener() : protocols::stepwise::screener::O2PrimeScreener
• O_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• O_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• oatom1_oatom2_distance() : protocols::toolbox::match_enzdes_util::LigandConformer
• oatom1_oatom2_oatom3_angle() : protocols::toolbox::match_enzdes_util::LigandConformer
• oatom2_oatom3_distance() : protocols::toolbox::match_enzdes_util::LigandConformer
• objective_function() : protocols::loophash::MPI_LoopHashRefine
• observe_after_metropolis() : protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver
• observers() : protocols::canonical_sampling::MetropolisHastingsMover
• obtain_new_job() : protocols::jd2::JobDistributor
• obtain_templates_names() : protocols::antibody::Ab_TemplateInfo
• occ_space() : protocols::match::downstream::DownstreamBuilder
• occ_space_bounding_box() : protocols::match::MatcherTask
• occ_space_hash() : protocols::match::Matcher
• occ_space_set() : protocols::match::downstream::DownstreamBuilder
• occupied() : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• OccupiedSpaceHash() : protocols::match::OccupiedSpaceHash
• off_rotamer_pack() : protocols::simple_moves::MinPackMover
• offset() : protocols::inputter::Inputter , protocols::simple_filters::Sigmoid , protocols::topology_broker::SequenceNumberResolver
• old_seqpos() : protocols::forge::remodel::ResidueVicinityInfo
• OligomericAverageDegreeFilter() : protocols::matdes::OligomericAverageDegreeFilter
• omega() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::simple_moves::MinMover , protocols::stepwise::modeler::protein::MainChainTorsionSet
• omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• omega1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• on_conf_change() : protocols::boinc::BoincCurrentPoseObserver
• on_connection_change() : protocols::viewer::ConformationViewer
• on_energy_change() : protocols::viewer::SilentObserver
• on_length_change() : protocols::forge::build::BuildInstruction , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• on_new_fragments() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::FragmentMover
• on_residue_append() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• on_residue_delete() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• on_residue_prepend() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• on_xyz_change() : protocols::viewer::ConformationViewer
• one_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• one_random_loop() : protocols::loops::Loops
• onebody_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• only_enumerate_non_match_redundant_ligand_rotamers() : protocols::match::MatcherTask
• OopCreatorMover() : protocols::ncbb::oop::OopCreatorMover
• OopDockDesignProtocol() : protocols::ncbb::oop::OopDockDesignProtocol
• OopDPuckMinusMover() : protocols::simple_moves::oop::OopDPuckMinusMover
• OopDPuckPlusMover() : protocols::simple_moves::oop::OopDPuckPlusMover
• OopMover() : protocols::simple_moves::oop::OopMover
• OopPatcher() : protocols::simple_moves::oop::OopPatcher
• OopPuckMinusMover() : protocols::simple_moves::oop::OopPuckMinusMover
• OopPuckPlusMover() : protocols::simple_moves::oop::OopPuckPlusMover
• OopRandomPuckMover() : protocols::simple_moves::oop::OopRandomPuckMover
• OopRandomSmallMover() : protocols::simple_moves::oop::OopRandomSmallMover
• OP_const_iterator() : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• open_channel() : protocols::jd2::MpiFileBuffer
• opening() : protocols::dna::DNABasepair
• operation() : protocols::simple_filters::Operator
• Operator() : protocols::simple_filters::Operator
• operator!=() : protocols::abinitio::PairingStatEntry , protocols::antibody::PDBLandmark , protocols::environment::claims::ClaimStrength , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator()() : protocols::abinitio::_HashEntry , protocols::abinitio::_MergableEntries , protocols::abinitio::AllResiduesChanged , protocols::abinitio::hConvergenceCheck , protocols::abinitio::OrderSortPredicate , protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck , protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::dna::PDBOutput , protocols::dna::ResTypeSequence_lt , protocols::dna::RotamerDNAHBondFilter , protocols::electron_density::BfactorMultifunc , protocols::environment::Comparator , protocols::features::DatabaseFilter , protocols::features::TopCountOfAllInputs , protocols::features::TopCountOfEachInput , protocols::features::TopPercentOfAllInputs , protocols::features::TopPercentOfEachInput , protocols::forge::build::CountFromLeft , protocols::forge::build::RelativeSequencePosition , protocols::frag_picker::CompareByScoreCombination , protocols::frag_picker::CompareQueryPosition , protocols::frag_picker::CompareScoreComponent , protocols::frag_picker::CompareTotalScore , protocols::frag_picker::FragmentComparatorBase , protocols::frag_picker::quota::missing_fraction_sorter_biggest_first , protocols::frag_picker::quota::quota_limits_sorter_biggest_first , protocols::frag_picker::quota::quota_limits_sorter_smallest_first , protocols::genetic_algorithm::EntityElementsEqual , protocols::genetic_algorithm::Vec1Hash , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::hybridization::AllResiduesChanged , protocols::hybridization::hConvergenceCheck , protocols::jd2::archive::SortPredicate , protocols::jd2::CompareTags , protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFElecFunction , protocols::ligand_docking::rdf::RDFEtableFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::loophash::LoopHashMap::by_index , protocols::loops::Loop_lt , protocols::loops::RationalLoopComparator , protocols::match::downstream::hash_upstream_hit , protocols::match::downstream::us_secmatch_hit_compare , protocols::match::match_lite_equals , protocols::match::match_lite_hasher , protocols::moves::MonteCarloExceptionConverge , protocols::moves::PoseCondition , protocols::noesy_assign::FoldResonance , protocols::noesy_assign::PeakCalibrator , protocols::normalmode::NormalModeMultifunc , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::EntityHistoryLT , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::PowExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::qsar::scoring_grid::AllAtomNormalization , protocols::qsar::scoring_grid::ChiAngleNormalization , protocols::qsar::scoring_grid::HeavyAtomNormalization , protocols::qsar::scoring_grid::MolecularWeightNormalization , protocols::qsar::scoring_grid::ScoreNormalization , protocols::rbsegment_relax::RB_lt , protocols::sasa_scores::Poly , protocols::sasa_scores::PPoly , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4 , protocols::sic_dock::AtomIDHashFunction , protocols::sic_dock::NoPoseXYX_Func , protocols::stepwise::modeler::rna::rigid_body::compare_base_bin , protocols::stepwise::modeler::rna::rigid_body::compare_int_pair , protocols::toolbox::SF_Replica , protocols::toolbox::task_operations::ProteinCore , protocols::wum::find_SilentStructOPs , protocols::wum::sort_SilentStructOPs
• operator*() : protocols::sic_dock::Rose , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator+() : protocols::sic_dock::Rose
• operator++() : protocols::match::VoxelSetIterator , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator+=() : protocols::match::MatcherOutputStats
• operator-() : protocols::sic_dock::Rose
• operator--() : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator->() : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator<() : protocols::dna::Reversion , protocols::environment::claims::ClaimStrength , protocols::forge::build::Interval , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::hotspot_hashing::HotspotStub , protocols::ligand_docking::Ligand_info , protocols::loops::Loop , protocols::match::downstream_hit , protocols::match::upstream_hit , protocols::motif_grafting::movers::MotifMatch , protocols::multistate_design::PosType , protocols::pockets::SmallMol , protocols::pockets::UnionEdge
• operator<<() : protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::evaluation::MetaPoseEvaluator
• operator<=() : protocols::environment::claims::ClaimStrength
• operator=() : protocols::abinitio::ClassicAbinitio , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::Anchor , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , protocols::antibody::design::ConservativeDesignOperation , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::PDBLandmark , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::boinc::BoincCurrentPoseObserver , protocols::branch_angle::BranchAngleOptimizer , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::comparative_modeling::LoopRelaxMover , protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::environment::ProtectedConformation , protocols::evaluation::EvaluatorFactory , protocols::farna::TorsionSet , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::OtherContextScoreFunction , protocols::floppy_tail::FloppyTailMover , 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::Interval , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelWorkingSet , protocols::frag_picker::VallResidue , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::hotspot_hashing::HotspotStub , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputter , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loophash::LoopHashMap , protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::LoopMoverFactory , protocols::loops::Loops , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::DownstreamAlgorithm , protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::output::MatchScoreWriter , protocols::match::upstream::BuildSet , protocols::matdes::SymDofMoverSampler , protocols::membrane::FlipMover , protocols::membrane::geometry::Embedding , protocols::membrane::geometry::EmbeddingDef , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::DualMonteCarlo , protocols::moves::FilterReporterMover , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::multistate_design::PosType , protocols::noesy_assign::ResonanceList , protocols::nonlocal::Chunk , protocols::pack_daemon::EntityCorrespondence , protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::VLB , protocols::qsar::scoring_grid::GridFactory , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::rpc::JSON_RPC , protocols::scoring::InterchainPotential , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::scoring::methods::pcs2::PcsInputCenter , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4 , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::DOFHistogramRecorder , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::RingConformationMover , protocols::simple_moves::UniformRotationMover , protocols::simple_moves::UniformTranslationMover , protocols::stepwise::modeler::protein::MainChainTorsionSet , protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::Attachment , protocols::stepwise::monte_carlo::SWA_Move , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::toolbox::AllowInsert , protocols::toolbox::DummyClass , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP > , protocols::toolbox::pose_metric_calculators::MetricValueGetter , protocols::toolbox::SF_Replica , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::topology_broker::TopologyBroker , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• operator==() : protocols::abinitio::PairingStatEntry , protocols::antibody::PDBLandmark , protocols::environment::claims::ClaimStrength , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::fldsgn::topology::HSSTriplet , protocols::forge::build::Interval , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::jumping::DisulfPairing , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::ResidueTorsionRestraints , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::match::downstream_hit , protocols::match::upstream_hit , protocols::multistate_design::PosType , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakAssignment , protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData , protocols::stepwise::modeler::rna::phosphate::PhosphateMove , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator>() : protocols::environment::claims::ClaimStrength
• operator>=() : protocols::environment::claims::ClaimStrength
• operator[]() : protocols::abinitio::StructureStore , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::cluster::Cluster , protocols::coarse_rna::SourcePositions , protocols::dna::DnaChains , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary , protocols::ligand_docking::DistributionMap , protocols::loops::Loops , protocols::loops::LoopsFileData , protocols::noesy_assign::MethylNameLibrary , protocols::noesy_assign::ResonanceList , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData , protocols::pack_daemon::TopEntitySet , protocols::rbsegment_relax::RBSegment
• operator_filter() : protocols::simple_filters::MultipleSigmoids
• oprod() : protocols::evaluation::PCA
• optE_type_from_name() : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• opte_weight_mixing_factor() : protocols::optimize_weights::IterativeOptEDriver
• OptEData() : protocols::optimize_weights::OptEData
• OptEMultifunc() : protocols::optimize_weights::OptEMultifunc
• OptEPositionData() : protocols::optimize_weights::OptEPositionData
• OptEVariableExpression() : protocols::optimize_weights::OptEVariableExpression
• optimize_angles() : protocols::branch_angle::BranchAngleOptimizer
• optimize_branch_angles() : protocols::backrub::BackrubMover
• optimize_cov_bond() : protocols::ub_e2c::ubi_e2c_modeler
• optimize_foldtree() : protocols::simple_moves::DesignRepackMover
• optimize_kurtosis() : protocols::toolbox::InteratomicVarianceMatrix
• optimize_orientation3() : protocols::ligand_docking::LigandDockProtocol
• optimize_weights() : protocols::optimize_weights::IterativeOptEDriver
• OptimizeThreadingMover() : protocols::rbsegment_relax::OptimizeThreadingMover
• options() : protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• options_type() : protocols::loophash::LoopHashLibraryOptionsCreator , protocols::loops::LoopsFileOptionsCreator , protocols::membrane::io::LipoFileOptionsCreator , protocols::membrane::io::SpanFileOptionsCreator , protocols::surface_docking::SurfaceVectorOptionsCreator
• or_by_box_liberal() : protocols::match::Bool3DGrid
• or_by_sphere() : protocols::match::BumpGrid
• or_by_sphere_conservative() : protocols::match::Bool3DGrid
• or_by_sphere_liberal() : protocols::match::Bool3DGrid
• or_by_spheres_conservative() : protocols::match::Bool3DGrid
• or_with() : protocols::match::Bool3DGrid , protocols::match::BumpGrid
• or_within_radius_of_backbone() : protocols::match::downstream::ActiveSiteGrid
• or_within_radius_of_residue() : protocols::match::downstream::ActiveSiteGrid
• or_within_radius_of_sidechain() : protocols::match::downstream::ActiveSiteGrid
• OrbitalsFeatures() : protocols::features::OrbitalsFeatures
• OrbitalsFeaturesCreator() : protocols::features::OrbitalsFeaturesCreator
• order_parameter() : protocols::toolbox::InteratomicVarianceMatrix
• order_strand() : protocols::fldsgn::topology::Sheet
• order_strands() : protocols::fldsgn::topology::Sheet
• order_vector() : protocols::frag_picker::VallResidue
• ordered_constrained_positions() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzdesCstCache
• OrderedSequentialSymmetrySlider() : protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider
• OrderSortPredicate() : protocols::abinitio::OrderSortPredicate
• orient() : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairing
• orient_strand() : protocols::fldsgn::topology::Sheet
• orient_strands() : protocols::fldsgn::topology::Sheet
• origin() : protocols::pockets::FingerprintBase
• original2modified() : protocols::forge::build::BuildManager
• original2modified_interval_endpoints() : protocols::forge::build::BuildManager
• original2modified_intervals() : protocols::forge::build::BuildManager
• original_deleted_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
• original_end() : protocols::grafting::GraftMoverBase
• original_fixed_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• original_i2p_deleted() : protocols::forge::build::BuildManager
• original_i2p_kept() : protocols::forge::build::BuildManager
• original_insertion_point() : protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ScaffoldBuildPoint
• original_interval() : protocols::forge::build::BuildInstruction
• original_interval_valid() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• original_intervals_containing_deleted_positions() : protocols::forge::build::BuildManager
• original_intervals_containing_kept_positions() : protocols::forge::build::BuildManager
• original_kept_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
• original_mutable_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• original_resid() : protocols::match::upstream::OriginalBackboneBuildPoint
• original_sequence() : protocols::forge::components::VarLengthBuild
• original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• OriginalBackboneBuildPoint() : protocols::match::upstream::OriginalBackboneBuildPoint
• OrSelector() : protocols::pose_selectors::OrSelector
• otfedge_note_substitution_accepted() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• OTFFlexbbEdge() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• OTFFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• OTFFlexbbNode() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• other_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_helix() : protocols::helical_bundle::PerturbBundleOptions
• other_pose() : protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• OtherContextScoreFunction() : protocols::flexpack::OtherContextScoreFunction
• out_path() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• outbound() : protocols::wum::WorkUnitManager
• outer_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• outer_loop_refinement_adsorbed() : protocols::surface_docking::FullatomRelaxMover
• outer_loop_refinement_solution() : protocols::surface_docking::FullatomRelaxMover
• output() : protocols::comparative_modeling::AlignmentCluster
• output_alternative_states() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• output_atom_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• output_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• output_buried_unsatisfied_hbonds() : protocols::dna::PDBOutput
• output_capture_clear() : protocols::rpc::JSON_RPC
• output_capture_start() : protocols::rpc::JSON_RPC
• output_capture_stop() : protocols::rpc::JSON_RPC
• output_centroid_silent_struct() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• output_chainTORS() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• output_constraints_file() : protocols::metal_interface::AddZincSiteConstraints
• output_count() : protocols::canonical_sampling::SidechainMetropolisHastingsMover
• output_counts() : protocols::stepwise::StepWiseSampleAndScreen
• output_debug_structure() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::Protocol , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::relax::RelaxProtocolBase
• output_design_tags() : protocols::dna::PDBOutput
• output_diagnosis() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• output_empty_minimizer_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_ensemble() : protocols::antibody::design::AntibodyDesignMover
• output_extra_RMSDs() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• output_file_name() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::jobdist::BasicJob , protocols::match::MatcherTask
• output_forward_backward_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• output_fragments() : protocols::frag_picker::FragmentPicker
• output_hbond_info() : protocols::dna::PDBOutput
• output_hit() : protocols::match::output::WriteUpstreamHitKinemage
• output_id() : protocols::fldsgn::filters::HSSTripletFilter
• output_info() : protocols::dna::PDBOutput
• output_info_on_random_trials() : protocols::stepwise::StepWiseSampleAndScreen
• output_lores_silent_file() : protocols::farna::RNA_DeNovoProtocol
• output_matchres_only() : protocols::match::MatcherTask
• output_membrane_vector() : protocols::topology_broker::TMHTopologySamplerClaimer
• output_minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::options::StepWiseBasicOptions
• output_movie() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• output_name() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• output_only_cluster_transitions() : protocols::canonical_sampling::CanonicalSamplingMover
• output_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_pdb() : protocols::dna::PDBOutput
• output_pose() : protocols::analysis::PeptideDeriverPoseOutputter , protocols::protein_interface_design::movers::MapHotspot
• output_pose_data_list() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• output_pose_wrapper() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_rep() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• output_repacked_poses() : protocols::simple_moves::SetReturningPackRotamersMover
• output_residue_pair_energies() : protocols::simple_filters::ScoreCutoffFilter
• output_results() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• output_score_info() : protocols::dna::PDBOutput
• output_scores() : protocols::match::MatcherTask
• output_silent() : protocols::frag_picker::FragmentCandidate
• output_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• output_silent_struct() : protocols::farna::RNA_DeNovoProtocol
• output_solution_state() : protocols::surface_docking::FullatomRelaxMover
• output_statistics() : protocols::backrub::BackrubSidechainMover
• output_string_real_pairs_begin() : protocols::jd2::Job
• output_string_real_pairs_end() : protocols::jd2::Job
• output_string_string_pairs_begin() : protocols::jd2::Job
• output_string_string_pairs_end() : protocols::jd2::Job
• output_strings_begin() : protocols::jd2::Job
• output_strings_end() : protocols::jd2::Job
• output_tag() : protocols::jobdist::BasicJob
• output_to_silent_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• output_type() : protocols::fldsgn::filters::HSSTripletFilter
• output_upstream_coordinates() : protocols::match::output::WriteUpstreamHitKinemage
• output_weighted_unfolded_energies() : protocols::optimize_weights::IterativeOptEDriver
• output_writer() : protocols::match::output::MatchProcessor
• output_writer_name() : protocols::match::MatcherTask
• outputpose() : protocols::rpc::JSON_RPC
• Outputter() : protocols::outputter::Outputter
• OutputWriter() : protocols::match::output::OutputWriter
• outq() : protocols::wum2::EndPoint
• overall_cstfilter_weight() : protocols::abinitio::IterativeBase
• overall_energy0() : protocols::branch_angle::BranchCoef1
• overall_Ktheta() : protocols::branch_angle::BranchCoef1
• overall_params() : protocols::branch_angle::BranchAngleOptimizer
• overall_theta0() : protocols::branch_angle::BranchCoef1
• overlap() : protocols::comparative_modeling::AlignmentCluster
• overlapping() : protocols::features::helixAssembly::HelixBundleFeatures
• overlaps() : protocols::match::BumpGrid
• override_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• override_secstruct() : protocols::farna::RNA_StructureParameters
• overwrite() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• owner() : protocols::environment::claims::EnvClaim , protocols::topology_broker::claims::DofClaim
• owner_nodes_and_locations() : protocols::toolbox::match_enzdes_util::InvrotCollector