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

- o -

• O() : protocols::fldsgn::topology::BB_Pos
• O2M_MutateMover() : protocols::simple_moves::O2M_MutateMover
• o2prime_green_packer_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• o2prime_instantiation_distance_cutoff_ : protocols::stepwise::screener::SugarInstantiator
• o2prime_legacy_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• o2prime_legacy_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• o2prime_pack_pose_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• o2prime_pack_scorefxn_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• o2prime_pack_task_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• o2prime_packer_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::screener::O2PrimeScreener
• o2prime_trials() : protocols::farna::RNA_Minimizer
• O2PrimePacker() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• O2PrimeScreener() : protocols::stepwise::screener::O2PrimeScreener
• O3_C5_distance : protocols::stepwise::modeler::rna::output_data_struct
• O_ : protocols::fldsgn::topology::BB_Pos
• O_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• O_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• O_index_ : protocols::fldsgn::topology::BB_Pos
• O_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• 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
• oats_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• obj_cut_increment_ : protocols::mpi_refinement::MultiObjective
• obj_dominant_cut_ : protocols::mpi_refinement::MultiObjective
• objective_function() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Master
• objective_function_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• objsfxnOPs_ : protocols::mpi_refinement::MultiObjective
• obligate_pairing_sets_ : protocols::farna::RNA_StructureParameters
• 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
• observers_ : protocols::canonical_sampling::MetropolisHastingsMover
• obtain_new_job() : protocols::jd2::JobDistributor
• obtain_templates_names() : protocols::antibody::Ab_TemplateInfo
• oc_sfxn_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• occ_space() : protocols::match::downstream::DownstreamBuilder
• occ_space_bounding_box() : protocols::match::MatcherTask
• occ_space_bounding_box_ : protocols::match::Matcher , protocols::match::MatcherTask
• occ_space_hash() : protocols::match::Matcher
• occ_space_hash_ : protocols::match::Matcher
• occ_space_set() : protocols::match::downstream::DownstreamBuilder
• occspace_rev_id_at_last_update_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• occupied() : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• OccupiedSpaceHash() : protocols::match::OccupiedSpaceHash
• off_rotamer_pack() : protocols::simple_moves::MinPackMover
• off_rotamer_pack_ : protocols::simple_moves::MinPackMover
• offset() : protocols::inputter::Inputter , protocols::loophash::LeapIndex , protocols::simple_filters::Sigmoid , protocols::topology_broker::SequenceNumberResolver
• offset_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::inputter::Inputter , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::simple_filters::Sigmoid
• offset_frags_ : protocols::antibody_legacy::AntibodyModeler
• offset_map_ : protocols::topology_broker::SequenceNumberResolver
• offset_map_reversed_ : protocols::topology_broker::SequenceNumberResolver
• offset_save1_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• offset_save2_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• offset_save_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• OffsetMap : protocols::topology_broker::SequenceNumberResolver
• offsets_ : protocols::rbsegment_relax::SequenceShiftMover
• oframe_in_D3frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ok_for_centroid_calculation_ : protocols::farna::MultipleDomainMover , protocols::rigid::RigidBodyPerturbMover
• ok_to_increment_ : protocols::stepwise::screener::StepWiseScreener
• old_batches_ : protocols::abinitio::HedgeArchive
• old_center_ : protocols::membrane::TranslationRotationMover
• old_chi_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_force : protocols::cartesian::CartesianAtom
• old_normal_ : protocols::membrane::RotationMover , protocols::membrane::TranslationRotationMover
• old_phi_ : protocols::simple_moves::BackboneMover
• old_position : protocols::cartesian::CartesianAtom
• old_psi_ : protocols::simple_moves::BackboneMover
• old_rama_score_ : protocols::simple_moves::BackboneMover
• old_seqpos() : protocols::forge::remodel::ResidueVicinityInfo
• old_seqpos_ : protocols::forge::remodel::ResidueVicinityInfo
• old_size_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• old_velocity : protocols::cartesian::CartesianAtom
• oldphi : protocols::simple_moves::BBConRotMover
• OligomericAverageDegreeFilter() : protocols::matdes::OligomericAverageDegreeFilter
• omega() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , 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
• omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• omega1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• omega1_ : protocols::helical_bundle::parameters::BundleParameters
• omega1_initial_ : protocols::helical_bundle::FitSimpleHelix
• omega1_val_output_ : protocols::helical_bundle::FitSimpleHelix
• omega_ : protocols::canonical_sampling::BiasEnergy , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::make_rot_lib::RotData , protocols::simple_moves::MinMover , protocols::stepwise::modeler::protein::MainChainTorsionSet
• OMEGA_ANGLES : protocols::sparta::Sparta::SpartaLib
• omega_cutoff_ : protocols::simple_filters::GeometryFilter
• OMEGA_MEAN_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• omg_ : protocols::make_rot_lib::MakeRotLibJob
• omg_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• OMIT : protocols::flxbb::LayerDesignOperation
• 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_body_energies_ : protocols::flexpack::interaction_graph::FlexbbNode
• one_group : protocols::analysis::InterfaceAnalyzerMover , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• one_random_loop() : protocols::loops::Loops
• onebody_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• onebody_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• OnePerStruct : protocols::hotspot_hashing::movers::PlaceProbeMover
• only_center_clusters_ : protocols::antibody::CDRSetOptions
• only_current_cluster_ : protocols::antibody::CDRSetOptions
• only_enumerate_non_match_redundant_ligand_rotamers() : protocols::match::MatcherTask
• only_enumerate_non_match_redundant_ligand_rotamers_ : protocols::match::MatcherTask
• only_remove_missing_density_flag_ : protocols::LoopRebuild
• only_seeds_chain_ : protocols::seeded_abinitio::SeedFoldTree
• only_stage4_ : protocols::abinitio::MembraneAbinitio
• oop_d_minus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_d_plus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_design_first_ : protocols::ncbb::oop::OopDockDesignProtocol
• oop_low_e_puck_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_minus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_plus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_post_pos_ : protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher
• oop_pre_pos_ : protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher
• oop_seq_positions_ : protocols::simple_moves::oop::OopRandomPuckMover , protocols::simple_moves::oop::OopRandomSmallMover
• 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 : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::FitnessFunction , protocols::genetic_algorithm::PositionSpecificRandomizer , protocols::multistate_design::MultiStateAggregateFunction , protocols::multistate_design::MultiStateFitnessFunction , protocols::multistate_design::PartitionAggregateFunction< T >
• op1_atom_idx_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• op2_atom_idx_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• op_ : protocols::canonical_sampling::PatchOperation
• OP_const_iterator() : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• open_buffers_ : protocols::jd2::MpiFileBuffer
• open_channel() : protocols::jd2::MpiFileBuffer
• open_files_ : protocols::jd2::MpiFileBuffer
• opening() : protocols::dna::DNABasepair
• opening_ : protocols::dna::DNABasepair
• operation() : protocols::simple_filters::Operator
• 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::jd2::InnerJob , protocols::jd2::Job , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::sic_dock::Rose , 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::branch_angle::BranchParam1 , protocols::branch_angle::BranchParam2 , protocols::dna::Reversion , protocols::environment::claims::ClaimStrength , protocols::farna::BasePairStepSequence , protocols::farna::BasePairType , 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::abinitio::PairingStatistics , protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::evaluation::MetaPoseEvaluator , protocols::farna::BasePairStep , protocols::farna::BasePairStepSequence , protocols::features::helixAssembly::HelicalFragment , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::Strand , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::jd2::archive::Batch , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jumping::JumpSample , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::Loops , protocols::loops::LoopsFileIO , protocols::match::output::MatchScoreWriter , protocols::motifs::Motif , protocols::motifs::MotifLibrary , protocols::motifs::SingleMotif , protocols::moves::MoverContainer , protocols::moves::TrialMover , protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData , protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::scoring::methods::pcs2::PcsInputCenter , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs2::PcsTensor , 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_file_data , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs::PCS_tensor , 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_file_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , 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_file_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , 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_file_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , 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_file_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4 , protocols::topology_broker::ClaimerMessage
• 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::jd2::InnerJob , protocols::jd2::Job , 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::sic_dock::Rose , 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::PairingStatEntry , protocols::abinitio::PairingStatistics , protocols::jd2::archive::Batch , protocols::sasa_scores::Poly , protocols::sasa_scores::PPoly
• 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_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• operator_filter() : protocols::simple_filters::MultipleSigmoids
• operatorF_ : protocols::simple_filters::MultipleSigmoids
• oprod() : protocols::evaluation::PCA
• optE_data_ : protocols::optimize_weights::IterativeOptEDriver
• opte_data_ : protocols::optimize_weights::OptEMultifunc
• optE_dof_expressions_ : protocols::optimize_weights::WrapperOptEMultifunc
• optE_type_2_optE_type_name_ : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_from_name() : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name_map_ : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name_map_initialized_ : protocols::optimize_weights::OptEPositionDataFactory
• opte_weight_mixing_factor() : protocols::optimize_weights::IterativeOptEDriver
• OptEData() : protocols::optimize_weights::OptEData
• OptEMultifunc() : protocols::optimize_weights::OptEMultifunc
• optEmultifunc_dof_order_ : protocols::optimize_weights::WrapperOptEMultifunc
• OptEPositionData() : protocols::optimize_weights::OptEPositionData
• OptEVariableExpression() : protocols::optimize_weights::OptEVariableExpression
• optimal : protocols::pockets::PocketExemplarMultifunc
• optimize_angles() : protocols::branch_angle::BranchAngleOptimizer
• optimize_branch_angles() : protocols::backrub::BackrubMover
• optimize_cov_bond() : protocols::ub_e2c::ubi_e2c_modeler
• optimize_cyclic_threshold_ : protocols::analysis::PeptideDeriverFilter
• optimize_foldtree() : protocols::simple_moves::DesignRepackMover
• optimize_foldtree_ : protocols::simple_moves::DesignRepackMover
• optimize_kurtosis() : protocols::toolbox::InteratomicVarianceMatrix
• optimize_mask_ : protocols::cryst::UpdateSolventMover
• optimize_memory_usage_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• optimize_only_kic_region_sidechains_after_move_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• optimize_orientation3() : protocols::ligand_docking::LigandDockProtocol
• optimize_params_ : protocols::cryst::UpdateSolventMover
• optimize_sequence_ : protocols::antibody::GraftCDRLoopsProtocol
• optimize_stems_ : protocols::antibody::GraftedStemOptimizer
• optimize_until_score_is_negative_ : protocols::ligand_docking::Transform
• optimize_weights() : protocols::optimize_weights::IterativeOptEDriver
• OptimizeThreadingMover() : protocols::rbsegment_relax::OptimizeThreadingMover
• option_cstfile_ : protocols::enzdes::AddOrRemoveMatchCsts
• option_file_ : protocols::ligand_docking::LigandDesign
• options : protocols::loophash::LoopHashLibrary , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• options2 : protocols::loophash::LoopHashLibrary
• options2_ : protocols::loophash::LocalInserter_SimpleMin
• options_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::jd2::archive::Batch , protocols::loophash::LocalInserter_SimpleMin , protocols::normalmode::NormalModeMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::wum::WorkUnitBase::WU_Header
• options_registered_ : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::docking::TemperedDocking , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::PeakFileFormat , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::sparta::Sparta , protocols::toolbox::DecoySetEvaluation , protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• options_type() : protocols::loophash::LoopHashLibraryOptionsCreator , protocols::loops::LoopsFileOptionsCreator , protocols::membrane::io::LipoFileOptionsCreator , protocols::membrane::io::SpanFileOptionsCreator , protocols::surface_docking::SurfaceVectorOptionsCreator
• opts : protocols::simple_moves::AddCavitiesMover
• 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
• orbital_score_ : protocols::ligand_docking::rdf::RDFOrbitalFunction
• OrbitalsFeatures() : protocols::features::OrbitalsFeatures
• OrbitalsFeaturesCreator() : protocols::features::OrbitalsFeaturesCreator
• order_ : protocols::frag_picker::VallResidue , protocols::pose_selectors::TopNByProperty
• order_of_atoms_ : protocols::frag_picker::CSTalosIO
• order_parameter() : protocols::toolbox::InteratomicVarianceMatrix
• order_strand() : protocols::fldsgn::topology::Sheet
• order_strands() : 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
• OrderedFragSetOP : protocols::forge::components::VarLengthBuild
• OrderedSequentialSymmetrySlider() : protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider
• OrderSortPredicate() : protocols::abinitio::OrderSortPredicate
• ori : protocols::kinmatch::KRSQuery , protocols::pockets::spherical_coor_triplet
• orient() : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairing
• orient_ : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairing
• orient_functional_group_ : protocols::simple_moves::chiral::ChiralMover
• orient_strand() : protocols::fldsgn::topology::Sheet
• orient_strands() : protocols::fldsgn::topology::Sheet
• orient_strands_ : protocols::fldsgn::topology::Sheet
• orientation : protocols::farna::BasePairType , protocols::farna::RNA_Pairing
• orientation_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• orig_bb_tors_ : protocols::simple_moves::GreenPacker
• orig_loop_ : protocols::loops::loop_closure::ccd::ShortLoopClosure
• orig_rot_2_curr_rot_ : protocols::simple_moves::GreenPacker
• orig_upstream_pose_ : protocols::match::output::PDBWriter
• origin() : protocols::pockets::FingerprintBase
• origin_ : protocols::pockets::FingerprintBase
• Original2Modified : protocols::forge::build::BuildManager
• original2modified() : protocols::forge::build::BuildManager
• Original2Modified : protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• original2modified_ : protocols::forge::build::BuildManager
• original2modified_interval_endpoints() : protocols::forge::build::BuildManager
• original2modified_intervals() : protocols::forge::build::BuildManager
• original_bb_rep_coords_ : protocols::simple_moves::GreenPacker
• original_constraint_set_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• 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_end_ : protocols::grafting::GraftMoverBase
• original_filenames_ : protocols::toolbox::KClusterData
• 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_fold_tree_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• original_geometry_weight_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• original_i2p_deleted() : protocols::forge::build::BuildManager
• original_i2p_kept() : protocols::forge::build::BuildManager
• original_index : protocols::forge::remodel::LineObject
• original_insertion_point() : protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ScaffoldBuildPoint
• original_interval() : protocols::forge::build::BuildInstruction
• 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_pose_ : protocols::loop_modeling::utilities::PrepareForFullatom
• original_rama2b_weight_ : protocols::loop_modeling::LoopProtocol
• original_rama_weight_ : protocols::loop_modeling::LoopProtocol
• original_repulsive_weight_ : protocols::loop_modeling::LoopProtocol
• original_resid() : protocols::match::upstream::OriginalBackboneBuildPoint
• original_resid_ : protocols::match::upstream::OriginalBackboneBuildPoint
• original_rotamers_ : protocols::simple_moves::GreenPacker
• original_scaffold_residue_bump_grids_ : protocols::match::Matcher
• original_sequence() : protocols::forge::components::VarLengthBuild
• original_sequence_ : protocols::abinitio::AllResiduesChanged , protocols::forge::components::VarLengthBuild , protocols::hybridization::AllResiduesChanged
• original_tags_ : protocols::toolbox::KClusterData
• original_type_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• original_weight : protocols::moves::TrialMover
• original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• original_weights_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• OriginalBackboneBuildPoint() : protocols::match::upstream::OriginalBackboneBuildPoint
• OriginalInterval2DesignString : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• originating_geom_cst_for_dspos : protocols::match::match_dspos1
• originnum : protocols::pockets::triplet_and_originnum
• OrSelector() : protocols::pose_selectors::OrSelector
• ostr_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• 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_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_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::WriteFileSFB , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::moves::FilterReporterMover
• out_p_ : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• out_path() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• out_path_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• out_tag_ : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• outbound() : protocols::wum::WorkUnitManager
• outbound_wu_buffer_size_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• outbound_wus_ : protocols::wum::WorkUnitManager
• outer_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• outer_cycles_ : protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• outer_loop_counter_ : protocols::optimize_weights::IterativeOptEDriver
• outer_loop_cycles_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• outer_loop_last_sequence_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• outer_loop_refinement_adsorbed() : protocols::surface_docking::FullatomRelaxMover
• outer_loop_refinement_solution() : protocols::surface_docking::FullatomRelaxMover
• outer_loop_seq_profile_cross_entropy_ : protocols::optimize_weights::IterativeOptEDriver
• outer_mc_ : protocols::antibody::H3PerturbCCD
• outer_radius_ : protocols::qsar::scoring_grid::AtrGrid
• outfile_ : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore
• outfile_name_ : protocols::jd2::AtomTreeDiffJobOutputter
• outmap_name_ : protocols::electron_density::ScaleMapIntensities
• output() : protocols::comparative_modeling::AlignmentCluster
• output_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• 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_cen_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• output_centroid : protocols::seeded_abinitio::GrowPeptides
• 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_dsgeom_for_geomcst_ : protocols::match::output::PDBWriter
• 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_extra_RMSDs_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• output_file_name() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::jobdist::BasicJob , protocols::match::MatcherTask
• output_file_name_ : protocols::jobdist::BasicJob , protocols::match::MatcherTask
• output_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• output_filters_ : protocols::farna::RNA_DeNovoProtocol
• output_forward_backward_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• output_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• output_fragments() : protocols::frag_picker::FragmentPicker
• output_frags_pdbs_ : protocols::frag_picker::nonlocal::NonlocalFrags
• output_full_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• output_hbond_info() : protocols::dna::PDBOutput
• output_header_ : protocols::match::output::MatchScoreWriter
• output_hit() : protocols::match::output::WriteUpstreamHitKinemage
• output_id() : protocols::fldsgn::filters::HSSTripletFilter
• output_id_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter
• output_idealized_ : protocols::frag_picker::nonlocal::NonlocalFrags
• output_info() : protocols::dna::PDBOutput
• output_info_on_random_trials() : protocols::stepwise::StepWiseSampleAndScreen
• output_level_ : protocols::rotamer_recovery::RRReporterSQLite
• output_lores_silent_file() : protocols::farna::RNA_DeNovoProtocol
• output_lores_silent_file_ : protocols::farna::RNA_DeNovoProtocol
• output_match_dspos1_for_geomcst_ : protocols::match::Matcher
• output_matches_as_singular_downstream_positioning_ : protocols::match::Matcher
• output_matchres_only() : protocols::match::MatcherTask
• output_matchres_only_ : protocols::match::MatcherTask
• output_matrix_ : protocols::contact_map::ContactMap
• output_membrane_vector() : protocols::topology_broker::TMHTopologySamplerClaimer
• output_minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::options::StepWiseBasicOptions
• output_minimized_pose_list_ : protocols::stepwise::options::StepWiseBasicOptions
• output_movie() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• output_mutant_structures_ : protocols::pmut_scan::PointMutScanDriver
• 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_name_ : protocols::canonical_sampling::MetropolisHastingsMover
• output_name_from_job_distributor_ : protocols::canonical_sampling::MetropolisHastingsMover
• output_observers_ : protocols::jd2::Job
• output_only_cluster_transition_ : protocols::canonical_sampling::CanonicalSamplingMover
• output_only_cluster_transitions() : protocols::canonical_sampling::CanonicalSamplingMover
• output_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_pdb() : protocols::dna::PDBOutput
• output_pdb_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• output_pdbs_ : protocols::flxbb::InterlockAroma
• output_period_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• output_pose() : protocols::analysis::PeptideDeriverPoseOutputter , protocols::protein_interface_design::movers::MapHotspot
• output_pose_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• output_pose_data_list() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• output_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• output_pose_wrapper() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_prefix_ : protocols::contact_map::ContactMap
• 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_round_silent_files_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• output_sampled_space_ : protocols::ligand_docking::Transform
• output_score_info() : protocols::dna::PDBOutput
• output_scores() : protocols::match::MatcherTask
• 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_type_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter
• output_upstream_coordinates() : protocols::match::output::WriteUpstreamHitKinemage
• output_value_ : protocols::fldsgn::filters::HSSTripletFilter
• output_weighted_unfolded_energies() : protocols::optimize_weights::IterativeOptEDriver
• output_writer() : protocols::match::output::MatchProcessor
• output_writer_name() : protocols::match::MatcherTask
• output_writer_name_ : protocols::match::MatcherTask
• outputpose() : protocols::rpc::JSON_RPC
• outputpose_ : protocols::rpc::JSON_RPC
• Outputter() : protocols::outputter::Outputter
• OutputWriter() : protocols::match::output::OutputWriter
• outq() : protocols::wum2::EndPoint
• outq_ : protocols::wum2::EndPoint
• outq_current_mem : protocols::wum2::StatusResponse
• outtag_ : protocols::sic_dock::LinkerScore
• overall_cstfilter_weight() : protocols::abinitio::IterativeBase
• overall_cstfilter_weight_ : protocols::abinitio::IterativeBase
• overall_energy0() : protocols::branch_angle::BranchCoef1
• overall_energy0_ : protocols::branch_angle::BranchCoef1
• overall_Ktheta() : protocols::branch_angle::BranchCoef1
• overall_Ktheta_ : protocols::branch_angle::BranchCoef1
• overall_params() : protocols::branch_angle::BranchAngleOptimizer
• overall_prob_set_ : protocols::antibody::design::ResidueProbDesignOperation
• overall_theta0() : protocols::branch_angle::BranchCoef1
• overall_theta0_ : protocols::branch_angle::BranchCoef1
• overhang_ : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover
• overhangs_ : protocols::antibody::design::AntibodyDesignModeler
• overlap() : protocols::comparative_modeling::AlignmentCluster
• overlap_ : protocols::hybridization::CartesianSampler
• overlap_chainbreaks_ : protocols::hybridization::FoldTreeHybridize
• overlapping() : protocols::features::helixAssembly::HelixBundleFeatures
• overlaps() : protocols::match::BumpGrid
• override_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• override_secstruct() : protocols::farna::RNA_StructureParameters
• oversample_ : protocols::analysis::PackStatMover , protocols::toolbox::pose_metric_calculators::PackstatCalculator
• overwrite() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• overwrite_ : protocols::jobdist::BaseJobDistributor , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover
• owner() : protocols::environment::claims::EnvClaim , protocols::topology_broker::claims::DofClaim
• owner_ : protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::VectorExpressionCreator
• owner_nodes_and_locations() : protocols::toolbox::match_enzdes_util::InvrotCollector
• owner_nodes_and_locations_ : protocols::toolbox::match_enzdes_util::InvrotCollector
• ozstream : protocols::dna::PDBOutput