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

- o -

• O() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• o1_ : core::scoring::func::CircularSigmoidalFunc
• o2_ : core::scoring::func::CircularSigmoidalFunc
• o2h_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• o2h_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• o2p_index_within_special_backbone_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• o2prime_green_packer_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• o2prime_index() : core::chemical::rna::RNA_ResidueType
• o2prime_index_ : core::chemical::rna::RNA_ResidueType
• o2prime_index_within_special_backbone_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• 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::movers::RNA_Minimizer
• O2PrimePacker() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• O2PrimeScreener() : protocols::stepwise::screener::O2PrimeScreener
• O3_C5_distance : protocols::stepwise::modeler::rna::output_data_struct
• o3prime_atom_index() : core::chemical::rna::RNA_ResidueType
• o3prime_c3prime_c2prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• o3prime_c3prime_c2prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• o3prime_index_ : core::chemical::rna::RNA_ResidueType
• o4prime_atom_index() : core::chemical::rna::RNA_ResidueType
• o4prime_c1prime_bond_length_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_bond_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_bond_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_dist_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_first_base_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_first_base_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_n1_9_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_n1_9_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_index_ : core::chemical::rna::RNA_ResidueType
• o5prime_atom_index() : core::chemical::rna::RNA_ResidueType
• o5prime_index_ : core::chemical::rna::RNA_ResidueType
• O_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• O_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• O_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• O_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• O_p_sp2 : core::scoring::orbitals::OrbitalsStatistics
• O_p_sp3 : core::scoring::orbitals::OrbitalsStatistics
• O_pi_sp2 : core::scoring::orbitals::OrbitalsStatistics
• 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
• obey_ENDMDL() : core::io::StructFileReaderOptions
• obey_ENDMDL_ : core::io::StructFileReaderOptions
• 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::setup::RNA_DeNovoParameters
• obligate_pairing_sets_ : protocols::farna::setup::RNA_DeNovoParameters
• 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
• observed_sufficient_hpatch_E_to_predict_min_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• observed_sufficient_surface_E_to_predict_min_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• observer_cache() : core::pose::Pose
• observer_cache_ : core::pose::Pose
• ObserverCache() : core::pose::datacache::ObserverCache , core::pose::Pose
• ObserverCacheOP : core::pose::Pose
• ObserverOPs : core::pose::datacache::ObserverCache
• observers() : protocols::canonical_sampling::MetropolisHastingsMover
• observers_ : protocols::canonical_sampling::MetropolisHastingsMover
• ObserverType : protocols::moves::PyMolObserver
• Obsolet_NamedAtomPairConstraint() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• obsolete() : core::pose::PDBInfo
• obsolete_ : core::pose::PDBInfo
• obtain_new_job() : protocols::jd2::JobDistributor
• obtain_templates_names() : protocols::antibody::Ab_TemplateInfo
• oc_sfxn_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• occ : core::scoring::packstat::SimplePDB_Atom
• occ_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• occ_hbond_sol_database_ : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::ScoringManager
• occ_radius_scaling_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occ_shells_ : core::scoring::rna::data::RNA_DMS_Potential
• 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
• occ_values_ : core::scoring::rna::data::RNA_DMS_Potential
• occluded_sites_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occluded_water_hbond_penalty() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• OccludedHbondSolEnergy() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• OccludedHbondSolEnergy_onebody() : core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• occspace_rev_id_at_last_update_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• occupancy : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord , core::pose::PDBInfo
• occupied() : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• occupied_xyz_bins_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• OccupiedSpaceHash() : protocols::match::OccupiedSpaceHash
• occurrence_data() : core::sequence::SequenceProfile
• occurrence_data_ : core::sequence::SequenceProfile
• Octree2D() : core::scoring::packstat::Octree2D
• off_rotamer_pack() : protocols::simple_moves::MinPackMover
• off_rotamer_pack_ : protocols::simple_moves::MinPackMover
• offset() : core::io::rna::RDAT , protocols::loophash::LeapIndex , protocols::simple_filters::Sigmoid , protocols::topology_broker::SequenceNumberResolver
• offset_ : core::io::rna::RDAT , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::KarplusFunc , core::scoring::rna::RNA_SuitePotential , protocols::frag_picker::scores::AtomPairConstraintsData , 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
• OffsetPeriodicBoundFunc() : core::scoring::constraints::OffsetPeriodicBoundFunc
• offsets_ : core::import_pose::atom_tree_diffs::AtomTreeDiff , protocols::rbsegment_relax::SequenceShiftMover
• ofrac : core::scoring::APBSConfig
• 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_bond_type_ : core::chemical::ChangeBondType
• old_center_ : protocols::membrane::TranslationRotationMover
• old_chi_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_dna_set() : core::io::NomenclatureManager
• old_eval_atom_derivative() : core::scoring::disulfides::FullatomDisulfideEnergy
• old_eval_dof_derivative() : core::scoring::methods::OmegaTetherEnergy
• 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() : protocols::hybridization::FragmentBiasAssigner
• old_rama_score_ : protocols::simple_moves::BackboneMover
• old_rna_set() : core::io::NomenclatureManager
• 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() : core::fragment::picking_old::vall::VallResidue , core::fragment::torsions , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , protocols::forge::remodel::RemodelGlobalFrame , 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
• omega0_copies_pitch_instead() : protocols::helical_bundle::PerturbBundleOptions
• omega0_copies_pitch_instead_ : protocols::helical_bundle::PerturbBundleOptions
• 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_ : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::scoring::ScoringManager , protocols::canonical_sampling::BiasEnergy , protocols::forge::remodel::RemodelGlobalFrame , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::make_rot_lib::RotData , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::pose_length_moves::InsertResMover , protocols::simple_moves::MinMover , protocols::stepwise::modeler::protein::MainChainTorsionSet
• OMEGA_ANGLES : protocols::sparta::Sparta::SpartaLib
• omega_cutoff_ : protocols::simple_filters::GeometryFilter
• omega_index() : core::scoring::OmegaTether
• OMEGA_MEAN_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• omega_mean_sd : core::chemical::carbohydrates::LinkageConformerData
• omega_mus_all_ : core::scoring::OmegaTether
• omega_mus_all_splines_ : core::scoring::OmegaTether
• omega_sigmas_all_ : core::scoring::OmegaTether
• omega_sigmas_all_splines_ : core::scoring::OmegaTether
• OmegaTether() : core::scoring::OmegaTether
• OmegaTetherEnergy() : core::scoring::methods::OmegaTetherEnergy
• omg() : core::scoring::motif::Xfres
• omg_ : core::scoring::motif::Xfres , protocols::make_rot_lib::MakeRotLibJob
• OMG_BINRANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• omg_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• OMIT : protocols::flxbb::LayerDesignOperation
• on_conf_change() : protocols::boinc::BoincCurrentPoseObserver
• on_conf_xyz_change() : core::pose::Pose
• on_connection_change() : core::pose::PDBInfo , core::scoring::constraints::ConstraintSet , protocols::viewer::ConformationViewer
• on_energy_change() : protocols::viewer::SilentObserver
• on_identity_change() : core::pose::PDBInfo
• on_length_change() : core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , core::pose::PDBInfo , core::scoring::constraints::ConstraintSet , protocols::forge::build::BuildInstruction , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• on_new_fragments() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::FragmentMover
• on_pose_conf_change() : core::pose::metrics::PoseMetricContainer
• on_pose_destruction_change() : core::pose::metrics::PoseMetricContainer
• on_pose_energy_change() : core::pose::metrics::PoseMetricContainer
• 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 : core::chemical::gasteiger::GasteigerAtomTypeData
• one2three() : protocols::membrane::MPMutateRelaxMover
• one_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• one_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• one_body_energy() : core::pack::interaction_graph::SimpleNode
• one_group : protocols::analysis::InterfaceAnalyzerMover , protocols::toolbox::CalcInterNeighborGroup , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• one_letter() : core::sequence::AnnotatedSequence
• one_letter_sequence() : core::io::silent::SilentStruct , core::sequence::AnnotatedSequence
• one_letter_sequence_ : core::sequence::AnnotatedSequence
• one_line_report() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• one_random_loop() : protocols::loops::Loops
• onebody_energies() : core::scoring::Energies , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• onebody_energies_ : core::scoring::Energies , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• onebody_enmeths_ : core::scoring::MinimizationNode
• OneBodyEnergies : core::scoring::MinimizationNode
• OneBodyEnergiesIterator : core::scoring::MinimizationNode
• OneBodyEnergy() : core::scoring::methods::OneBodyEnergy
• OneGaussianScattering() : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering
• OnePerStruct : protocols::hotspot_hashing::movers::PlaceProbeMover
• OneToAllEnergyContainer() : core::scoring::OneToAllEnergyContainer
• OneToAllNeighborConstIterator() : core::scoring::OneToAllNeighborConstIterator
• OneToAllNeighborIterator() : core::scoring::OneToAllNeighborIterator
• only_c_term_ : protocols::simple_filters::SSElementMotifContactFilter
• 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_helices_ : protocols::simple_filters::LeastNativeLike9merFilter
• only_loops_ : protocols::simple_moves::StructProfileMover
• only_n_term_ : protocols::simple_filters::SSElementMotifContactFilter
• only_remove_missing_density_flag_ : protocols::LoopRebuild
• only_seeds_chain_ : protocols::seeded_abinitio::SeedFoldTree
• only_stage4_ : protocols::abinitio::MembraneAbinitio
• OnTheFlyEdge() : core::pack::interaction_graph::OnTheFlyEdge
• OnTheFlyInteractionGraph() : core::pack::interaction_graph::OnTheFlyInteractionGraph
• OnTheFlyNode() : core::pack::interaction_graph::OnTheFlyNode
• 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() : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset
• 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
• op1_atom_index() : core::chemical::rna::RNA_ResidueType
• op1_atom_index_ : core::chemical::rna::RNA_ResidueType
• op2_atom_idx_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• op2_atom_index() : core::chemical::rna::RNA_ResidueType
• op2_atom_index_ : core::chemical::rna::RNA_ResidueType
• op_ : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , 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
• operate_on_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex1_ : core::pack::task::ResidueLevelTask_
• operate_on_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex2_ : core::pack::task::ResidueLevelTask_
• operate_on_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex3_ : core::pack::task::ResidueLevelTask_
• operate_on_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex4_ : core::pack::task::ResidueLevelTask_
• OperateOnCertainResidues() : core::pack::task::operation::OperateOnCertainResidues
• OperateOnResidueSubset() : core::pack::task::operation::OperateOnResidueSubset
• operating_on_pos1_ : core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• operation() : protocols::simple_filters::Operator
• operation_ : protocols::simple_filters::Operator
• OperationList : core::pack::task::TaskFactory
• operations_ : core::chemical::PatchCase , core::pack::task::TaskFactory
• Operator() : protocols::simple_filters::Operator
• operator!= : core::chemical::ResConnID , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::environment::LocalPosition , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::AtomID , core::id::AtomID_Map< T > , core::id::DOF_ID , core::id::DOF_ID_Map< T > , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedAtomID_Map< T > , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::ResidueInformation , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots , core::pose::full_model_info::FullModelParameters , core::pose::full_model_info::SubMotifInfo , core::scoring::constraints::Constraint , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::EMapVector , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::func::Func , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ScoreFunctionInfo , protocols::abinitio::PairingStatEntry , protocols::antibody::PDBLandmark , protocols::environment::claims::ClaimStrength , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob , protocols::jd3::PoseInputSource , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T > , protocols::sic_dock::Rose , protocols::stepwise::monte_carlo::mover::StepWiseMove , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator()() : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::CopyEdge< Graph1, Graph2 > , core::chemical::CopyVertex< Graph1, Graph2 > , core::chemical::ElectronConfiguration , core::chemical::GraphvizPropertyWriter , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::PolarHydrogenFilter , core::chemical::RealFilter , core::chemical::RerootEdgeSorter , core::conformation::DefaultCubeHash , core::conformation::ExactResidueMatcher , core::conformation::ResidueMatcher , core::conformation::WatsonCrickResidueMatcher , core::environment::LengthChecker , core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::import_pose::atom_tree_diffs::ScoreLessThanComparator , core::indexed_structure_store::less_then_match_rmsd , core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent , core::optimization::ArmijoLineMinimization , core::optimization::AtomTreeMultifunc , core::optimization::BrentLineMinimization , core::optimization::CartesianMultifunc , core::optimization::ConvergenceTest , core::optimization::DFPMinConvergedAbsolute , core::optimization::DFPMinConvergedFractional , core::optimization::func_1d , core::optimization::LineMinimizationAlgorithm , core::optimization::Multifunc , core::optimization::SingleResidueMultifunc , core::optimization::sort_pred , core::optimization::StrongWolfeLineMinimization , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::rotamer_set::RotamerOperation , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::pack::task::operation::NoResFilter , core::pack::task::operation::ResFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResidueTypeFilter , core::scoring::AtomVDW , core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::DockingScoreFunction , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::ExcludedResPredicate , core::scoring::func::ConformationXYZ , core::scoring::func::FourPointsFunc , core::scoring::func::ResiduePairXYZ , core::scoring::func::ResidueXYZ , core::scoring::func::XYZ_Func , core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::IsProteinCAPredicate , core::scoring::MinScoreScoreFunction , core::scoring::motif::MyHash , core::scoring::motif::MyPred , core::scoring::motif::RMSandEnergyCMP , core::scoring::packstat::Array2D , core::scoring::packstat::HTL_EventX , core::scoring::packstat::OrderCavBallOnR , core::scoring::packstat::OrderCavBallOnRmAnb , core::scoring::packstat::OrderCavBallOnRmE , core::scoring::packstat::OrderCavBallOnX , core::scoring::packstat::OrderCBC , core::scoring::packstat::OrderSphereOnID , core::scoring::packstat::OrderSphereOnX , core::scoring::Predicate , core::scoring::ResRangePredicate , core::scoring::saxs::DistanceHistogram , core::scoring::sc::CloserToAtom , core::scoring::ScoreFunction , core::scoring::SelectedResPredicate , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::vdwaals::VDWTrieCountPair1B , core::sequence::DP_Matrix , core::sequence::SequenceAlignmentHasher , 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::denovo_design::components::SolutionSorter , protocols::dna::PDBOutput , protocols::dna::ResTypeSequence_lt , protocols::dna::RotamerDNAHBondFilter , protocols::electron_density::BfactorMultifunc , protocols::electron_density::RBfitResultComparitor , protocols::electron_density::RefinementResultComparitor , protocols::electron_density::VoxelSpacingMultifunc , 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::ncbb::SecStructMinimizeMultiFunc , 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::Mean , 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::pose_length_moves::FinalRMSDComparator , protocols::pose_length_moves::StubRMSDComparator , 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::sewing::basis_pair_equal_to , protocols::sewing::basis_pair_hash , protocols::sewing::coord_equal_to , protocols::sewing::coord_hash , protocols::sic_dock::AtomIDHashFunction , protocols::sic_dock::NoPoseXYX_Func , protocols::simple_moves::less_then_match_rmsd , 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*() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::scoring::EMapVector , protocols::sic_dock::Rose , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator*=() : core::scoring::EMapVector
• operator+() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , protocols::sic_dock::Rose
• operator++() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , protocols::match::VoxelSetIterator , protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T > , 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+=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector , protocols::match::MatcherOutputStats
• operator-() : protocols::sic_dock::Rose
• operator--() : core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator-=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector
• operator->() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator< : core::chemical::ResConnID , core::chemical::sdf::BondData , core::environment::LocalPosition , core::fragment::FragID , core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::AtomID , core::id::DOF_ID , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::kinematics::Edge , core::optimization::DOF_Node , core::pose::PDBPoseMap::ResidueKey , core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing , core::scoring::elec::ElecAtom , core::scoring::etable::EtableOptions , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotif , core::scoring::packstat::CavityBall , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::branch_angle::BranchParam1 , protocols::branch_angle::BranchParam2 , protocols::denovo_design::task_operations::SurroundingSS , protocols::dna::Reversion , protocols::environment::claims::ClaimStrength , protocols::farna::libraries::BasePairStepSequence , protocols::farna::libraries::BasePairType , protocols::features::helixAssembly::FragmentPair , protocols::features::Segment , 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 , protocols::sewing::Basis , protocols::sewing::HashValue , protocols::sewing::Model , protocols::sewing::SewSegment
• operator<< : core::chemical::AtomType , core::chemical::Bond , core::chemical::Orbital , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmetryInfo , core::fragment::FragSet , core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::AtomID , core::id::DOF_ID , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::indexed_structure_store::FragmentSpecification , core::io::CrystInfo , core::io::pose_to_sfr::PoseToStructFileRepConverter , core::io::RemarkInfo , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::RT , core::pack::task::PackerTask , core::pose::full_model_info::FullModelParameters , core::pose::full_model_info::SubMotifInfo , core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::Energies , core::scoring::etable::EtableOptions , core::scoring::func::ConstantFunc , core::scoring::func::EtableFunc , core::scoring::func::GaussianFunc , core::scoring::func::MixtureFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::Hairpin , core::scoring::Hairpins , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondSet , core::scoring::Helices , core::scoring::loop_graph::Loop , core::scoring::loop_graph::LoopCycle , core::scoring::methods::FreeDOF_Options , core::scoring::mm::MMBondAngleResidueTypeParam , core::scoring::motif::MotifHash , core::scoring::motif::MotifHits , core::scoring::motif::ResPairMotif , core::scoring::motif::ResPairMotifQuery , core::scoring::motif::RPM_FilterStats , core::scoring::motif::XformScore , core::scoring::motif::Xfres , core::scoring::packing::HolesParams , core::scoring::packstat::SimplePDB , core::scoring::packstat::SimplePDB_Atom , core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::Strands , core::scoring::vdwaals::VDWAtom , core::sequence::ChemicalShiftSequence , core::sequence::DP_Matrix , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile , 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::denovo_design::components::BondInfo , protocols::denovo_design::components::NamedSegment , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::Connection::Motif , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::evaluation::MetaPoseEvaluator , protocols::farna::base_pairs::BasePairStep , protocols::farna::libraries::BasePairStepSequence , protocols::features::helixAssembly::HelicalFragment , protocols::fldsgn::ResiduePair , 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::jd3::InnerLarvalJob , 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::sewing::Assembly , protocols::sewing::HashEdge , protocols::sewing::ModelNode , protocols::topology_broker::ClaimerMessage
• operator<=() : core::scoring::sc::Atom , protocols::environment::claims::ClaimStrength
• operator=() : core::chemical::Atom , core::chemical::AtomProperties , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::orbitals::OrbitalTypeMapper , core::chemical::ResConnID , core::chemical::ResidueProperties , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::chemical::rings::RingConformerSet , core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::conformation::Conformation , core::conformation::membrane::LipidAccInfo , core::conformation::membrane::MembraneInfo , core::conformation::membrane::Span , core::conformation::membrane::SpanningTopology , core::conformation::PseudoBond , core::conformation::Residue , core::conformation::signals::ConnectionEvent , core::conformation::signals::GeneralEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::conformation::signals::XYZEvent , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmetricConformation , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::IndependentBBTorsionSRFD , core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_ , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallResidue , core::graph::Array0< T > , core::graph::Edge , core::graph::EdgeList , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::graph::Graph , core::graph::Node , core::graph::UpperEdgeGraph< V, E > , core::id::SequenceMapping , core::import_pose::PDBSilentStruct , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentStruct , core::io::silent::SilentStructFactory , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::ResidueCoordinateChangeList , core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::Multifunc , core::pack::annealer::MultiCoolAnnealer , core::pack::dunbrack::cenrot::CenrotLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FirstClassEdge< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::pack::scmin::SidechainStateAssignment , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::TaskFactory , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , core::pose::metrics::CalculatorFactory , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , core::pose::PDBPoseMap , core::pose::Pose , core::pose::rna::RNA_SuiteName , core::pose::signals::ConformationEvent , core::pose::signals::DestructionEvent , core::pose::signals::EnergyEvent , core::pose::signals::GeneralEvent , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::ContextGraph , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DipolarCoupling , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::DockingScoreFunction , core::scoring::EMapVector , core::scoring::Energies , core::scoring::EnergyGraph , core::scoring::etable::EtableOptions , core::scoring::Hairpin , core::scoring::Hairpins , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBondOptions , core::scoring::Helices , core::scoring::loop_graph::Loop , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::LinearChainbreakEnergy , core::scoring::MinimizationGraph , core::scoring::MinScoreScoreFunction , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidualDipolarCoupling , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData , core::scoring::rna::data::RNA_DataInfo , core::scoring::ScoreFunction , core::scoring::ScoreFunctionInfo , core::scoring::SecondaryStructureWeights , core::scoring::solid_surface::SurfaceEnergies , core::scoring::Strands , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , core::sequence::AnnotatedSequence , core::sequence::Cell , core::sequence::ChemicalShiftSequence , core::sequence::CompositeSequence , core::sequence::DerivedSequenceMapping , core::sequence::Line , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceCoupling , core::sequence::SequenceFactory , core::sequence::SequenceProfile , protocols::abinitio::ClassicAbinitio , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::Anchor , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , 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::IgnoreSubsetConstraintSet , protocols::comparative_modeling::LoopRelaxMover , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::environment::ProtectedConformation , protocols::evaluation::EvaluatorFactory , protocols::farna::fragments::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::JobsContainer , 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::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::TiltMover , 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::moves::PyMolObserver , 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::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::rpc::JSON_RPC , protocols::scoring::InterchainPotential , 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::sewing::sampling::requirements::RequirementFactory , 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::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , 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::ConservativeDesignOperation , 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==() : core::chemical::Atom , core::chemical::AtomProperties , core::chemical::ResConnID , core::chemical::sdf::BondData , core::conformation::PseudoBond , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::environment::LocalPosition , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::AtomID , core::id::AtomID_Map< T > , core::id::BondID , core::id::DOF_ID , core::id::DOF_ID_Map< T > , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::ResidueInformation , core::io::silent::EnergyNames , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::Stub , core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBDepScoreInterpData< N > , core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResidueRotamerLibrary , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::pose::full_model_info::FullModelParameters , core::pose::full_model_info::SubMotifInfo , core::pose::rna::BasePair , core::scoring::aa_composition_energy::AACompositionConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing , core::scoring::elec::ElecAtom , core::scoring::EMapVector , core::scoring::etable::EtableOptions , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondSet , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::loop_graph::Loop , core::scoring::loop_graph::LoopCycle , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::FreeDOF_Options , core::scoring::methods::LK_SigmoidalFunc , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotif , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::sc::Atom , core::scoring::ScoreFunctionInfo , core::scoring::SecondaryStructureWeights , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , core::sequence::DerivedSequenceMapping , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile , protocols::abinitio::PairingStatEntry , protocols::antibody::PDBLandmark , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::denovo_design::components::BondInfo , protocols::environment::claims::ClaimStrength , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::farna::base_pairs::BasePairStep , protocols::features::helixAssembly::FragmentPair , protocols::fldsgn::topology::HSSTriplet , protocols::forge::build::Interval , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob , protocols::jd3::PoseInputSource , protocols::jumping::ChainbreakDistFunc , protocols::jumping::DisulfPairing , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::ResidueTorsionRestraints , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::make_rot_lib::RotData , 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::pockets::EggshellGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketConstraint , protocols::pockets::PocketGrid , protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T > , protocols::sewing::SewSegment , protocols::sic_dock::Rose , protocols::stepwise::modeler::rna::phosphate::PhosphateMove , protocols::stepwise::monte_carlo::mover::Attachment , protocols::stepwise::monte_carlo::mover::StepWiseMove , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator>() : protocols::environment::claims::ClaimStrength
• operator>=() : protocols::environment::claims::ClaimStrength
• operator>> : core::conformation::symmetry::SymmetryInfo , core::id::NamedAtomID , core::id::NamedStubID , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::RT , core::pose::full_model_info::FullModelParameters , core::pose::full_model_info::SubMotifInfo , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::packstat::SimplePDB , core::scoring::packstat::SimplePDB_Atom , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::abinitio::PairingStatEntry , protocols::abinitio::PairingStatistics , protocols::jd2::archive::Batch , protocols::sasa_scores::Poly , protocols::sasa_scores::PPoly
• operator[]() : core::chemical::AtomTypeSet , core::chemical::ElementSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueTypeSelector , core::chemical::ResidueTypeSelectorSingle , core::chemical::Selector_AA , core::chemical::Selector_CMDFLAG , core::chemical::Selector_MATCH_VARIANTS , core::chemical::Selector_NAME1 , core::chemical::Selector_NAME3 , core::chemical::Selector_NO_VARIANTS , core::chemical::Selector_PROPERTY , core::chemical::Selector_UPPER_POSITION , core::chemical::Selector_VARIANT_TYPE , core::conformation::UltraLightResidue , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::graph::Array0< T > , core::graph::ArrayPoolElement< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::io::silent::SilentFileData , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::rotamer_set::RotamerCouplings , core::pack::rotamer_set::WaterPackingInfo , core::scoring::dna::BasePartner , core::scoring::EMapVector , core::scoring::EnergyEdge , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::lkball::LKB_ResiduesInfo , core::scoring::ScoreFunction , core::sequence::Sequence , 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::jd2::JobsContainer , 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
• oprev_cprev_n_h_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• oprev_cprev_n_h_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• oprod() : protocols::evaluation::PCA
• opt_mem_ : protocols::membrane::MPQuickRelaxMover
• OptCysHG() : core::pack::task::operation::OptCysHG
• 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
• OptH() : core::pack::task::operation::OptH
• optimal : protocols::pockets::PocketExemplarMultifunc
• optimization_loop() : protocols::relax::LocalRelax
• optimize1_ : protocols::docking::membrane::MPDockingSetupMover
• optimize2_ : protocols::docking::membrane::MPDockingSetupMover
• optimize_angles() : protocols::branch_angle::BranchAngleOptimizer
• optimize_branch_angles() : protocols::backrub::BackrubMover
• optimize_cdrs_ : protocols::antibody::AntibodyCDRGrafter
• 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_h() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• optimize_H_ : core::pack::task::PackerTask_
• optimize_H_mode_ : core::pack::task::ResidueLevelTask_
• optimize_kurtosis() : protocols::toolbox::InteratomicVarianceMatrix
• optimize_mask_ : protocols::cryst::UpdateSolventMover
• optimize_membrane() : protocols::membrane::MPQuickRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• optimize_membrane_center() : protocols::membrane::OptimizeMembranePositionMover
• optimize_membrane_normal() : protocols::membrane::OptimizeMembranePositionMover
• optimize_memory_usage_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• 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_speed_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• optimize_stems_ : protocols::antibody::GraftedStemOptimizer
• optimize_until_score_is_negative_ : protocols::ligand_docking::Transform
• optimize_weights() : protocols::optimize_weights::IterativeOptEDriver
• OptimizeMembranePositionMover() : protocols::membrane::OptimizeMembranePositionMover
• OptimizeProteinEmbeddingMover() : protocols::membrane::OptimizeProteinEmbeddingMover
• optimizeSolventMask() : core::scoring::cryst::PhenixInterface
• optimizeSolvParams() : core::scoring::cryst::PhenixInterface
• optimizeSolvParamsAndMask() : core::scoring::cryst::PhenixInterface
• OptimizeThreadingMover() : protocols::rbsegment_relax::OptimizeThreadingMover
• option_cstfile_ : protocols::enzdes::AddOrRemoveMatchCsts
• option_file_ : protocols::ligand_docking::LigandDesign
• options() : protocols::farna::RNA_DeNovoProtocol , protocols::loophash::LoopHashLibrary , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• options2 : protocols::loophash::LoopHashLibrary
• options2_ : protocols::loophash::LocalInserter_SimpleMin
• options_ : core::io::pose_from_sfr::PoseFromSFRBuilder , core::io::pose_to_sfr::PoseToStructFileRepConverter , core::optimization::Minimizer , core::optimization::NelderMeadSimplex , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::HBondSet , core::scoring::methods::FreeDOF_Energy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , protocols::farna::movers::RNA_Minimizer , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo , 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::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::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::wum::WorkUnitBase::WU_Header
• options_registered_ : core::scoring::FACTSPotential , 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() : core::chemical::ResidueLoaderOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator , core::import_pose::ImportPoseOptionsCreator , core::io::silent::SilentFileOptionsCreator , core::scoring::electron_density::ElectronDensityOptionsCreator , core::scoring::fiber_diffraction::FiberDiffractionOptionsCreator , protocols::loophash::LoopHashLibraryOptionsCreator , protocols::loops::LoopsFileOptionsCreator , protocols::surface_docking::SurfaceVectorOptionsCreator
• optmem_ : protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• opts : protocols::simple_moves::AddCavitiesMover
• or_adducts() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• 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_double_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex3_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex4_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_exdna_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_fix_his_tautomer() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_flip_HNQ() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_include_current() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_include_virtual_side_chain() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_linmem_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_multi_cool_annealer() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_operate_on_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_optimize_h() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_optimize_h_mode() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_preserve_c_beta() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_properties_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• 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
• orb_orb_rules() : core::scoring::orbitals::OrbitalsScore
• OrbHdist_cosAOH_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbHdist_cosDHO_energy() : core::scoring::orbitals::OrbitalsLookup
• Orbital() : core::chemical::Orbital
• orbital() : core::chemical::ResidueType
• orbital_e_neg_pos_ : core::chemical::gasteiger::GasteigerAtomTypeData
• orbital_enum() : core::chemical::orbitals::OrbitalType
• orbital_icoor_data() : core::chemical::ResidueType
• orbital_index() : core::chemical::ResidueType
• orbital_name() : core::chemical::orbitals::OrbitalType , core::conformation::Residue
• orbital_name_ : core::chemical::orbitals::OrbitalType
• orbital_score_ : protocols::ligand_docking::rdf::RDFOrbitalFunction
• orbital_set_tag() : core::chemical::ResidueLoaderOptions
• orbital_set_tag_ : core::chemical::ResidueLoaderOptions
• orbital_type() : core::chemical::ResidueType , core::conformation::Residue
• orbital_type_2_enum_ : core::chemical::orbitals::OrbitalTypeMapper , core::scoring::orbitals::OrbitalsStatistics
• orbital_type_enum_ : core::chemical::orbitals::OrbitalType
• orbital_type_index() : core::chemical::Orbital , core::chemical::orbitals::OrbitalTypeSet , core::conformation::Residue
• orbital_type_index_ : core::chemical::Orbital , core::chemical::orbitals::OrbitalTypeSet
• orbital_type_name : core::scoring::orbitals::OrbitalsStatistics
• orbital_type_name_ : core::chemical::orbitals::OrbitalType
• orbital_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueTypeSet
• orbital_type_sets_ : core::chemical::ChemicalManager
• orbital_types_ : core::chemical::ResidueType , core::chemical::ResidueTypeSet
• orbital_types_ptr() : core::chemical::ResidueType
• orbital_xyz() : core::conformation::Residue
• orbitals_ : core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueType , core::conformation::Residue
• orbitals_index_ : core::chemical::ResidueType
• orbitals_lookup_table_ : core::scoring::ScoringManager
• OrbitalsFeatures() : protocols::features::OrbitalsFeatures
• OrbitalsFeaturesCreator() : protocols::features::OrbitalsFeaturesCreator
• OrbitalsLookup() : core::scoring::orbitals::OrbitalsLookup
• OrbitalsScore() : core::scoring::orbitals::OrbitalsScore
• OrbitalsStatistics() : core::scoring::orbitals::OrbitalsStatistics
• OrbitalType() : core::chemical::orbitals::OrbitalType
• OrbitalTypeMapper() : core::chemical::orbitals::OrbitalTypeMapper
• OrbitalTypeSet() : core::chemical::orbitals::OrbitalTypeSet
• OrbitalTypeSets : core::chemical::ChemicalManager
• OrbitalXYZCoords() : core::conformation::orbitals::OrbitalXYZCoords
• OrbOrbDist_cosAOD_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbOrbDist_cosDOA_energy() : core::scoring::orbitals::OrbitalsLookup
• Orbtype_ : core::chemical::orbitals::AssignOrbitals
• order() : core::chemical::Bond
• order_ : core::chemical::Bond , core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , protocols::pose_selectors::TopNByProperty
• order_atoms() : core::chemical::ResidueType
• order_by_energy() : core::io::silent::SilentFileData
• order_by_energy_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• 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() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• ordered_atoms_ : core::chemical::ResidueType
• ordered_constrained_positions() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzdesCstCache
• ordered_move_from_partition() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• OrderedFragSet() : core::fragment::OrderedFragSet , core::fragment::OrderedFragSetIterator_
• OrderedFragSetIterator_() : core::fragment::OrderedFragSetIterator_
• 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_onto_residue() : core::conformation::Residue
• orient_onto_residue_peptoid() : core::conformation::Residue
• orient_rotamer_set_to_symmetric_partner() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• orient_strand() : protocols::fldsgn::topology::Sheet
• orient_strands() : protocols::fldsgn::topology::Sheet
• orient_strands_ : protocols::fldsgn::topology::Sheet
• orientation() : core::pose::rna::BasePair , core::pose::rna::BaseStack
• Orientation() : core::scoring::dssp::Pairing
• orientation : protocols::farna::libraries::BasePairType , protocols::fldsgn::ResiduePair
• orientation_ : core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::dssp::Pairing
• orientation_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• orientation_dep_rna_ch_o_bonds_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• orientation_vectors_ : core::scoring::methods::LK_hack
• orig : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• 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_rotamer_id_for_moltenres() : core::pack::scmin::SidechainStateAssignment
• orig_upstream_pose_ : protocols::match::output::PDBWriter
• origin : core::scoring::electron_density::ElectronDensity , protocols::jd3::PoseInputSource , protocols::pockets::FingerprintBase
• origin_ : protocols::jd3::PoseInputSource , protocols::pockets::FingerprintBase , protocols::simple_moves::PeriodicBoxMover
• 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::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_layer_lines_I : core::scoring::fiber_diffraction::FiberDiffraction
• original_layer_lines_R : core::scoring::fiber_diffraction::FiberDiffraction
• 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_position() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• 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_residue_type_ : core::pack::task::ResidueLevelTask_
• original_rotamer_id_ : core::pack::scmin::SidechainStateAssignment
• 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
• originalPose_ : protocols::pose_length_moves::PossibleLoop
• originating_geom_cst_for_dspos : protocols::match::match_dspos1
• originnum : protocols::pockets::triplet_and_originnum
• OrResidueSelector() : core::select::residue_selector::OrResidueSelector
• OrSelector() : protocols::pose_selectors::OrSelector
• ortho_check() : core::kinematics::Jump , core::kinematics::RT
• 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 : core::chemical::gasteiger::GasteigerAtomTypeData
• other_atom() : core::id::BondID
• other_atoms() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• other_atoms_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• OTHER_DETAILS : core::io::HeaderInformation
• other_distances_ : core::scoring::func::GaussianChainFunc
• other_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_helix() : protocols::helical_bundle::PerturbBundleOptions
• other_neighbor_atom_indices() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• other_neighbor_id() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• 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
• other_pose_list() : core::pose::full_model_info::FullModelInfo
• other_pose_list_ : core::pose::full_model_info::FullModelInfo
• other_res_index() : core::scoring::PolymerBondedEnergyContainer
• other_struct_list() : core::io::silent::SilentStruct
• other_struct_list_ : core::io::silent::SilentStruct
• OtherContextScoreFunction() : protocols::flexpack::OtherContextScoreFunction
• OtherPoseEnergy() : core::scoring::methods::OtherPoseEnergy
• out_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::WriteFileSFB , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::moves::FilterReporterMover
• out_file_tag_ : protocols::farna::RNA_FragmentMonteCarlo
• out_filename_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• out_of_bounds() : core::scoring::PoissonBoltzmannPotential
• out_of_bounds_func() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• out_p_ : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• out_path() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• out_path_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• out_scorefilename_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• 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_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• outer_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• outer_cycles_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• outer_end_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• outer_kt_ : protocols::antibody::design::AntibodyDesignMover
• 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
• outeriterations_ : core::pack::annealer::SimAnnealerBase
• outeriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• OuterIterator : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• outfile_ : protocols::cryst::ReportGradientsMover , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore
• outfile_name_ : protocols::jd2::AtomTreeDiffJobOutputter
• outmap_name_ : protocols::electron_density::ScaleMapIntensities
• outnml : core::scoring::sc::_DOT
• output() : protocols::comparative_modeling::AlignmentCluster
• output_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• output_all_ : protocols::pose_length_moves::NearNativeLoopCloser
• 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_base_stats() : protocols::sewing::RepeatAssemblyMover
• 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_closed_ : protocols::pose_length_moves::NearNativeLoopCloser
• output_cluster_size() : protocols::stepwise::options::StepWiseBasicOptions
• output_cluster_size_ : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• output_connectivity() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• output_constraints_file() : protocols::metal_interface::AddZincSiteConstraints
• output_count() : protocols::canonical_sampling::SidechainMetropolisHastingsMover
• output_counts() : protocols::stepwise::StepWiseSampleAndScreen
• output_data() : core::io::rna::RDAT
• 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_dimacs() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• output_dsgeom_for_geomcst_ : protocols::match::output::PDBWriter
• output_empty_minimizer_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseMinimizer
• output_ensemble() : protocols::antibody::design::AntibodyDesignProtocol
• output_etable() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• 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::membrane::MPMutateRelaxMover
• output_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• output_filters() : protocols::farna::options::RNA_DeNovoProtocolOptions
• output_filters_ : protocols::farna::options::RNA_DeNovoProtocolOptions
• output_forward_backward_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• output_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• output_fragment_debug() : protocols::pose_length_moves::PossibleLoop
• 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_ignore_water_warning_once() : core::io::pose_from_sfr::PoseFromSFRBuilder
• output_info() : protocols::dna::PDBOutput
• output_info_on_random_trials() : protocols::stepwise::StepWiseSampleAndScreen
• output_level_ : protocols::rotamer_recovery::RRReporterSQLite
• output_local_prediction() : core::scoring::methods::ProQ_Energy
• output_lores_silent_file() : protocols::farna::options::RNA_DeNovoProtocolOptions
• output_lores_silent_file_ : protocols::farna::options::RNA_DeNovoProtocolOptions
• 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_mg_into_one_PDB() : protocols::magnesium::MgScanner
• output_mg_to_silent_file() : protocols::magnesium::MgScanner
• output_minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• output_minimized_pose_list_ : protocols::stepwise::options::StepWiseBasicOptions
• output_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• 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_pair_counts() : protocols::frag_picker::FragmentPicker
• output_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• output_pdb() : core::scoring::packing::PoseBalls , protocols::dna::PDBOutput , protocols::magnesium::MgMonteCarlo , protocols::magnesium::MgScanner
• output_pdb_ : protocols::magnesium::MgMonteCarlo , protocols::magnesium::MgScanner , 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_pdb_name() : protocols::jd3::pose_outputters::PDBPoseOutputter
• 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::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_rdat_header() : core::io::rna::RDAT
• output_rdat_to_file() : core::io::rna::RDAT
• output_rep() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• output_repacked_poses() : protocols::simple_moves::SetReturningPackRotamersMover
• output_residue() : core::chemical::sdf::MolWriter
• 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_sqc_file() : core::io::sequence_comparation::DesignContrast
• output_statistics() : protocols::backrub::BackrubSidechainMover
• output_stats() : protocols::sewing::AssemblyMover , protocols::sewing::LoophashAssemblyMover
• 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_subunit_ : core::conformation::symmetry::SymmData
• output_tag() : protocols::jobdist::BasicJob
• output_tags() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• output_to_silent_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• output_torsions() : core::io::StructFileRepOptions
• output_torsions_ : core::io::StructFileRepOptions
• 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_virtual() : core::io::StructFileRepOptions
• output_virtual_ : core::io::StructFileRepOptions
• output_virtual_zero_occ() : core::io::StructFileRepOptions
• output_virtual_zero_occ_ : core::io::StructFileRepOptions
• 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
• outputed() : protocols::pose_length_moves::PossibleLoop
• outputed_ : protocols::pose_length_moves::PossibleLoop
• outputpose() : protocols::rpc::JSON_RPC
• outputpose_ : protocols::rpc::JSON_RPC
• outputProfile_ : protocols::simple_moves::StructProfileMover
• outputted_ignored_water_warning_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• OutputWriter() : protocols::match::output::OutputWriter
• outtag_ : protocols::sic_dock::LinkerScore
• OUTWARDS : core::scoring::dssp::Pairing
• 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::toolbox::task_operations::ResidueProbDesignOperation
• overall_theta0() : protocols::branch_angle::BranchCoef1
• overall_theta0_ : protocols::branch_angle::BranchCoef1
• overhang_ : protocols::antibody::design::AntibodyDesignMover
• overhangs_ : protocols::antibody::design::GeneralAntibodyModeler
• overlap() : core::scoring::packstat::Circle , protocols::comparative_modeling::AlignmentCluster
• overlap1() : core::scoring::motif::ResPairMotifQuery
• overlap1_ : core::scoring::motif::ResPairMotifQuery
• overlap2() : core::scoring::motif::ResPairMotifQuery
• overlap2_ : core::scoring::motif::ResPairMotifQuery
• overlap_ : core::select::residue_selector::SecondaryStructureSelector , protocols::denovo_design::connection::BridgeChains , protocols::hybridization::CartesianSampler
• overlap_chainbreaks_ : protocols::hybridization::FoldTreeHybridize
• overlap_exposed() : core::pack::interaction_graph::InvRotamerDots
• overlap_location_pose_ : protocols::simple_moves::MergePDBMover
• overlap_max_length_ : protocols::simple_moves::MergePDBMover
• overlap_range_ : protocols::simple_moves::MergePDBMover
• overlapping_with_region() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet
• overlaps() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::RotamerDots , protocols::match::BumpGrid
• override_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• override_secstruct() : protocols::farna::setup::RNA_DeNovoPoseSetup
• 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
• overwrite_current_refpose_ : protocols::simple_moves::StorePoseSnapshot
• ownbuf_ : core::io::serialization::BUFFER
• owner() : core::scoring::Energies , protocols::environment::claims::EnvClaim , protocols::topology_broker::claims::DofClaim
• owner_ : core::graph::Edge , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::graph::Node , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::Energies , 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
• oxygen_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• ozstream : protocols::dna::PDBOutput