- o -

• 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_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_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
• O3_C5_distance : protocols::stepwise::modeler::rna::output_data_struct
• 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_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_index_ : core::chemical::rna::RNA_ResidueType
• O_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• O_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• O_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• O_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• oats_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• 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_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
• 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
• observers_ : protocols::canonical_sampling::MetropolisHastingsMover
• obsolete_ : core::pose::PDBInfo
• 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_bounding_box_ : protocols::match::Matcher , protocols::match::MatcherTask
• occ_space_hash_ : protocols::match::Matcher
• occ_values_ : core::scoring::rna::data::RNA_DMS_Potential
• occluded_sites_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occspace_rev_id_at_last_update_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• occupancy : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord
• occupied_xyz_bins_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• occurrence_data_ : core::sequence::SequenceProfile
• off_rotamer_pack_ : protocols::simple_moves::MinPackMover
• offset : protocols::loophash::LeapIndex
• 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
• 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_force : protocols::cartesian::CartesianAtom
• old_normal_ : protocols::membrane::RotationMover , protocols::membrane::TranslationRotationMover
• old_phi_ : protocols::simple_moves::BackboneMover
• old_position : protocols::cartesian::CartesianAtom
• old_psi_ : protocols::simple_moves::BackboneMover
• old_rama_score_ : protocols::simple_moves::BackboneMover
• old_seqpos_ : protocols::forge::remodel::ResidueVicinityInfo
• old_size_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• old_velocity : protocols::cartesian::CartesianAtom
• oldphi : protocols::simple_moves::BBConRotMover
• omega : core::fragment::torsions , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• omega0_copies_pitch_instead_ : protocols::helical_bundle::PerturbBundleOptions
• 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_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
• 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
• 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_letter_sequence_ : core::sequence::AnnotatedSequence
• onebody_energies_ : core::scoring::Energies , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• onebody_enmeths_ : core::scoring::MinimizationNode
• 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_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
• 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
• op1_atom_idx_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• 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
• op_ : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , protocols::canonical_sampling::PatchOperation
• open_buffers_ : protocols::jd2::MpiFileBuffer
• open_files_ : protocols::jd2::MpiFileBuffer
• opening_ : protocols::dna::DNABasepair
• operate_on_ex1_ : core::pack::task::ResidueLevelTask_
• operate_on_ex2_ : core::pack::task::ResidueLevelTask_
• operate_on_ex3_ : core::pack::task::ResidueLevelTask_
• operate_on_ex4_ : core::pack::task::ResidueLevelTask_
• operating_on_pos1_ : core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• operation_ : protocols::simple_filters::Operator
• operations_ : core::chemical::PatchCase , core::pack::task::TaskFactory
• operator_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• operatorF_ : protocols::simple_filters::MultipleSigmoids
• oprev_cprev_n_h_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• opt_mem_ : protocols::membrane::MPQuickRelaxMover
• 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_name_map_ : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name_map_initialized_ : protocols::optimize_weights::OptEPositionDataFactory
• optEmultifunc_dof_order_ : protocols::optimize_weights::WrapperOptEMultifunc
• optimal : protocols::pockets::PocketExemplarMultifunc
• optimize1_ : protocols::docking::membrane::MPDockingSetupMover
• optimize2_ : protocols::docking::membrane::MPDockingSetupMover
• optimize_cdrs_ : protocols::antibody::AntibodyCDRGrafter
• optimize_cyclic_threshold_ : protocols::analysis::PeptideDeriverFilter
• optimize_foldtree_ : protocols::simple_moves::DesignRepackMover
• optimize_H_ : core::pack::task::PackerTask_
• optimize_H_mode_ : core::pack::task::ResidueLevelTask_
• optimize_mask_ : protocols::cryst::UpdateSolventMover
• 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_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
• option_cstfile_ : protocols::enzdes::AddOrRemoveMatchCsts
• option_file_ : protocols::ligand_docking::LigandDesign
• options : protocols::loophash::LoopHashLibrary
• 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
• optmem_ : protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• opts : protocols::simple_moves::AddCavitiesMover
• or_properties_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• orbital_e_neg_pos_ : core::chemical::gasteiger::GasteigerAtomTypeData
• orbital_name_ : core::chemical::orbitals::OrbitalType
• orbital_score_ : protocols::ligand_docking::rdf::RDFOrbitalFunction
• orbital_set_tag_ : core::chemical::ResidueLoaderOptions
• 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
• orbital_type_name_ : core::chemical::orbitals::OrbitalType
• orbital_type_sets_ : core::chemical::ChemicalManager
• orbital_types_ : core::chemical::ResidueType , core::chemical::ResidueTypeSet
• orbitals_ : core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueType , core::conformation::Residue
• orbitals_index_ : core::chemical::ResidueType
• orbitals_lookup_table_ : core::scoring::ScoringManager
• Orbtype_ : core::chemical::orbitals::AssignOrbitals
• order_ : core::chemical::Bond , core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , protocols::pose_selectors::TopNByProperty
• order_by_energy_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• order_of_atoms_ : protocols::frag_picker::CSTalosIO
• order_strands_ : protocols::fldsgn::topology::Sheet
• ordered_atoms_ : core::chemical::ResidueType
• 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_functional_group_ : protocols::simple_moves::chiral::ChiralMover
• orient_strands_ : protocols::fldsgn::topology::Sheet
• 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_upstream_pose_ : protocols::match::output::PDBWriter
• origin : core::scoring::electron_density::ElectronDensity
• origin_ : protocols::jd3::PoseInputSource , protocols::pockets::FingerprintBase , protocols::simple_moves::PeriodicBoxMover
• original2modified_ : protocols::forge::build::BuildManager
• original_bb_rep_coords_ : protocols::simple_moves::GreenPacker
• original_constraint_set_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• original_end_ : protocols::grafting::GraftMoverBase
• original_filenames_ : protocols::toolbox::KClusterData
• original_fold_tree_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• original_geometry_weight_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• original_index : protocols::forge::remodel::LineObject
• original_interval_ : protocols::forge::build::BuildInstruction
• original_layer_lines_I : core::scoring::fiber_diffraction::FiberDiffraction
• original_layer_lines_R : core::scoring::fiber_diffraction::FiberDiffraction
• original_pose_ : protocols::loop_modeling::utilities::PrepareForFullatom
• original_rama2b_weight_ : protocols::loop_modeling::LoopProtocol
• original_rama_weight_ : protocols::loop_modeling::LoopProtocol
• original_repulsive_weight_ : protocols::loop_modeling::LoopProtocol
• original_resid_ : protocols::match::upstream::OriginalBackboneBuildPoint
• original_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::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
• originalPose_ : protocols::pose_length_moves::PossibleLoop
• originating_geom_cst_for_dspos : protocols::match::match_dspos1
• originnum : protocols::pockets::triplet_and_originnum
• ostr_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• other_atoms_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• other_distances_ : core::scoring::func::GaussianChainFunc
• other_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_pose_list_ : core::pose::full_model_info::FullModelInfo
• other_struct_list_ : core::io::silent::SilentStruct
• 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_p_ : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• out_path_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• out_scorefilename_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• out_tag_ : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• 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::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_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
• 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::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• output_all_ : protocols::pose_length_moves::NearNativeLoopCloser
• output_cen_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• output_centroid : protocols::seeded_abinitio::GrowPeptides
• output_closed_ : protocols::pose_length_moves::NearNativeLoopCloser
• output_cluster_size_ : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• output_dsgeom_for_geomcst_ : protocols::match::output::PDBWriter
• output_extra_RMSDs_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• output_file_name_ : protocols::jobdist::BasicJob , protocols::match::MatcherTask
• output_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• output_filters_ : protocols::farna::options::RNA_DeNovoProtocolOptions
• output_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• output_frags_pdbs_ : protocols::frag_picker::nonlocal::NonlocalFrags
• output_full_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• output_header_ : protocols::match::output::MatchScoreWriter
• output_id_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter
• output_idealized_ : protocols::frag_picker::nonlocal::NonlocalFrags
• output_level_ : protocols::rotamer_recovery::RRReporterSQLite
• 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_matrix_ : protocols::contact_map::ContactMap
• output_minimized_pose_list_ : protocols::stepwise::options::StepWiseBasicOptions
• output_mutant_structures_ : protocols::pmut_scan::PointMutScanDriver
• 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_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_pdbs_ : protocols::flxbb::InterlockAroma
• output_period_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• output_pose_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• output_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• output_prefix_ : protocols::contact_map::ContactMap
• output_round_silent_files_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• output_sampled_space_ : protocols::ligand_docking::Transform
• output_scores_ : protocols::match::MatcherTask
• output_subunit_ : core::conformation::symmetry::SymmData
• output_torsions_ : core::io::StructFileRepOptions
• output_type_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter
• output_value_ : protocols::fldsgn::filters::HSSTripletFilter
• output_virtual_ : core::io::StructFileRepOptions
• output_virtual_zero_occ_ : core::io::StructFileRepOptions
• output_writer_name_ : protocols::match::MatcherTask
• outputed_ : protocols::pose_length_moves::PossibleLoop
• outputpose_ : protocols::rpc::JSON_RPC
• outputProfile_ : protocols::simple_moves::StructProfileMover
• outputted_ignored_water_warning_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• outtag_ : protocols::sic_dock::LinkerScore
• OUTWARDS : core::scoring::dssp::Pairing
• overall_cstfilter_weight_ : protocols::abinitio::IterativeBase
• overall_energy0_ : protocols::branch_angle::BranchCoef1
• overall_Ktheta_ : protocols::branch_angle::BranchCoef1
• overall_prob_set_ : protocols::toolbox::task_operations::ResidueProbDesignOperation
• overall_theta0_ : protocols::branch_angle::BranchCoef1
• overhang_ : protocols::antibody::design::AntibodyDesignMover
• overhangs_ : protocols::antibody::design::GeneralAntibodyModeler
• overlap1_ : 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_location_pose_ : protocols::simple_moves::MergePDBMover
• overlap_max_length_ : protocols::simple_moves::MergePDBMover
• overlap_range_ : protocols::simple_moves::MergePDBMover
• oversample_ : protocols::analysis::PackStatMover , protocols::toolbox::pose_metric_calculators::PackstatCalculator
• 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::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
• oxygen_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential