- o -

• o2prime_green_packer_ : protocols::stepwise::sampling::rna::o2prime::O2PrimePacker
• o2prime_instantiation_distance_cutoff_ : protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler , protocols::stepwise::screener::SugarInstantiator
• o2prime_pack_pose_ : protocols::stepwise::sampling::rna::o2prime::O2PrimePacker
• o2prime_pack_scorefxn_ : protocols::stepwise::sampling::legacy::RigidBodySampler , protocols::stepwise::sampling::rna::o2prime::O2PrimePacker
• o2prime_pack_task_ : protocols::stepwise::sampling::rna::o2prime::O2PrimePacker
• o2prime_packer_ : protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler , protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler , protocols::stepwise::screener::O2PrimeScreener
• o2prime_trials_ : protocols::stepwise::sampling::legacy::RigidBodySampler
• O3_C5_distance : protocols::stepwise::sampling::rna::output_data_struct
• O_ : protocols::fldsgn::topology::BB_Pos
• O_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• O_index_ : protocols::fldsgn::topology::BB_Pos
• o_opt : protocols::hybridization::TMalign
• O_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• oats_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• objective_function : protocols::loophash::MPI_LoopHashRefine_Master
• objective_function_ : protocols::loophash::MPI_LoopHashRefine
• obligate_pairing_sets_ : protocols::farna::RNA_StructureParameters
• observers_ : protocols::canonical_sampling::MetropolisHastingsMover
• oc_sfxn_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• occ_space_bounding_box_ : protocols::match::Matcher , protocols::match::MatcherTask
• occ_space_hash_ : protocols::match::Matcher
• occspace_rev_id_at_last_update_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• off_rotamer_pack_ : protocols::simple_moves::MinPackMover
• offset : protocols::loophash::LeapIndex
• offset_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::inputter::Inputter , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::simple_filters::Sigmoid
• offset_frags_ : protocols::antibody_legacy::AntibodyModeler
• offset_map_ : protocols::topology_broker::SequenceNumberResolver
• offset_map_reversed_ : protocols::topology_broker::SequenceNumberResolver
• offset_save1_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• offset_save2_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• offset_save_ : protocols::rotamer_sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampling::rna::legacy::RNA_AnalyticLoopCloser
• offsets_ : protocols::rbsegment_relax::SequenceShiftMover
• oframe_in_D3frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ok_for_centroid_calculation_ : protocols::farna::MultipleDomainMover , protocols::rigid::RigidBodyPerturbMover
• ok_to_increment_ : protocols::stepwise::screener::StepWiseScreener
• old_batches_ : protocols::abinitio::HedgeArchive
• old_chi_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• old_force : protocols::cartesian::CartesianAtom
• 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 : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• omega_ : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::MakeRotLib::RotData , protocols::stepwise::sampling::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::sampling::protein::StepWiseProteinLoopBridger
• OMEGA_SCALE_FACTOR_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• omg_ : protocols::motif_hash::Xfres
• one_body_energies_ : protocols::flexpack::interaction_graph::FlexbbNode
• onebody_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• only_dock_preexisting_chunks_ : protocols::stepwise::monte_carlo::SWA_MoveSelector
• only_enumerate_non_match_redundant_ligand_rotamers_ : protocols::match::MatcherTask
• only_remove_missing_density_flag_ : protocols::LoopRebuild
• only_seeds_chain_ : protocols::seeded_abinitio::SeedFoldTree
• only_stage4_ : protocols::abinitio::MembraneAbinitio
• oop_d_minus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_d_plus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_design_first_ : protocols::ncbb::oop::OopDockDesignProtocol
• oop_low_e_puck_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_minus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_plus_positions_ : protocols::ncbb::oop::OopCreatorMover
• oop_post_pos_ : protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher
• oop_pre_pos_ : protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher
• oop_seq_positions_ : protocols::simple_moves::oop::OopRandomPuckMover , protocols::simple_moves::oop::OopRandomSmallMover
• op1_atom_idx_ : protocols::stepwise::sampling::rna::phosphate::PhosphateMover
• op2_atom_idx_ : protocols::stepwise::sampling::rna::phosphate::PhosphateMover
• op_ : protocols::canonical_sampling::PatchOperation
• open_buffers_ : protocols::jd2::MpiFileBuffer
• open_files_ : protocols::jd2::MpiFileBuffer
• openers_ : protocols::loop_modeling::openers::OpenerCollection
• opening_ : protocols::dna::DNABasepair
• operation_ : protocols::simple_filters::Operator
• operatorF_ : protocols::simple_filters::MultipleSigmoids
• opt_to_fsc_ : protocols::electron_density::BfactorFittingMover
• 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
• optimize_foldtree_ : protocols::simple_moves::DesignRepackMover
• optimize_mask_ : protocols::cryst::UpdateSolventMover
• optimize_memory_usage_ : protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer
• 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_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_ : protocols::jd2::archive::Batch , protocols::loophash::LocalInserter_SimpleMin , protocols::normalmode::NormalModeMinimizer , protocols::stepwise::monte_carlo::rna::AddOrDeleteMover , protocols::stepwise::monte_carlo::rna::DeleteMover , protocols::stepwise::monte_carlo::rna::ResampleMover , protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo , protocols::stepwise::sampling::protein::StepWiseProteinModeler , protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler , protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler , protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler , protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer , protocols::stepwise::sampling::rna::StepWiseRNA_Modeler , protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler , protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD , protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::screener::SimplePoseSelection , protocols::wum::WorkUnitBase::WU_Header
• options_registered_ : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MpiHamiltonianExchange , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , 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::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::moves::CanonicalSamplingMover , 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
• opts : protocols::simple_moves::AddCavitiesMover
• orbital_score_ : protocols::ligand_docking::rdf::RDFOrbitalFunction
• order_ : protocols::frag_picker::VallResidue , protocols::pose_selectors::TopNByProperty
• order_of_atoms_ : protocols::frag_picker::CSTalosIO
• order_strands_ : protocols::fldsgn::topology::Sheet
• ori : protocols::kinmatch::KRSQuery
• 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::BasePairType , protocols::farna::RNA_Pairing
• orientation_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• orig_bb_tors_ : protocols::simple_moves::GreenPacker
• orig_loop_ : protocols::loops::loop_closure::ccd::ShortLoopClosure
• orig_rot_2_curr_rot_ : protocols::simple_moves::GreenPacker
• orig_upstream_pose_ : protocols::match::output::PDBWriter
• origin_ : protocols::pockets::FingerprintBase
• original2modified_ : protocols::forge::build::BuildManager
• original_bb_rep_coords_ : protocols::simple_moves::GreenPacker
• original_constraint_set_ : protocols::stepwise::sampling::rna::sugar::StepWiseRNA_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::sampling::rna::StepWiseRNA_Minimizer
• original_index : protocols::forge::remodel::LineObject
• original_interval_ : protocols::forge::build::BuildInstruction
• original_resid_ : protocols::match::upstream::OriginalBackboneBuildPoint
• 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_tree_ : protocols::loop_modeling::LoopProtocol
• original_type_ : protocols::rotamer_sampler::copy_dofs::ResidueAlternativeRotamer
• original_weight : protocols::moves::TrialMover
• original_weights_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• originating_geom_cst_for_dspos : protocols::match::match_dspos1
• ostr_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• other_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_residues_base_list_ : protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler
• out_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::WriteFileSFB , protocols::jobdist::AtomTreeDiffJobDistributor
• out_path_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo
• outbound_wu_buffer_size_ : protocols::loophash::MPI_LoopHashRefine_Master
• outbound_wus_ : protocols::wum::WorkUnitManager
• outer_cycles_ : protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• outer_loop_counter_ : protocols::optimize_weights::IterativeOptEDriver
• outer_loop_cycles_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• outer_loop_last_sequence_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• outer_loop_seq_profile_cross_entropy_ : protocols::optimize_weights::IterativeOptEDriver
• outer_mc_ : protocols::antibody::H3PerturbCCD
• outer_radius_ : protocols::qsar::scoring_grid::AtrGrid
• outfile_ : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore
• outfile_name_ : protocols::jd2::AtomTreeDiffJobOutputter
• outmap_name_ : protocols::electron_density::ScaleMapIntensities
• output_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• output_cen_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• output_centroid : protocols::seeded_abinitio::GrowPeptides
• output_dsgeom_for_geomcst_ : protocols::match::output::PDBWriter
• output_extra_RMSDs_ : protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
• output_file_name_ : protocols::jobdist::BasicJob , protocols::match::MatcherTask
• output_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer
• output_filters_ : protocols::farna::RNA_DeNovoProtocol
• 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::RNA_DeNovoProtocol
• output_match_dspos1_for_geomcst_ : protocols::match::Matcher
• output_matches_as_singular_downstream_positioning_ : protocols::match::Matcher
• output_matchres_only_ : protocols::match::MatcherTask
• output_matrix_ : protocols::contact_map::ContactMap
• output_minimized_pose_list_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions , protocols::stepwise::sampling::protein::StepWiseProteinModelerOptions , protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
• 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::JobOutputter
• output_only_cluster_transition_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• output_pdb_ : protocols::stepwise::sampling::rna::checker::AtrRepChecker , protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup , protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer , protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
• output_pdbs_ : protocols::flxbb::InterlockAroma
• output_period_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• output_pose_count : protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct
• output_pose_list_ : protocols::stepwise::sampling::general::StepWiseClusterer
• output_prefix_ : protocols::contact_map::ContactMap
• output_sampled_space_ : protocols::ligand_docking::Transform
• output_scores_ : protocols::match::MatcherTask
• output_to_silent_file_ : protocols::stepwise::screener::PoseSelectionScreener
• output_type_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter
• output_value_ : protocols::fldsgn::filters::HSSTripletFilter
• output_writer_name_ : protocols::match::MatcherTask
• outputpose_ : protocols::rpc::JSON_RPC
• outq_ : protocols::wum2::EndPoint
• outq_current_mem : protocols::wum2::StatusResponse
• outtag_ : protocols::sic_dock::LinkerScore
• overall_cstfilter_weight_ : protocols::abinitio::IterativeBase
• overall_energy0_ : protocols::branch_angle::BranchCoef1
• overall_Ktheta_ : protocols::branch_angle::BranchCoef1
• overall_prob_set_ : protocols::antibody::design::ResidueProbDesignOperation
• overall_theta0_ : protocols::branch_angle::BranchCoef1
• overhang_ : protocols::antibody::design::AntibodyGraftDesigner
• overlap_ : protocols::hybridization::CartesianSampler
• overlap_chainbreaks_ : protocols::hybridization::FoldTreeHybridize
• oversample_ : protocols::analysis::PackStatMover , protocols::toolbox::pose_metric_calculators::PackstatCalculator
• overwrite_ : protocols::jobdist::BaseJobDistributor , protocols::simple_filters::SavePoseConstraintToFileFilter
• owner : protocols::environment::claims::RTElement , protocols::environment::claims::TorsionElement
• owner_ : protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::VectorExpressionCreator
• owner_nodes_and_locations_ : protocols::toolbox::match_enzdes_util::InvrotCollector