- r -

• r : core::optimization::EItem , core::scoring::packstat::Circle
• r0 : core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_struct , core::scoring::data_structDaR
• r0_ : core::scoring::ResidualDipolarCoupling
• r1 : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_structDaR , protocols::hybridization::TMalign , protocols::sparta::PDB , protocols::sparta::Sparta::SpartaLib
• r1_ : core::scoring::ResidualDipolarCoupling
• r2 : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_structDaR , protocols::hybridization::TMalign
• r2_ : core::scoring::ResidualDipolarCoupling
• R_ : core::scoring::ResidualDipolarCoupling
• r_ : core::scoring::packing::Ball
• r_cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_cell_dimensions : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_cell_volume : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_chi2 : core::scoring::saxs::FastSAXSEnergy
• r_ids_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• r_ik : protocols::cluster::Exemplar
• r_kk : protocols::cluster::DataPoint
• r_param : core::scoring::APBSConfig
• rad : protocols::sparta::RingData
• radii_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::InvRotamerDots , core::scoring::sc::MolecularSurfaceCalculator
• radii_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• radius : core::scoring::PQR , core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere , core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::Atom
• radius_ : core::chemical::SetNbrRadius , core::scoring::packstat::CavityBall , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::qsar::scoring_grid::RepGrid , protocols::toolbox::GreedyKCenter
• radmax : core::scoring::sc::MolecularSurfaceCalculator
• ram_counts_ : core::scoring::Ramachandran
• ram_energ_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• ram_energ_left_ : core::scoring::Ramachandran2B
• ram_energ_right_ : core::scoring::Ramachandran2B
• ram_entropy_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• ram_entropy_left_ : core::scoring::Ramachandran2B
• ram_entropy_right_ : core::scoring::Ramachandran2B
• ram_probabil_ : core::scoring::Ramachandran
• rama2b_ : core::scoring::ScoringManager
• rama_ : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , core::scoring::ScoringManager
• rama_delta_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• rama_energy_splines_ : core::scoring::Ramachandran
• rama_initialized_ : core::scoring::Ramachandran
• rama_params : protocols::relax::CentroidRelax::parameters
• rama_sampling_factor_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• rama_sampling_table_ : core::scoring::Ramachandran
• rama_sampling_table_by_torsion_bin_ : core::scoring::Ramachandran
• rama_sampling_thold_ : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• rama_score_limit_ : core::scoring::Ramachandran2B
• rama_type_ : protocols::relax::CentroidRelax
• ramachandran_ : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• ramady_ : protocols::relax::FastRelax
• ramady_cutoff_ : protocols::relax::FastRelax
• ramady_force_ : protocols::relax::FastRelax
• ramady_num_rebuild_ : protocols::relax::FastRelax
• ramady_rms_limit_ : protocols::relax::FastRelax
• ramp_ : protocols::abinitio::CoordinateConstraintKC
• ramp_cst_cycles_ : protocols::abinitio::FoldConstraints
• ramp_down_constraints_ : protocols::relax::RelaxProtocolBase
• ramp_fa_rep : protocols::flexpep_docking::FlexPepDockingFlags , protocols::simple_moves::ShakeStructureMover
• ramp_iterations_ : protocols::abinitio::FoldConstraints
• ramp_one_weight_ : protocols::moves::RampingMover
• ramp_rama : protocols::flexpep_docking::FlexPepDockingFlags
• ramp_rama_ : protocols::relax::CentroidRelax
• ramp_temperature_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• ramp_vdw_ : protocols::relax::CentroidRelax
• ramp_weight : protocols::moves::TrialMover
• ramp_width_A2_ : core::scoring::methods::LK_BallEnergy
• ramping_funcs_for_weights_ : protocols::moves::RampingMover
• ramping_scorefxn_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• ran_annealing_since_pair_energy_table_cleared_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• rand_ : protocols::rbsegment_relax::RBSegmentRelax
• randmove_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• random_conformer_ : protocols::docking::ConformerSwitchMover
• random_counter_ : protocols::jobdist::BaseJobDistributor
• random_flush_frequency_ : protocols::jd2::SilentFileJobOutputter
• random_grow_loops_by_ : protocols::topology_broker::RigidChunkClaimer
• random_loop_flag_ : protocols::LoopRebuild
• random_order_ : protocols::loops::loop_mover::IndependentLoopMover
• random_perturbation_ : protocols::rna::RNA_HelixAssembler
• random_phi_psi_pert : protocols::flexpep_docking::FlexPepDockingFlags
• random_phi_psi_pert_size : protocols::flexpep_docking::FlexPepDockingFlags
• random_sheets_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• random_step_ : protocols::rigid::UniformSphereTransMover
• random_store_ : protocols::jobdist::BaseJobDistributor
• random_template_ : protocols::hybridization::ChunkTrialMover
• random_torsion_strings_ : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• randomize1_ : protocols::docking::DockingInitialPerturbation
• randomize2_ : protocols::docking::DockingInitialPerturbation
• randomize_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval
• randomize_cut_ : protocols::protein_interface_design::movers::Splice
• randomize_equiv_frag_ : protocols::forge::remodel::RemodelMover::instruction_flags
• randomize_input_sequence_ : protocols::anchored_design::AnchoredDesignMover
• randomize_loop_ : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• randomize_loop_coords_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• randomize_loops_ : protocols::forge::remodel::RemodelLoopMover
• randomize_missing_coords_ : core::io::pdb::FileDataOptions
• randomize_order_ : protocols::ligand_docking::CompoundTranslate
• randomness_ : protocols::rbsegment_relax::RBSegmentRelax
• randomRBstart : protocols::flexpep_docking::FlexPepDockingFlags
• range1_ : protocols::simple_filters::AtomicContactFilter
• range_ : protocols::simple_filters::DeltaFilter
• range_pair_ : core::scoring::Hairpin
• rank : core::graph::DS_Node , protocols::wum2::StatusResponse , protocols::wum2::StatusRequest
• rank2tlevel_ : protocols::canonical_sampling::ParallelTempering
• rank_ : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::ParallelTempering , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::moves::ReplicaExchangeMC
• rank_by_bsasa_ : protocols::forge::remodel::RemodelMover::instruction_flags
• rank_by_filter_ : protocols::simple_moves::GenericMonteCarloMover
• ranking_cenfilter_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ranking_fafilter_ : protocols::loophash::LoopHashMoverWrapper
• rate_threshold_ : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• ratio_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• ratio_cutoff_goodfrag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• ratios_ : protocols::frag_picker::scores::ABEGO_SS_Score
• raw_probs_ : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• rawfile_name_ : protocols::jobdist::PlainRawJobDistributor
• rb_center : core::kinematics::Jump
• rb_chunks_ : protocols::rbsegment_relax::AutoRBMover
• rb_delta : core::kinematics::Jump
• rb_delta_ : protocols::rigid::RigidBodyPerturbMover
• rb_jump_ : core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface , protocols::docking::DockingSlideIntoContact , protocols::docking::FaDockingSlideIntoContact , protocols::enzdes::LigInterfaceEnergyFilter , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::rigid::RigidBodyMover , protocols::scoring::InterfaceInfo , protocols::simple_filters::DdgFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ddG , protocols::simple_moves::MutateResidue , protocols::surface_docking::SlideIntoSurface , protocols::surface_docking::FaSlideIntoSurface , protocols::surface_docking::FaSlideAwayFromSurface , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2
• rb_jump_num_ : protocols::rigid::RotateJumpAxisMover
• rb_jumps_ : protocols::docking::FaDockingSlideIntoContact , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover
• rb_min_ : protocols::enzdes::EnzdesBaseProtocol
• rb_minimizable_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• rb_mover_ : protocols::docking::DockingLowRes , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockingLowRes
• rb_movers_ : protocols::rna::MultipleDomainMover
• rb_rot_size : protocols::flexpep_docking::FlexPepDockingFlags
• rb_trans_size : protocols::flexpep_docking::FlexPepDockingFlags
• rbMCM : protocols::flexpep_docking::FlexPepDockingFlags
• rbs_new_pair_ : protocols::swa::rna::RNA_LoopCloseSampler
• rbsegs_input_ : protocols::rbsegment_relax::RBSegmentRelax
• rbsegs_remap_ : protocols::rbsegment_relax::RBSegmentRelax
• rbstub_minimization_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• RC_Tab : protocols::sparta::Sparta::SpartaLib
• RCCO_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• RcellDimensions : core::scoring::electron_density::ElectronDensity
• rcFileName : protocols::sparta::Sparta::SpartaLib
• rcgs_ : protocols::forge::components::VarLengthBuild
• rdc : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_structDaR
• rdc_atom_names_ : protocols::frag_picker::scores::RDCScore
• rdc_atoms_ : protocols::frag_picker::scores::RDCScore
• rdc_data_ : protocols::abinitio::IterativeBase , protocols::frag_picker::scores::RDCScore , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::SelectRDC_Evaluator
• rdc_file_ : protocols::frag_picker::scores::RDCScore , protocols::simple_filters::SelectRDC_Evaluator
• rdc_raw_data_ : protocols::frag_picker::scores::RDCScore
• rdc_segments_ : protocols::scoring::ResidualDipolarCouplingRigidSegments
• rdcconst : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_structDaR
• rdcconst_ : core::scoring::ResidualDipolarCoupling
• rdcs_ : protocols::simple_filters::TruncatedScoreEvaluator
• rdcweight : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structR , core::scoring::data_structDaR
• rdcweight_ : core::scoring::ResidualDipolarCoupling
• Rdimers : protocols::simple_filters::SymmetricMotifFilter
• reached_ : core::kinematics::AtomWithDOFChange
• read_fold_tree_ : core::import_pose::ImportPoseOptions
• read_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• read_gridlig_file_ : protocols::match::Matcher
• read_swap_limit_ : protocols::wum::WorkUnitQueue_Swapped
• read_type_ : protocols::jd2::parser::FragmentReader
• ready_to_align_ : protocols::swa::StepWisePoseSetup
• ready_to_go_ : protocols::swa::StepWiseDoNothingSampleGenerator
• real_dof_deriviative_expressions_ : protocols::optimize_weights::WrapperOptEMultifunc
• realatomdata_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• realatomdata_index : core::scoring::rna::chemical_shift::ChemicalShiftData
• realign_domains_ : protocols::hybridization::HybridizeProtocol
• realign_domains_stage2_ : protocols::hybridization::HybridizeProtocol
• rebuild_bulge_mode_ : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler
• rebuild_filter_ : protocols::comparative_modeling::LoopRelaxMover
• received_by_ : protocols::topology_broker::ClaimerMessage
• recent_history_hash_count_ : core::pack::annealer::FASTERAnnealer
• recent_history_hash_values_ : core::pack::annealer::FASTERAnnealer
• recent_history_head_ : core::pack::annealer::FASTERAnnealer
• recent_history_size_ : core::pack::annealer::FASTERAnnealer
• recent_network_state_history_ : core::pack::annealer::FASTERAnnealer
• recent_quota_score_ : protocols::frag_picker::scores::FragmentScoreMap
• recent_total_ : protocols::frag_picker::scores::FragmentScoreMap
• recenter_ : core::conformation::symmetry::SymmData
• receptor_anchor_pos : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_protector_oper_ : protocols::flexpep_docking::FlexPepDockingProtocol
• record_source_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• record_statistics_ : protocols::backrub::BackrubSidechainMover
• recorder_stream_ : protocols::canonical_sampling::MetricRecorder
• recover_centroid_structure_for_pool_ : protocols::abinitio::IterativeBase
• recover_low_ : protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• recover_low_stages_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler
• recover_original_on_failure_ : protocols::forge::components::VarLengthBuild
• recover_sidechains_ : protocols::docking::DockingProtocol
• recover_sidechains_filename_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• recovery_score_m2_ : protocols::rotamer_recovery::RRReporterHuman
• recovery_score_mean_ : protocols::rotamer_recovery::RRReporterHuman
• recovery_threshold_ : protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• recv_wu_time_ : protocols::wum::MPI_WorkUnitManager
• recv_wu_time_n_ : protocols::wum::MPI_WorkUnitManager
• redesign_loop : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub
• redesign_loop_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• redesign_loop_neighborhood_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• Reduced_Jdipolar_ : core::scoring::RDC , core::scoring::RDC_Rohl
• reduced_scofx_ : protocols::enzdes::SecondaryMatchProtocol
• reduced_sfxn_ : protocols::enzdes::EnzdesBaseProtocol
• ref_baseline_ : protocols::simple_filters::DeltaFilter
• REF_CS_Tab : protocols::sparta::Sparta
• ref_end_ : protocols::simple_moves::SuperimposeMover
• ref_energy_ : core::pack::dunbrack::SingleLigandRotamerLibrary
• ref_gunn_data_ : protocols::frag_picker::scores::GunnCostScore
• ref_motifs_ : protocols::simple_filters::SymmetricMotifFilter
• ref_pose_ : protocols::design_opt::GreedyOptMutationMover , protocols::enzdes::PoseFoundResiduesCombination , protocols::match::downstream::ScoringSecMatchRPE , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::simple_moves::SuperimposeMover , protocols::toolbox::DecoySetEvaluation
• ref_pose_list_ : protocols::rna::RNA_IdealCoord
• ref_poses_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• ref_profile_ : protocols::simple_moves::FavorSequenceProfile
• ref_residue_total_energies_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• ref_start_ : protocols::simple_moves::SuperimposeMover
• ref_start_struct_ : protocols::flexpep_docking::FlexPepDockingFlags
• ref_structure_ : protocols::toolbox::DecoySetEvaluation
• ref_tags_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• refCSFileName : protocols::sparta::Sparta
• reference_axes_ : protocols::swa::RigidBodySampler
• reference_centroid_ : protocols::swa::RigidBodySampler
• reference_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• reference_coords_ : core::scoring::NeighborList
• reference_energies_inner_loop_ : protocols::optimize_weights::IterativeOptEDriver
• reference_energy_ : protocols::swa::RigidBodySampler
• reference_intensities_ : core::scoring::saxs::SAXSEnergy
• reference_moltenres_2_resid_ : protocols::simple_moves::GreenPacker
• reference_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• reference_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• reference_pose_ : protocols::abinitio::IterativeBase , protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::features::ProteinRMSDFeatures , protocols::fldsgn::MatchResidues , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::GunnCostScore , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::simple_filters::DeltaFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• reference_res : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• reference_resid_2_moltenres_ : protocols::simple_moves::GreenPacker
• reference_residue_types_ : protocols::dna::DnaInterfacePacker
• reference_residues_indexes_ : protocols::fldsgn::MatchResidues
• reference_rotamer_sets_ : protocols::simple_moves::GreenPacker
• reference_task_ : protocols::simple_moves::GreenPacker
• reference_task_factory_ : protocols::simple_moves::GreenPacker
• reference_xyz_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• refine_ : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• refine_CCD_off_ : protocols::anchored_design::AnchoredRefineMover
• refine_cycles_ : protocols::anchored_design::AnchoredRefineMover
• refine_h3_ : protocols::antibody2::AntibodyModelerProtocol
• refine_input_loop_ : protocols::antibody::CDRH3Modeler , protocols::antibody2::H3RefineCCD , protocols::antibody2::RefineOneCDRLoopCentroid
• refine_KIC_off_ : protocols::anchored_design::AnchoredRefineMover
• refine_mode_ : protocols::antibody2::RefineOneCDRLoop
• refine_only_ : protocols::anchored_design::AnchoredDesignMover
• refine_repack_cycles_ : protocols::anchored_design::AnchoredRefineMover
• refine_temp_ : protocols::anchored_design::AnchoredRefineMover
• refinement_angle_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• refinement_distance_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• refinement_mode_ : protocols::ub_e2c::ubi_e2c_modeler
• refinement_pattern_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• refinement_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• refinement_scorefxn_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• region : core::util::Line
• region1_ : protocols::simple_filters::RegionalConnections
• region1_region2_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• region2_ : protocols::simple_filters::RegionalConnections
• region_ : protocols::nonlocal::Chunk , protocols::topology_broker::FragmentClaimer
• registered_makers_ : protocols::frag_picker::scores::FragmentScoreManager
• registry_shift_ : protocols::hybridization::InsertChunkMover
• reinitialize_CCD_torsions_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• REJECTED : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• rejected_ : protocols::moves::MoverStatistics
• rel_deriv_dev : core::optimization::symmetry::MinDebug
• rel_deriv_dev_ : core::optimization::SimpleDerivCheckResult
• relative_pose_names_ : protocols::simple_filters::Operator
• relative_tmh_ori_ : core::scoring::MembraneTopology
• relax : protocols::comparative_modeling::LoopRelaxThreadingMover
• relax_ : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• relax_bound_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• relax_constraint_to_design_ : protocols::flxbb::FlxbbDesign
• relax_cycles_ : protocols::rna::RNA_Relaxer
• relax_frags_repeats_ : protocols::frag_picker::nonlocal::NonlocalFrags
• relax_input_ : protocols::frag_picker::nonlocal::NonlocalFrags
• relax_input_with_coordinate_constraints_ : protocols::frag_picker::nonlocal::NonlocalFrags
• relax_mover_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_moves::ddG
• relax_protocol_ : protocols::abinitio::AbrelaxMover
• relax_repeats_ : protocols::hybridization::HybridizeProtocol
• relax_structure_ : protocols::rna::RNA_DeNovoProtocol
• relax_unbound_ : protocols::simple_filters::DeltaFilter
• relaxed1_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed2_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed_state_ : core::pack::interaction_graph::FASTERNode
• relevant_atom_ids_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• relevant_atom_names_ : protocols::features::AtomAtomPairFeatures
• relevant_chains_fname : protocols::moves::StructureRestrictor
• relevant_downstream_atoms_ : protocols::match::Matcher , protocols::match::MatcherTask
• relevant_elements_ : protocols::features::AtomAtomPairFeatures
• relevant_scoreterms_ : protocols::enzdes::EnzdesScorefileFilter
• rely_on_loopfile_indices_ : protocols::loops::GuardedLoopsFromFile
• remap_symm_ : core::scoring::electron_density::ElectronDensity
• remark_ : protocols::motifs::Motif
• REMARKS : protocols::sparta::GDB
• remarks : core::io::pdb::FileData
• remarks_ : core::pose::PDBInfo
• remember_unrecognized_res_ : core::io::pdb::FileDataOptions
• remember_unrecognized_water_ : core::io::pdb::FileDataOptions
• remembered_pose_ : protocols::simple_moves::ReturnSidechainMover
• remodel : protocols::comparative_modeling::LoopRelaxThreadingMover
• remodel_ : protocols::antibody2::ModelCDRH3 , protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• remodel_data_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::forge::remodel::RemodelMover
• remodel_kic_attempts_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• remodel_max_length_ : protocols::enzdes::EnzdesFlexibleRegion
• remodel_min_length_ : protocols::enzdes::EnzdesFlexibleRegion
• remodel_mover_ : protocols::antibody2::ModelCDRH3
• remodelable_ : protocols::enzdes::EnzdesFlexibleRegion
• remove_cterminus_variant_ : protocols::swa::StepWisePoseSetup
• remove_nonprotein_res_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• remove_nterminus_variant_ : protocols::swa::StepWisePoseSetup
• remove_shove_variant_ : protocols::protein_interface_design::movers::ShoveResidueMover
• remove_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• remove_xray_virt_ : protocols::features::ReportToDB
• rename_tag_ : protocols::swa::rna::StepWiseRNA_Minimizer
• rename_tags_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• renumber_decoys_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• rep : protocols::ligand_docking::Ligand_info
• rep_cutoff_ : protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• rep_radius_ : protocols::qsar::scoring_grid::ClassicGrid
• rep_ramp_cycles : protocols::flexpep_docking::FlexPepDockingFlags
• rep_ramp_cycles_ : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy
• rep_scorefxn_ : protocols::swa::rna::RNA_LoopCloseSampler
• rep_weight_ : core::scoring::etable::EtableEvaluator
• repack_ : protocols::enzdes::EnzRepackMinimize , protocols::relax::FastRelax , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ddG
• repack_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• repack_bound_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• repack_buffer_ : protocols::abinitio::ResolutionSwitcher
• repack_c_terminus_ : protocols::toolbox::task_operations::RestrictToTerminiOperation
• repack_chain1_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain2_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_cst_set_mut_ : protocols::ddg::ddGMover
• repack_cst_set_wt_ : protocols::ddg::ddGMover
• repack_every_Nth_ : protocols::ligand_docking::HighResDocker
• repack_foldpose_ : protocols::seeded_abinitio::SeedSetupMover
• repack_fragments_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• repack_mut_types_ : protocols::ddg::ddGMover
• repack_n_terminus_ : protocols::toolbox::task_operations::RestrictToTerminiOperation
• repack_neighbors_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• repack_no_lig_ : protocols::enzdes::EnzdesScorefileFilter
• repack_non_ala_ : protocols::simple_moves::DesignRepackMover
• repack_non_designed_residues_ : protocols::flxbb::LayerDesignOperation
• repack_only_ : protocols::enzdes::DetectProteinLigandInterface
• repack_partner1_ : protocols::simple_moves::DesignRepackMover
• repack_partner2_ : protocols::simple_moves::DesignRepackMover
• repack_period_ : protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::symmetric_docking::SymDockingHiRes
• repack_query_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• repack_rate_ : protocols::dna::DesignProteinBackboneAroundDNA
• repack_rest_ : protocols::toolbox::task_operations::LayerOperations
• repack_sc_ : protocols::relax::CentroidRelax
• repack_scorefxn_ : protocols::topology_broker::TopologyBroker
• repack_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• repack_switch_ : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• repack_target_ : protocols::seeded_abinitio::SeedSetupMover
• repack_wt_types_ : protocols::ddg::ddGMover
• repacked_poses_ : protocols::simple_moves::SetReturningPackRotamersMover
• repacker_ : protocols::pack_daemon::PackDaemon
• repacking_ : core::pack::task::ResidueLevelTask_
• repacking_radius_ : protocols::simple_filters::RotamerBoltzmannWeight , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• repeat_job_ : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• repeat_pose_ : protocols::forge::remodel::RemodelLoopMover
• repeat_tail_length_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• repeats : protocols::ligand_docking::Transform_info
• repeats_ : protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::PackStatFilter , protocols::simple_moves::ddG
• replace_ : protocols::seeded_abinitio::CAcstGenerator
• replaces_residue_type_ : core::chemical::Patch
• replicates_ : protocols::filters::ReplicateFilter
• report_all_ : protocols::protein_interface_design::filters::FilterScanFilter
• report_aln_components_ : protocols::evaluation::AlignEvaluator
• report_CA_rmsd_ : protocols::idealize::IdealizeMover
• report_call_order_ : protocols::rosetta_scripts::ParsedProtocol
• report_filter_name_ : protocols::simple_filters::ReportFilter
• report_gdt_components_ : protocols::comparative_modeling::Align_RmsdEvaluator , protocols::simple_filters::RmsdEvaluator
• report_residue_pair_energies_ : protocols::simple_filters::ScoreCutoffFilter
• report_string_ : protocols::simple_filters::ReportFilter
• report_this_as_effective_sequence_separation_ : core::scoring::constraints::MultiConstraint
• report_type_ : protocols::fldsgn::filters::NcontactsFilter
• reporter_ : protocols::rotamer_recovery::RotamerRecovery
• reporter_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• reporters_ : protocols::features::Report
• reporting_ : protocols::docking::DockingProtocol
• representative_downstream_algorithm_ : protocols::match::Matcher
• representative_dspos_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• representative_group_matches_ : protocols::match::output::CloudPDBWriter
• representative_target_res_for_geom_cst_ : protocols::toolbox::match_enzdes_util::InvrotTarget
• reps_for_nonzero_rank_ccs_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• repulsive : core::scoring::etable::AtomPairEnergy
• repulsive_ramp_ : protocols::antibody2::RefineBetaBarrel
• reqfile_name_ : protocols::enzdes::EnzdesScorefileFilter
• require_mm_bend_ : protocols::backrub::BackrubMover
• required_connections_ : protocols::simple_filters::RegionalConnections
• required_connections_between_regions_ : protocols::simple_filters::PackerNeighborGraphFilter
• required_connections_per_res_ : protocols::simple_filters::PackerNeighborGraphFilter
• required_context_graphs_ : core::scoring::Energies
• rerun_motifsearch_ : protocols::motifs::MotifSearch
• res : core::scoring::packstat::SimplePDB_Atom , protocols::cartesian::CartesianAtom
• res1 : core::scoring::rna::Base_pair , core::scoring::rna::Base_stack
• res1_ : core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC , protocols::fldsgn::topology::DimerPairing , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::SidechainRmsdFilter
• res1_atom1_index_ : protocols::motifs::Motif
• res1_atom1_int_ : protocols::motifs::Motif
• res1_atom1_name_ : protocols::motifs::Motif
• res1_atom2_index_ : protocols::motifs::Motif
• res1_atom2_int_ : protocols::motifs::Motif
• res1_atom2_name_ : protocols::motifs::Motif
• res1_atom3_index_ : protocols::motifs::Motif
• res1_atom3_int_ : protocols::motifs::Motif
• res1_atom3_name_ : protocols::motifs::Motif
• res1_conn_dist_ : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• res1_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res1_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res1_dat_ : core::scoring::hbonds::HBondResPairMinData
• res1_inds_ : core::scoring::disulfides::DisulfMinData
• res1_nb_ : core::scoring::hbonds::HBondEnergy
• res1_pbconn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2 : core::scoring::rna::Base_pair , core::scoring::rna::Base_stack
• res2_ : core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC , protocols::fldsgn::topology::DimerPairing , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::SidechainRmsdFilter
• res2_atom1_index_ : protocols::motifs::Motif
• res2_atom1_int_ : protocols::motifs::Motif
• res2_atom1_name_ : protocols::motifs::Motif
• res2_atom2_index_ : protocols::motifs::Motif
• res2_atom2_int_ : protocols::motifs::Motif
• res2_atom2_name_ : protocols::motifs::Motif
• res2_atom3_index_ : protocols::motifs::Motif
• res2_atom3_int_ : protocols::motifs::Motif
• res2_atom3_name_ : protocols::motifs::Motif
• res2_conn_dist_ : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• res2_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res2_dat_ : core::scoring::hbonds::HBondResPairMinData
• res2_inds_ : core::scoring::disulfides::DisulfMinData
• res2_nb_ : core::scoring::hbonds::HBondEnergy
• res2_pbconn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2jumps_ : core::kinematics::ShortestPathInFoldTree
• res3_ : core::scoring::CSA
• res_ : core::scoring::constraints::BigBinConstraint , core::scoring::RDC_Rohl
• res_aa : core::scoring::rna::chemical_shift::ChemicalShiftData
• res_aa_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• res_collections_ : core::pack::scmin::AtomTreeCollection
• res_energy1_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_energy2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_first : protocols::rbsegment_relax::RBResidueRange
• res_id_ : core::chemical::ResConnID
• res_ids_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• res_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• res_indices_to_output_ : protocols::dna::PDBOutput
• res_interactions_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• res_interacts_with_asymmetric_unit_ : core::optimization::symmetry::SymMinimizerMap
• res_labels_ : core::scoring::packstat::SimplePDB
• res_last : protocols::rbsegment_relax::RBResidueRange
• res_list_ : core::scoring::methods::ReferenceEnergyNoncanonical , protocols::noesy_assign::FloatingResonance
• res_map_ : core::id::AtomID_Map< T > , protocols::rna::ChunkSet
• res_min_data_ : core::scoring::MinimizationNode
• res_move_ : protocols::protein_interface_design::movers::Splice
• res_name1_ : protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::ReportPSSMDifferences
• res_name2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_name_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , protocols::simple_moves::MutateResidue
• res_num_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_num_cur_ : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• res_num_total_ : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• res_pair_min_data_ : core::scoring::MinimizationEdge
• res_recovered_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• res_scores_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• res_size_ : core::scoring::packing::HolesParamsRes
• res_switch_ : protocols::abinitio::KinematicTaskControl
• res_to_average_hASA_ : core::pack::interaction_graph::SurfacePotential
• res_to_superimpose_ : protocols::enzdes::EnzdesBaseProtocol
• res_type_linking_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• res_types_ : protocols::simple_filters::ResidueCountFilter
• resA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::CstResInteractions
• resA_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• resA_basename_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_modname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resB_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• resB_basename_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_modname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• rescore_only_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer
• reserve_size_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• reset_baselines_ : protocols::simple_moves::GenericMonteCarloMover
• reset_count_ : protocols::contact_map::ContactMap
• reset_delta_filters_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• reset_grid_bb_ : protocols::match::downstream::ActiveSiteGrid
• reset_slide_ : protocols::simple_moves::symmetry::SymmetrySlider
• resfile_ : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::docking::DockTaskFactory , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::forge::components::BDR , protocols::ligand_docking::HighResDocker , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• resfile_1_ : protocols::anchored_design::AnchorMoversData
• resfile_2_ : protocols::anchored_design::AnchorMoversData
• resfile_filename_ : core::pack::task::operation::ReadResfile
• resfile_general_property_ : protocols::outputter::ResFileOutputter , protocols::protein_interface_design::filters::FilterScanFilter
• resfile_name_ : protocols::protein_interface_design::filters::FilterScanFilter , protocols::pack_daemon::StructureFileNames
• resfilename_ : protocols::enzdes::DetectProteinLigandInterface
• resi_ : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• resID : core::scoring::SelfNeighInfo , protocols::sparta::RingData
• resid : core::io::pdb::ResidueInformation
• resid1_ : protocols::enzdes::DiffAtomSasaFilter
• resID1_ : core::io::pdb::LinkInformation
• resid2_ : protocols::enzdes::DiffAtomSasaFilter
• resID2_ : core::io::pdb::LinkInformation
• resid_ : core::pack::rotamer_set::RotamerSet , core::pack::task::operation::ExtraChiCutoff , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::ExtraRotamers , protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::ResidueTorsionRestraints , protocols::moves::ResId , protocols::protein_interface_design::movers::BBDofs , protocols::toolbox::task_operations::DesignAroundOperation
• resid_2_bgenumeration_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• resid_2_connid_map_ : core::scoring::trie::RotamerTrieBase
• resid_2_disulfide_index_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• resid_2_entity_id_ : protocols::pack_daemon::EntityCorrespondence
• resid_2_moltenres_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• resid_2_moltenresid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• resid_to_replace_ : protocols::match::output::PoseInserter
• reside_type_param_map_ : core::scoring::mm::MMBondAngleResidueTypeParamSet
• residList : protocols::sparta::GDB , protocols::sparta::PDB , protocols::sparta::Sparta::SpartaLib
• residListOne : protocols::sparta::PDB
• resids_to_entries_map_ : protocols::frag_picker::CSTalosIO
• residue : core::scoring::sc::_ATOM_RADIUS , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::scoring::sc::Atom
• residue1_ : protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter
• residue2_ : protocols::simple_filters::AtomicDistanceFilter
• residue_ : protocols::hotspot_hashing::HotspotStub , protocols::qsar::qsarPoint , protocols::qsar::qsarMap
• residue_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• residue_base2_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• residue_base_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• residue_begin : protocols::features::SecondaryStructureSegment
• residue_bur_unsat_polars_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• residue_calculators_ : protocols::enzdes::EnzdesScorefileFilter
• residue_change_id_ : core::kinematics::ResidueCoordinateChangeList
• residue_conformation_features_ : protocols::features::ProteinSilentReport
• residue_connection_data_ : core::scoring::etable::etrie::CountPairDataGeneric
• residue_connections_ : core::chemical::ResidueType
• residue_connid_for_entry_connid_ : core::scoring::trie::CPDataCorrespondence
• residue_coord_workspace_ : core::pack::scmin::CartSCMinMinimizerMap
• residue_coordinates_need_updating_ : core::conformation::Conformation
• residue_dbio_ : protocols::features::ResidueTypesFeatures
• residue_decomposition_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_dEdN_ : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• residue_E_ : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_end : protocols::features::SecondaryStructureSegment
• residue_features_ : protocols::features::ProteinSilentReport
• residue_fraction_buried_ : protocols::simple_filters::ResidueBurialFilter
• residue_group_for_rotamers_ : core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• residue_group_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• residue_id_ : core::conformation::AtomGraphVertexData
• residue_index_ : protocols::ligand_docking::AddHydrogen
• residue_indices_ : core::pack::task::operation::OperateOnCertainResidues
• residue_info_ : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• residue_level_tasks_for_placed_hotspots_ : protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• residue_list_ : protocols::simple_moves::carbohydrates::RingConformationMover
• residue_N_ : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_name_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• residue_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• residue_nlscore_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• residue_num_ : protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data
• residue_numbers_ : protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_moves::SwitchChainOrderMover
• residue_packed_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• residue_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• residue_pair_ : protocols::fldsgn::topology::StrandPairing
• residue_pair_constraints_ : core::scoring::constraints::ConstraintSet
• residue_pair_jump_ : protocols::topology_broker::MetalloClaimer
• residue_rec_ : core::pose::PDBInfo
• residue_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator
• residue_scores_ : protocols::analysis::PackStatMover
• residue_selection_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::PreventRepacking , protocols::comparative_modeling::ExtraThreadingMover
• residue_selection_big_frags_ : protocols::hybridization::hConvergenceCheck
• residue_selection_small_frags_ : protocols::hybridization::hConvergenceCheck
• residue_semiexpl_score_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• residue_set_ : core::coarse::TranslatorSet , protocols::inputter::FastaInputter
• residue_set_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_surface_energy_ : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• residue_tasks_ : core::pack::task::PackerTask_
• residue_torsions_need_updating_ : core::conformation::Conformation
• residue_total_energies_ : core::scoring::Energies
• residue_total_energies_uptodate_ : core::scoring::Energies
• residue_total_energy_ : core::scoring::Energies
• residue_total_energy_uptodate_ : core::scoring::Energies
• residue_type_ : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::rna::RNA_ResidueType , protocols::simple_moves::MinimalRotamer
• residue_type_for_rotamers_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_type_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_type_set_ : core::chemical::ResidueType , core::import_pose::ImportPoseOptions , protocols::simple_moves::ExtendedPoseMover
• residue_type_set_tag_ : core::chemical::ResidueLoaderOptions
• residue_type_sets_ : core::chemical::ChemicalManager
• residue_types_ : protocols::simple_filters::NeighborTypeFilter , core::chemical::ResidueTypeSet , core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• residue_types_const_ : core::chemical::ResidueTypeSet
• residue_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• residue_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_variants_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• ResiduePairJumps_ : protocols::jumping::ResiduePairJumpSetup
• residues : protocols::forge::remodel::Segment , protocols::ligand_docking::Ligand_info
• residues1_ : protocols::simple_filters::ShapeComplementarityFilter
• residues2_ : protocols::simple_filters::ShapeComplementarityFilter
• residues_ : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::frag_picker::VallChunk , core::conformation::Conformation , core::scoring::packing::HolesParamsRes , protocols::jumping::ResiduePairJump , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::pockets::PocketConstraint , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::viewer::ConformationViewer
• residues_considered_ : protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• residues_contact_screen : protocols::swa::rna::SillyCountStruct
• residues_in_interface_threshold_ : protocols::simple_filters::ResiduesInInterfaceFilter
• residues_info_ : core::scoring::methods::LKB_ResiduesInfo
• residues_to_mutate_ : protocols::ddg::ddGMover
• residues_to_prevent_ : core::pack::task::operation::PreventRepacking
• residues_to_restrict_to_repacking_ : core::pack::task::operation::RestrictResidueToRepacking
• residueType_ : protocols::jumping::ResiduePairJumpSingle
• resindex_ : protocols::loops::ResidueIndexDescription
• resl_params_ : core::scoring::packing::HolesEnergy
• resl_score : core::scoring::packing::HolesResult
• reslibraries_ : core::pack::dunbrack::RotamerLibrary
• resn_ : protocols::protein_interface_design::movers::BBDofs
• resName : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation , protocols::sparta::CORdata , protocols::sparta::RingData
• resname : protocols::forge::remodel::LineObject
• resName1_ : core::io::pdb::LinkInformation
• resName2_ : core::io::pdb::LinkInformation
• resname_ : protocols::contact_map::ContactPartner , protocols::jd2::parser::BluePrint , protocols::simple_moves::HelicalPeptideLengthMover
• resnames_ : protocols::protein_interface_design::movers::HotspotHasherMover
• resno_ : protocols::scoring::ImplicitFastClashCheck
• resnum : core::scoring::packstat::SimplePDB_Atom
• resNum : protocols::sparta::CORdata
• resnum_ : core::pack::interaction_graph::SimpleNode , protocols::comparative_modeling::features::ResidueFeature , protocols::enzdes::EnzScoreFilter , protocols::jd2::parser::BluePrint , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::SetTorsion , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::protein_interface_design::movers::SetAtomTree , core::pack::task::operation::AppendResidueRotamerSet
• resnum_map_ : protocols::jd2::parser::BluePrint
• resnums_ : protocols::simple_filters::ResidueIEFilter
• reso : core::scoring::electron_density::ElectronDensity
• resolution_ : protocols::qsar::scoring_grid::GridManager
• resolve_ : core::coarse::CoarseEtable
• resolved_anchor_residue_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• resonance1_ : protocols::noesy_assign::PeakAssignment
• resonance2_ : protocols::noesy_assign::PeakAssignment
• resonances_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakFileFormat
• respair_evaluators_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respos_from_external_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• resSeq : core::io::pdb::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey , core::io::pdb::AtomInformation
• ResSurfaceFullList : protocols::sparta::PDB
• ResSurfacePartList : protocols::sparta::PDB
• REST_ALL : core::coarse::Rule
• REST_SIDECHAIN : core::coarse::Rule
• restart_mode_ : protocols::forge::components::VarLengthBuild
• restore_pose_ : protocols::rosetta_scripts::SavePoseMover
• restraints_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• restrict_identities_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_restypes_ : protocols::flxbb::LayerDesignOperation
• restrict_to_interface_ : protocols::docking::DockTaskFactory
• restrict_to_nbrhood_ : protocols::ddg::ddGMover
• restrict_to_repacking_ : protocols::simple_moves::DesignRepackMover , protocols::enzdes::PackRotamersMoverPartGreedy
• restrict_to_wt_ : protocols::motifs::MotifSearch
• restricted_aatypes_for_selection_ : protocols::toolbox::SelectResiduesByLayer
• restrictSize_ : protocols::pockets::PocketGrid
• restype_ : core::chemical::AutomorphismIterator , protocols::match::upstream::BuildSet , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::downstream::ClassicMatchAlgorithm , core::chemical::orbitals::AssignOrbitals , protocols::simple_filters::ResidueIEFilter
• restype_atom_id_2_nonchi_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• restype_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• restype_geom_ : protocols::match::upstream::BuildSet
• restype_group_for_rotamers_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• restype_id_2_collision_check_id_ : protocols::toolbox::match_enzdes_util::LigandConformer
• restype_index_ : core::pack::scmin::ResidueAtomTreeCollectionMomento
• restype_name1_ : protocols::motifs::Motif
• restype_name2_ : protocols::motifs::Motif
• restype_name_ : protocols::match::upstream::UpstreamResTypeGeometry
• restype_set_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo , protocols::enzdes::EnzdesBaseProtocol , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• restypegroup_adjacency_ : core::pack::interaction_graph::SymmOnTheFlyEdge
• result : core::scoring::APBSWrapper
• result_query_string_ : protocols::wum::DatabaseEntryWorkUnit
• resulting_cutoff_ : protocols::frag_picker::DiversifyCrmsdByClustering
• results : core::scoring::sc::MolecularSurfaceCalculator
• retrieve_index : protocols::loophash::FilterBucket
• retry_count_ : protocols::jd2::FileSystemJobDistributor
• return_centroid_ : protocols::abinitio::Protocol
• return_pseudo_hits_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_val_ : core::scoring::constraints::ConstantFunc
• reverse_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• reverse_mapping_ : protocols::abinitio::Template
• reversion_scan_ : protocols::dna::DnaInterfacePacker
• revision_id_ : protocols::match::OccupiedSpaceHash , core::scoring::constraints::ConstraintSet
• revision_id_current_ : core::scoring::constraints::ConstraintSet
• REWARD : protocols::frag_picker::scores::SequenceIdentity , protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity
• reweight_stride_ : protocols::canonical_sampling::SimulatedTempering
• rg : core::scoring::methods::RG_MinData
• rg_ : core::scoring::rna::RG_Energy_RNA
• rgstr_shift_ : protocols::fldsgn::topology::StrandPairing
• rh_ : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcs2::PcsTensor
• rho : protocols::pockets::spherical_coor_triplet
• rho_ : core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore
• rho_calc : core::scoring::electron_density::ElectronDensity
• rho_calc_as : core::scoring::electron_density::ElectronDensity
• rho_calc_atms : core::scoring::electron_density::ElectronDensity
• rho_calc_sum : core::scoring::electron_density::ElectronDensity
• rhq_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• rhs_ : core::scoring::ResidualDipolarCoupling
• right : protocols::forge::build::Interval
• right_ : core::pack::dunbrack::BBIndNRChiSample< P > , core::scoring::interface::DDPlookup , protocols::topology_broker::DofClaim
• right_position_ : protocols::forge::build::ConnectRight
• right_ram_probabil_ : core::scoring::Ramachandran2B
• right_rama_sampling_table_ : core::scoring::Ramachandran2B
• right_rama_sampling_table_by_torsion_bin_ : core::scoring::Ramachandran2B
• right_stub_atoms_ : protocols::forge::build::ConnectRight
• rigid_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator , protocols::topology_broker::CoordConstraintClaimer
• rigid_body_confs_ : protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
• rigid_body_cycles_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• rigid_body_info_ : protocols::docking::DockSetupMover , protocols::docking::DockingInitialPerturbation
• rigid_body_mover_ : protocols::rna::RNA_DeNovoProtocol
• rigid_core_ : protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::RigidChunkClaimer
• rigid_loops_ : protocols::abinitio::DoubleLayerKinematicAbinitio
• rigid_min_ : protocols::forge::remodel::RemodelMover::instruction_flags
• rigid_rot_mag_ : protocols::docking::TemperedDocking
• rigid_segment_in_refinement_ : protocols::forge::remodel::RemodelMover::instruction_flags
• rigid_segs_ : protocols::rbsegment_relax::AutoRBMover
• rigid_trans_mag_ : protocols::docking::TemperedDocking
• ring_height_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_intensity_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_radius_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_size_ : core::chemical::carbohydrates::CarbohydrateInfo
• ringFact : protocols::sparta::RingData
• RingNo : protocols::sparta::PDB
• Rings : protocols::sparta::PDB
• rise_ : protocols::dna::DNABasestep
• rltoc_map_ : core::pack::task::operation::ResLvlTaskOperationFactory
• rm_virt_phosphate_ : protocols::swa::rna::StepWiseRNA_Minimizer
• rmax_ : core::scoring::constraints::MixtureFunc
• rmdl_attempts_ : protocols::fldsgn::BluePrintBDR
• rms_ : protocols::optimize_weights::SingleStructureData , protocols::seeded_abinitio::SegmentHybridizer
• rms_all_rpked_ : protocols::enzdes::RepackWithoutLigandFilter
• rms_cutoff_ : protocols::protein_interface_design::movers::Splice
• rms_group_cutoff_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• rms_limit_ : protocols::loophash::MPI_LoopHashRefine
• rms_target_ : core::scoring::methods::RMS_Energy
• rms_threshold_ : protocols::enzdes::RepackWithoutLigandFilter
• RMSD : protocols::swa::rna::Cluster_Member
• rmsd : protocols::swa::rna::output_data_struct
• rmsd_ : protocols::anchored_design::AnchoredDesignMover , core::scoring::ResidualDipolarCoupling
• rmsd_ca_list_ : protocols::toolbox::KClusterData
• rmsd_count : protocols::swa::rna::SillyCountStruct
• rmsd_cutoff_ : protocols::swa::PoseFilter_RMSD_Screen , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener , protocols::fldsgn::filters::FragQualFilter , protocols::swa::RigidBodySampler
• rmsd_cutoff_1_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_cutoff_2_ : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• rmsd_cutoff_goodfrag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• rmsd_max_cutoff_ : protocols::rna::RNA_Relaxer
• rmsd_min_cutoff_ : protocols::rna::RNA_Relaxer
• RMSD_only_this_ : protocols::anchored_design::AnchoredDesignMover
• RMSD_only_this_pose_ : protocols::anchored_design::AnchoredDesignMover
• rmsd_pool_ : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• rmsd_pose_ : protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SymmetricRmsdEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::LoopRmsdEvaluator
• rmsd_res_list_ : protocols::swa::rna::StepWiseRNA_JobParameters
• rmsd_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• rmsd_threshold_ : protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SidechainRmsdFilter
• rmsd_unique_cutoff_ : protocols::match::downstream::LigandConformerBuilder
• rmsd_wrt_correct_minimized : protocols::swa::rna::output_data_struct
• rmsd_wrt_minimized : protocols::swa::rna::output_data_struct
• rmsd_wt_ : protocols::simple_filters::SymmetricMotifFilter
• rN : protocols::sparta::Sparta::SpartaLib , protocols::sparta::PDB
• rna_ : core::import_pose::ImportPoseOptions
• rna_add_mover_ : protocols::swa::monte_carlo::RNA_AddOrDeleteMover
• rna_add_or_delete_mover_ : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• rna_atom_vdw_ : core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::RNA_FA_Stack , core::scoring::ScoringManager
• rna_axis_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_potential_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_weight_ : core::scoring::rna::RNA_LowResolutionPotential
• RNA_backbone_oxygen_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_backbone_xy_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_radius_cutoff2_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_radius_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_stagger_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_xy_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_bond_geometry_energy_ : core::scoring::constraints::ConstraintEdge
• rna_centroid_info_ : core::scoring::rna::RNA_ScoringInfo , protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• rna_ch_o_bond_distance_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_chemical_shift_potential_ : core::scoring::ScoringManager , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy
• rna_chunk_library_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• rna_cos_theta_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_cos_theta_fade_zone_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_cs_params_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• rna_data_ : core::scoring::rna::RNA_DataInfo
• rna_data_file_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_data_info_ : core::scoring::rna::RNA_ScoringInfo , protocols::rna::RNA_DataReader
• rna_data_reader_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_delete_mover_ : protocols::swa::monte_carlo::RNA_AddOrDeleteMover
• rna_filtered_base_base_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_fitted_torsion_info_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer , protocols::swa::monte_carlo::RNA_TorsionMover
• rna_fragment_mover_ : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Relaxer
• rna_fragments_ : protocols::rna::RNA_FragmentMover
• rna_jump_library_ : protocols::rna::RNA_StructureParameters
• rna_loop_closer_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::MultipleDomainMover , protocols::rna::RNA_DeNovoProtocol
• rna_low_resolution_potential_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::ScoringManager , core::scoring::rna::RNA_BaseBaseEnergy
• rna_mg_knowledge_based_potential_ : core::scoring::rna::RNA_Mg_Energy
• rna_minimizer_ : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Relaxer
• rna_o2star_mover_ : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• rna_pairing_list_ : protocols::rna::RNA_StructureParameters
• rna_pairing_template_map_ : protocols::rna::RNA_JumpLibrary
• rna_params_file_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_raw_base_base_info_ : core::scoring::rna::RNA_ScoringInfo , core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_relaxer_ : protocols::rna::RNA_DeNovoProtocol
• rna_repulse_all_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_max_penalty_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_screen_scale_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_weight_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_residuetype_ : core::chemical::ResidueType
• rna_secstruct_ : protocols::rna::RNA_SecStructInfo , protocols::rna::RNA_StructureParameters
• rna_stagger_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_structure_parameters_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_sugar_close_constraints_ : core::scoring::rna::RNA_SugarCloseEnergy
• rna_tight_torsions_ : core::scoring::rna::RNA_FittedTorsionInfo , core::scoring::rna::RNA_TorsionPotential
• rna_torsion_mover_ : protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• rna_torsion_potential_ : core::scoring::rna::RNA_TorsionEnergy , core::scoring::ScoringManager
• rna_vdw_atom_ : core::scoring::rna::RNA_AtomVDW
• rna_vdw_parameter_ : core::scoring::rna::RNA_AtomVDW
• rna_verbose_ : core::scoring::rna::RNA_LowResolutionPotential , core::scoring::rna::RNA_FilteredBaseBaseInfo
• rnl_pose_ : protocols::enzdes::EnzdesScorefileFilter
• role_available_mem_ : protocols::wum2::EndPoint
• roll_ : protocols::dna::DNABasestep
• root_ : core::kinematics::AtomTree , core::conformation::symmetry::SymmData , protocols::jumping::ResiduePairJumpSetup , protocols::topology_broker::CoordConstraintClaimer
• root_at_first_rigid_body_ : protocols::rna::RNA_StructureParameters , protocols::rna::RNA_DeNovoProtocol
• root_expression_ : protocols::pack_daemon::SurrogateVariableExpression
• root_from_label_ : protocols::topology_broker::CoordConstraintClaimer
• rooted_chunk_indices_ : protocols::hybridization::HybridizeFoldtreeDynamic
• rosetta2methyl_ : protocols::noesy_assign::MethylNames
• rosetta2nmr_ : protocols::noesy_assign::MethylNames
• ROSETTA_SASA_radii_ : core::pack::interaction_graph::RotamerDotsRadiusData
• rot : core::pack::dunbrack::ChiSet
• rot_ : core::pack::dunbrack::CoarseRotamer
• rot_bin_ : core::pack::dunbrack::DunbrackConstraint
• rot_center_ : protocols::rigid::RigidBodyMover
• rot_db : protocols::constraints_additional::BindingSiteConstraint
• rot_freq_ : core::pack::annealer::SimAnnealerBase
• rot_level_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rot_mag_ : protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::rigid::RigidBodyPerturbMover , protocols::antibody2::LHSnugFitLegacy , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::antibody2::LHRepulsiveRampLegacy , protocols::rigid::RigidBodyDofPerturbMover , protocols::antibody2::LHRepulsiveRamp , protocols::rna::MultipleDomainMover
• rot_magnitude_ : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes
• rot_mat_ : protocols::pockets::PocketGrid
• rot_number_ : protocols::optimize_weights::PNatAAOptERotamerData
• rot_prob_accumulation_limit_ : protocols::match::upstream::BuildSet
• rot_sets_ : protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::BasicSimAnnealerRepacker
• rot_to_pack_ : core::pack::annealer::RotamerAssigningAnnealer
• rot_vec_pos_ : core::pack::dunbrack::DunbrackConstraint
• rot_well_ : core::pack::dunbrack::DunbrackRotamerSampleData
• ROT_X : core::kinematics::Jump
• ROT_Y : core::kinematics::Jump
• ROT_Z : core::kinematics::Jump
• rotamer_ : core::pack::interaction_graph::RotamerDots , core::pack::dunbrack::RotamericData< T > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::InvRotamerDots
• rotamer_aa_ : core::chemical::ResidueType
• rotamer_boltzmann_weight_ : protocols::features::RotamerBoltzmannWeightFeatures
• rotamer_centers_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• rotamer_combo_indexer_ : protocols::match::output::SameRotamerComboGrouper
• rotamer_couplings_ : core::pack::task::operation::SetRotamerCouplings , core::pack::task::PackerTask_ , core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• rotamer_energies_ : core::pack::interaction_graph::DoubleDensePDNode
• rotamer_generator_list_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• rotamer_id : protocols::loophash::BBExtraData
• rotamer_id_ : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• rotamer_index_ : protocols::optimize_weights::PNatRotOptERotamerData
• rotamer_is_glycine_ : protocols::flexpack::interaction_graph::OTFFlexbbNode
• rotamer_is_proline_ : protocols::flexpack::interaction_graph::OTFFlexbbNode
• rotamer_it_ : protocols::protein_interface_design::movers::TryRotamers
• rotamer_library_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , core::pack::dunbrack::RotamerLibrary
• rotamer_library_name_ : core::chemical::ResidueType
• rotamer_links_ : core::pack::task::PackerTask_ , core::pack::task::operation::SetRotamerLinks , core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• rotamer_list_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• rotamer_offsets_require_update_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• rotamer_operation_ : core::pack::task::operation::AppendRotamer
• rotamer_operations_ : core::pack::task::ResidueLevelTask_
• rotamer_probabilities_ : protocols::simple_filters::RotamerBoltzmannWeight
• rotamer_probability_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotamer_recovery_ : protocols::rotamer_recovery::RotamerRecoveryMover
• rotamer_recovery_context_poses_ : protocols::optimize_weights::IterativeOptEDriver
• rotamer_representatives_ : core::pack::interaction_graph::SymmOnTheFlyNode
• rotamer_seq_sep_ : core::scoring::hbonds::HBondEnergy
• rotamer_set_ : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::interaction_graph::OnTheFlyNode
• rotamer_set_operation_ : core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::AppendResidueRotamerSet
• rotamer_sets_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::annealer::FASTERAnnealer , protocols::simple_moves::PackRotamersMover , core::pack::annealer::RotamerAssigningAnnealer , core::pack::rotamer_set::ContinuousRotamerSets , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , protocols::motifs::IRCollection
• rotamer_well_counts_ : protocols::optimize_weights::PNatRotOptEPositionData
• rotamers_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::CoarseRotamerSet , core::pack::rotamer_set::RotamerSubset , protocols::flexpack::interaction_graph::OTFFlexbbNode , core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::rotamer_set::RotamerSet_ , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamers_in_subtree_ : core::scoring::trie::TrieNode< AT, CPDATA >
• rotamers_recovered_ : protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• rotamers_vector_ : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• rotamersets_p_ : protocols::multistate_design::PackingState
• rotate_atom_ : protocols::ligand_docking::RigidSearchMover
• rotate_deg_ : protocols::ligand_docking::RigidSearchMover
• rotate_info_ : protocols::ligand_docking::Rotate
• rotate_rsd_ : protocols::ligand_docking::RigidSearchMover
• rotates_ : protocols::ligand_docking::Rotates
• rotation : core::kinematics::RT
• rotation_mag_ : protocols::rigid::MembraneNormalPerturbationMover
• rotation_matrices_ : core::conformation::symmetry::SymmData
• rotation_matrix_ : protocols::rigid::RigidBodyRandomizeMover
• rotE_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophipsi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecopsi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotlib_ : core::pack::dunbrack::RotamerConstraint
• rotno_2_packed_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• rots2add_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rots_for_nodes_ : core::pack::annealer::RotamerAssigningAnnealer
• rotset_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::protein_interface_design::movers::TryRotamers
• rotsetops_ : core::pack::task::ResidueLevelTask_
• rotsets_ : protocols::jumping::ResiduePairJump , protocols::flexpack::annealer::FlexbbSimAnnealer
• rottrials_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• rotwell_ : core::pack::dunbrack::DunbrackRotamer< S, P > , core::pack::dunbrack::RotamerLibraryScratchSpace
• rotwell_exists_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• rotx : protocols::loophash::LegacyLeapIndex
• roty : protocols::loophash::LegacyLeapIndex
• rotz : protocols::loophash::LegacyLeapIndex
• rounds_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::relax::CentroidRelax , protocols::rna::RNA_Minimizer
• row_format_ : protocols::contact_map::ContactMap
• row_map_ : protocols::wum::DatabaseEntryWorkUnit
• row_names_ : protocols::contact_map::ContactMap
• rp : core::scoring::sc::MolecularSurfaceCalculator
• rp_ : protocols::forge::build::RelativeConnectRight
• rsd1_ : core::id::JumpID , core::scoring::constraints::ResiduePairXYZ , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• rsd1_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd2_ : core::id::JumpID , core::scoring::constraints::ResiduePairXYZ , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• rsd2_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd_ : protocols::kinmatch::FunGroupTK , core::id::TorsionID , core::scoring::constraints::ResidueXYZ , core::id::NamedAtomID , core::id::AtomID , core::scoring::AtomNeighbor
• rsd_id_ : core::optimization::SingleResidueMultifunc
• rsd_layer_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• rsd_sasa_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• rsd_set : protocols::rna::RNA_HelixAssembler
• rsd_set_ : protocols::jd2::PoseInputStreamJobInputter , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWiseClusterer , protocols::swa::StepWisePoseSetup , protocols::swa::InputStreamWithResidueInfo , protocols::swa::protein::StepWiseProteinPoseSetup , protocols::swa::monte_carlo::RNA_AddMover
• rsd_type_ : core::conformation::Residue
• rsd_type_name3_ : core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::NonResidueTypeConstraint
• rsd_type_name_ : core::pack::dunbrack::RotamerConstraint
• rsd_type_set_ : protocols::topology_broker::SequenceClaimer , protocols::swa::StepWiseClusterer
• rsigma_dot_ : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rsigma_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• rswitch_ : core::scoring::constraints::BoundFunc
• RT : core::scoring::dna::DirectReadoutPotential
• rt_ : protocols::jumping::PairingTemplate , protocols::forge::build::ConnectRight , protocols::jumping::DisulfTemplate , core::fragment::DownJumpSRFD , core::kinematics::Jump
• rt_min_ : protocols::antibody2::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::CDRsMinPackMin
• rtmin_ : protocols::symmetric_docking::SymDockProtocol , protocols::docking::DockMCMCycle , protocols::design_opt::PointMutationCalculator , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::GreedyOptMutationMover , protocols::symmetric_docking::SymDockingHiRes , protocols::simple_filters::RelativePoseFilter , protocols::protein_interface_design::filters::FilterScanFilter
• rtmin_mover_ : protocols::docking::DockingPrepackProtocol , protocols::docking::DockingEnsemblePrepackProtocol
• rts_ : protocols::forge::build::BuildInstruction
• rules_ : core::coarse::RuleSet , core::coarse::Rule
• run_ : core::scoring::sc::MolecularSurfaceCalculator , protocols::abinitio::FoldConstraints
• run_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• run_motifs_ : protocols::motifs::MotifDnaPacker
• RV : core::scoring::electron_density::ElectronDensity
• rv_infos_ : protocols::forge::remodel::ResidueVicinityRCG
• rvjump_pose : protocols::forge::remodel::WorkingRemodelSet