- r -

• r : core::optimization::EItem , core::scoring::packstat::Circle
• r0 : core::scoring::data_struct
• r0_ : core::scoring::ResidualDipolarCoupling , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• r1 : core::scoring::data_struct , protocols::hybridization::TMalign , protocols::sparta::PDB , protocols::sparta::Sparta::SpartaLib
• r1_ : core::scoring::ResidualDipolarCoupling , protocols::helical_bundle::parameters::BundleParameters
• r1_guesses_ : protocols::helical_bundle::FitSimpleHelix
• r1_initial_ : protocols::helical_bundle::FitSimpleHelix
• r1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• r2 : core::scoring::data_struct , protocols::hybridization::TMalign
• r21 : protocols::normalmode::ContactStruct
• r2_ : core::scoring::ResidualDipolarCoupling
• r_ : core::scoring::packing::Ball
• R_ : core::scoring::ResidualDipolarCoupling
• 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_handed_ : protocols::simple_filters::RepeatParameterFilter
• 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
• r_pose_ : protocols::simple_filters::MultipleSigmoids
• rad : protocols::sparta::RingData
• radial_disp_ : protocols::matdes::GetRBDOFValues
• radial_disp_deltas_ : protocols::matdes::SymDofMover
• radial_disp_steps_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• radial_disps_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• radial_disps_range_max_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• radial_disps_range_min_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• radial_offsets_ : protocols::matdes::SymDofMover
• radii_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots , core::scoring::sc::MolecularSurfaceCalculator
• radii_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• radii_set_ : core::scoring::sasa::SasaMethod
• radius : core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere , core::scoring::PQR , 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::forge::remodel::RemodelGlobalFrame , protocols::pose_selectors::ClusterPoseSelector , protocols::qsar::scoring_grid::RepGrid , protocols::toolbox::GreedyKCenter
• radius_exp_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• radmax : core::scoring::sc::MolecularSurfaceCalculator
• ram_counts_ : core::scoring::Ramachandran
• ram_energ_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• ram_energ_left_ : core::scoring::Ramachandran2B
• ram_energ_right_ : core::scoring::Ramachandran2B
• ram_entropy_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• ram_entropy_left_ : core::scoring::Ramachandran2B
• ram_entropy_right_ : core::scoring::Ramachandran2B
• ram_probabil_ : core::scoring::Ramachandran
• rama2b_ : core::scoring::ScoringManager
• rama_ : core::scoring::ScoringManager , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• rama_cutoff_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• rama_energy_splines_ : core::scoring::Ramachandran
• rama_params : protocols::relax::CentroidRelax::parameters
• rama_pp_ : core::scoring::ScoringManager
• rama_pp_splines_ : core::scoring::RamaPrePro
• rama_sampling_factor_ : core::scoring::Ramachandran
• rama_sampling_thold_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• rama_score_limit_ : core::scoring::Ramachandran2B
• rama_splines_ : core::scoring::RamaPrePro
• rama_table_type_by_res_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• rama_threshhold_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• rama_type_ : protocols::relax::CentroidRelax
• ramachandran_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• 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_cart_ : protocols::relax::LocalRelax
• 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_schedule_ : protocols::relax::LocalRelax
• ramp_sfxn_rama_ : protocols::loop_modeling::LoopProtocol
• ramp_sfxn_rep_ : protocols::loop_modeling::LoopProtocol
• ramp_temp_ : protocols::loop_modeling::LoopProtocol
• ramp_temperature_ : protocols::canonical_sampling::CanonicalSamplingMover
• ramp_vdw_ : protocols::relax::CentroidRelax
• ramp_weight : protocols::moves::TrialMover
• ramp_width_A2_ : core::scoring::lkball::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
• rand_checkpoint_file_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• rand_drop_rate_ : protocols::abinitio::abscript::ConstraintPreparer
• rand_range_ : protocols::membrane::SpinAroundPartnerMover
• randfragprob_ : protocols::hybridization::CartesianHybridize
• randfragprob_stage2_ : protocols::hybridization::HybridizeProtocol
• randmove_ : protocols::canonical_sampling::CanonicalSamplingMover
• random_ : protocols::stepwise::sampler::StepWiseSamplerBase
• random_access_ : protocols::simple_moves::AddChainMover
• random_angle_ : protocols::membrane::FlipMover , protocols::membrane::TiltMover
• random_chain_closed_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• random_conformer_ : protocols::docking::ConformerSwitchMover
• random_counter_ : protocols::jobdist::BaseJobDistributor
• random_entry_ : protocols::protein_interface_design::PatchdockReader
• random_flush_frequency_ : protocols::jd2::SilentFileJobOutputter
• random_grow_loops_by_ : protocols::topology_broker::RigidChunkClaimer
• random_loop_flag_ : protocols::LoopRebuild
• random_mover_ : protocols::abinitio::abscript::AbscriptStageMover
• random_order_ : protocols::loops::loop_mover::IndependentLoopMover
• random_perturbation_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• random_phi_psi_pert : protocols::flexpep_docking::FlexPepDockingFlags
• random_phi_psi_pert_size : protocols::flexpep_docking::FlexPepDockingFlags
• random_point_on_ellipsoid_ : protocols::docking::EllipsoidalRandomizationMover
• random_roll_ : protocols::rigid::RollMover
• random_roll_angle_ : protocols::rigid::RollMover
• random_roll_trans_ : protocols::rigid::RollMover
• random_set_ : protocols::simple_moves::SetTorsion
• 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::BaseTabooPerturber
• 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_equiv_frag_ : protocols::forge::remodel::RemodelMover::instruction_flags
• randomize_input_ : protocols::jd2::MSDJobDistributor
• 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::StructFileRepOptions
• randomize_order_ : protocols::ligand_docking::CompoundTranslate
• randomize_resnum_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• randomly_cycle_appearance : protocols::boinc::BoincSharedMemory
• randomness_ : protocols::rbsegment_relax::RBSegmentRelax
• randomRBstart : protocols::flexpep_docking::FlexPepDockingFlags
• range1_ : protocols::simple_filters::AtomicContactFilter
• range2_is_bound_ : core::conformation::symmetry::SymDof
• range_ : protocols::membrane::SpinAroundPartnerMover , protocols::simple_filters::DeltaFilter
• range_pair_ : core::scoring::Hairpin
• range_squared_ : protocols::ligand_docking::ComputeLigandRDF
• rank : core::graph::DS_Node
• rank2tlevel_ : protocols::canonical_sampling::ParallelTempering
• rank_ : protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest , protocols::canonical_sampling::AsyncMPITemperingBase , 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 , protocols::simple_filters::MutationsFilter
• 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_parent_ : core::kinematics::tree::Atom_
• 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_ : protocols::docking::DockingSlideIntoContact , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::enzdes::LigInterfaceEnergyFilter , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , 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::UniformRotationMover , protocols::simple_moves::UniformTranslationMover , 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::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqTransMover
• rb_min_ : protocols::enzdes::EnzdesBaseProtocol
• rb_min_jumps_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzRepackMinimize
• rb_min_post_graft_ : protocols::antibody::design::AntibodyDesignMover
• rb_minimizable_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• rb_mover_ : protocols::docking::DockingLowRes , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockingLowRes
• rb_mover_stage1_weight_ : protocols::topology_broker::TMHTopologySamplerClaimer
• rb_movers_ : protocols::farna::MultipleDomainMover
• rb_rot_size : protocols::flexpep_docking::FlexPepDockingFlags
• rb_trans_size : protocols::flexpep_docking::FlexPepDockingFlags
• rbMCM : protocols::flexpep_docking::FlexPepDockingFlags
• 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::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• rd1_model : protocols::ss_prediction::SS_predictor
• rd2_model : protocols::ss_prediction::SS_predictor
• rdc : core::scoring::data_struct
• rdc_data_ : protocols::abinitio::IterativeBase , 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
• rdcconst_ : core::scoring::ResidualDipolarCoupling
• rdcs_ : protocols::simple_filters::TruncatedScoreEvaluator
• rdcweight : core::scoring::data_struct
• rdcweight_ : core::scoring::ResidualDipolarCoupling
• rdf_functions_ : protocols::ligand_docking::ComputeLigandRDF
• Rdimers : protocols::simple_filters::SymmetricMotifFilter
• reached_ : core::kinematics::AtomWithDOFChange
• reactivity_ : core::io::rna::RDAT
• reactivity_error_ : core::io::rna::RDAT
• read_fold_tree_ : core::import_pose::ImportPoseOptions
• read_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• read_gridlig_file_ : protocols::match::Matcher
• read_link_records_ : core::io::StructFileReaderOptions
• read_pdb_header_ : core::io::StructFileReaderOptions
• read_type_ : protocols::jd2::parser::FragmentReader
• ready_for_exchange_ : protocols::canonical_sampling::AsyncMPITemperingBase
• ready_to_align_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• real_dof_deriviative_expressions_ : protocols::optimize_weights::WrapperOptEMultifunc
• real_groups : core::indexed_structure_store::FragmentStore
• real_value_ : protocols::simple_moves::AddJobPairData
• realatomdata_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• realatomdata_index : core::scoring::rna::chemical_shift::ChemicalShiftData
• realign_domains_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• realign_domains_stage2_ : protocols::hybridization::HybridizeProtocol
• realVector_groups : core::indexed_structure_store::FragmentStore
• rebuild_bulge_mode_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• rebuild_cycles_ : protocols::rbsegment_relax::OptimizeThreadingMover
• rebuild_filter_ : protocols::comparative_modeling::LoopRelaxMover
• rebuild_fold_tree_ : protocols::cyclic_peptide::DeclareBond
• recal_foldtree : protocols::flexpep_docking::FlexPepDockingFlags
• 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 , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• 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
• record_annealer_trajectory_ : core::pack::annealer::FixbbSimAnnealer
• record_definitions_ : core::io::pdb::RecordCollection
• record_source_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• record_statistics_ : protocols::backrub::BackrubSidechainMover
• recorder_stream_ : protocols::canonical_sampling::MetricRecorder
• recover_low_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins
• recv_buf_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• recv_level_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• 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_IG_as_L_ : protocols::moves::DsspMover
• Reduced_Jdipolar_ : core::scoring::RDC , core::scoring::RDC_Rohl
• reduced_scofx_ : protocols::enzdes::SecondaryMatchProtocol
• reduced_sfxn_ : protocols::enzdes::EnzdesBaseProtocol
• ref_atom_ : core::scoring::sc::CloserToAtom
• ref_baseline_ : protocols::simple_filters::DeltaFilter
• REF_CS_Tab : protocols::sparta::Sparta
• ref_cst_maxdist_ : protocols::hybridization::CartesianSampler
• ref_cst_weight_ : protocols::hybridization::CartesianSampler
• ref_end_ : protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::simple_moves::SuperimposeMover
• ref_energy_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::rotamers::SingleLigandRotamerLibrary
• ref_gunn_data_ : protocols::frag_picker::scores::GunnCostScore
• ref_mini_pose_list_ : core::pose::rna::RNA_IdealCoord
• ref_model_ : protocols::hybridization::CartesianSampler
• ref_motifs_ : protocols::simple_filters::SymmetricMotifFilter
• ref_pKa_ : protocols::simple_moves::IonizableResidue
• ref_pose_ : core::scoring::cryst::PhenixInterface , protocols::design_opt::GreedyOptMutationMover , protocols::enzdes::PoseFoundResiduesCombination , protocols::match::downstream::ScoringSecMatchRPE , protocols::matdes::MatDesGreedyOptMutationMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::simple_moves::SuperimposeMover , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::toolbox::DecoySetEvaluation
• ref_pose_name_ : protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::SimpleGlycosylateMover
• 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_sfxn1_ : protocols::membrane::benchmark::SampleTiltAngles
• ref_sfxn2_ : protocols::membrane::benchmark::SampleTiltAngles
• ref_sfxn3_ : protocols::membrane::benchmark::SampleTiltAngles
• ref_shift : core::scoring::rna::chemical_shift::ChemicalShiftData
• ref_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter , 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
• ref_xyz_ : protocols::md::MDBase
• refCSFileName : protocols::sparta::Sparta
• reference_atom_ : protocols::helical_bundle::FitSimpleHelix
• reference_atom_name_ : protocols::stepwise::screener::AnchorSugarScreener
• reference_centroid_ : protocols::stepwise::screener::CentroidDistanceScreener
• reference_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , 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_intensities_ : core::scoring::saxs::SAXSEnergy
• reference_moltenres_2_resid_ : protocols::simple_moves::GreenPacker
• reference_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• reference_pdb_id_ : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• reference_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• reference_pose_ : protocols::abinitio::IterativeBase , protocols::denovo_design::constraints::CoordinateConstraintGenerator , protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::fldsgn::MatchResidues , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::GunnCostScore , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::simple_filters::DeltaFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::packer::SideChainCopier , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• reference_pose_local_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• reference_pose_map_ : core::pose::reference_pose::ReferencePoseSet
• reference_pose_name_ : protocols::simple_moves::StorePoseSnapshot
• reference_pose_set_ : core::pose::Pose
• reference_res : protocols::stepwise::modeler::rna::sugar::SugarModeling
• reference_res_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::TagDefinition
• reference_resid_2_moltenres_ : protocols::simple_moves::GreenPacker
• reference_residue_ : protocols::helical_bundle::FitSimpleHelix
• reference_residue_types_ : protocols::dna::DnaInterfacePacker
• reference_residues_indexes_ : protocols::fldsgn::MatchResidues
• reference_rotamer_sets_ : protocols::simple_moves::GreenPacker
• reference_shifts_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• reference_stub_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::screener::StubDistanceScreener
• reference_task_ : protocols::simple_moves::GreenPacker
• reference_task_factory_ : protocols::simple_moves::GreenPacker
• reference_xyz_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• refinable_lattice_ : protocols::cryst::MakeLatticeMover
• refine_ : protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , 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_from_silent_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• refine_h3_ : protocols::antibody::AntibodyModelerProtocol
• refine_input_loop_ : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody_legacy::CDRH3Modeler
• refine_KIC_off_ : protocols::anchored_design::AnchoredRefineMover
• refine_mode_ : protocols::antibody::RefineOneCDRLoop
• refine_only_ : protocols::anchored_design::AnchoredDesignMover
• refine_pose_ : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::RNA_FragmentMonteCarlo
• refine_pose_list_ : protocols::farna::RNA_DeNovoProtocol
• 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
• refiners_ : protocols::loop_modeling::LoopProtocol
• refpose_ : protocols::relax::AtomCoordinateCstMover
• refresh_normalmode_ : protocols::normalmode::NormalModeRelaxMover
• refx_ : protocols::simple_filters::AngleToVector
• refy_ : protocols::simple_filters::AngleToVector
• refz_ : protocols::simple_filters::AngleToVector
• reg_only_movers_ : protocols::environment::EnvMover
• region : core::sequence::Line
• region1_ : protocols::simple_filters::RegionalConnections
• region1_region2_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• region2_ : protocols::simple_filters::RegionalConnections
• region_ : protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::nonlocal::Chunk , protocols::topology_broker::FragmentClaimer
• regional_avg_per_residue_dG : protocols::analysis::PerResidueInterfaceData
• regional_avg_per_residue_dSASA : protocols::analysis::PerResidueInterfaceData
• regional_avg_per_residue_energy_int : protocols::analysis::PerResidueInterfaceData
• regional_avg_per_residue_energy_sep : protocols::analysis::PerResidueInterfaceData
• regional_avg_per_residue_SASA_int : protocols::analysis::PerResidueInterfaceData
• regional_avg_per_residue_SASA_sep : protocols::analysis::PerResidueInterfaceData
• registered_makers_ : protocols::frag_picker::scores::FragmentScoreManager
• registered_movers_ : protocols::environment::Environment
• registry_shift_ : protocols::hybridization::InsertChunkMover
• regular_half_width : core::pose::rna::RNA_SuiteName
• reinitialize_CCD_torsions_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• reject_failed_loops_ : protocols::pose_length_moves::FixAllLoopsMover
• 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
• rel_hydrophobic_sasa_by_charge_ : core::scoring::sasa::SasaCalc
• relative_pose_names_ : protocols::simple_filters::Operator
• relative_tmh_ori_ : core::scoring::MembraneTopology
• relax : protocols::comparative_modeling::LoopRelaxThreadingMover
• relax_ : protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , protocols::membrane::MPMutateRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• relax_bb_for_disulf_ : protocols::forge::remodel::RemodelMover
• relax_bound_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• relax_constraint_to_design_ : protocols::flxbb::FlxbbDesign
• relax_cycles_ : protocols::farna::movers::RNA_Relaxer , protocols::hybridization::MRMover
• 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_max_iter_ : protocols::hybridization::MRMover
• relax_mover_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , 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 , protocols::relax::membrane::MPFastRelaxMover
• relax_repeats_ : protocols::hybridization::HybridizeProtocol
• relax_structure_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• relax_type : protocols::mpi_refinement::MethodParams
• 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
• relaxmode_ : protocols::normalmode::NormalModeRelaxMover
• relevant_atom_ids_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• relevant_atom_indices_ : protocols::enzdes::ResidueConformerFilter
• 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_residues_ : protocols::features::ReportToDB
• relevant_residues_mode_ : protocols::features::FeaturesReporter , protocols::features::ReportToDB
• relevant_scoreterms_ : protocols::enzdes::EnzdesScorefileFilter
• rely_on_loopfile_indices_ : protocols::loops::GuardedLoopsFromFile
• remap_pdb_atom_names_ : core::chemical::ResidueType
• remap_symm_ : core::scoring::electron_density::ElectronDensity
• remapped_atom_names_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• remark_ : protocols::motifs::Motif
• REMARK_NUM : protocols::denovo_design::components::StructureData
• REMARKS : protocols::sparta::GDB
• remarks_ : core::io::StructFileRep , core::pose::PDBInfo
• remember_unrecognized_res_ : core::io::StructFileRepOptions
• remember_unrecognized_water_ : core::io::StructFileRepOptions
• remembered_pose_ : protocols::simple_moves::ReturnSidechainMover
• remodel : protocols::comparative_modeling::LoopRelaxThreadingMover
• remodel_ : protocols::antibody::ModelCDRH3 , protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• remodel_data_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , 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::antibody::ModelCDRH3
• remodelable_ : protocols::enzdes::EnzdesFlexibleRegion
• removable_ : protocols::simple_moves::VirtualRootMover
• remove_ : protocols::protein_interface_design::movers::AddChainBreak , protocols::simple_moves::VirtualRootMover
• remove_antigen_ : protocols::antibody::design::AntibodyDesignProtocol
• remove_cterminus_variant_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• remove_non_contiguous_assembly_ : protocols::sewing::MonteCarloAssemblyMover
• 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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• remove_shove_variant_ : protocols::protein_interface_design::movers::ShoveResidueMover
• remove_singletons_ : protocols::pose_selectors::ClusterPoseSelector
• remove_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• remove_xray_virt_ : protocols::features::ReportToDB
• rename_tags_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• renumber_decoys_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• renumber_pdb_ : core::io::StructFileRepOptions , protocols::simple_filters::SaveResfileToDiskFilter
• rep : protocols::ligand_docking::Ligand_info
• rep_cutoff_ : protocols::moves::SimulatedTempering , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::screener::PartitionContactScreener
• rep_radius_ : protocols::qsar::scoring_grid::ClassicGrid
• rep_ramp_cycles : protocols::flexpep_docking::FlexPepDockingFlags
• rep_ramp_cycles_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy
• rep_scorefxn_ : protocols::moves::SimulatedTempering
• 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
• repack_again_ : protocols::relax::RangeRelaxMover
• 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_mutation_only_ : protocols::membrane::MPMutateRelaxMover
• 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::loop_modeling::refiners::RepackingRefiner , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::symmetric_docking::SymDockingHiRes
• repack_query_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• repack_radius_ : protocols::membrane::MPMutateRelaxMover
• repack_rate_ : protocols::dna::DesignProteinBackboneAroundDNA
• repack_residues_ : protocols::membrane::MPMutateRelaxMover
• repack_sc_ : protocols::relax::CentroidRelax
• repack_scorefxn_ : protocols::topology_broker::TopologyBroker
• repack_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , 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_unbound_ : protocols::simple_moves::ddG
• 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_length_ : protocols::forge::remodel::RemodelLoopMover
• repeat_pose_ : protocols::forge::remodel::RemodelLoopMover
• repeat_tail_length_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• repeat_without_replacing_pose_ : protocols::simple_moves::RepeatPropagationMover
• repeating_unit_offset_ : protocols::helical_bundle::parameters::BundleParameters
• repeats : protocols::ligand_docking::Transform_info
• repeats_ : protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::PackStatFilter , protocols::simple_moves::bin_transitions::PerturbByBins , 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_as_silent_ : protocols::md::MDBase
• report_avg_ : protocols::simple_filters::SSElementMotifContactFilter
• report_CA_rmsd_ : protocols::idealize::IdealizeMover
• report_call_order_ : protocols::rosetta_scripts::ParsedProtocol
• report_diffs_ : protocols::simple_filters::DdGScan
• report_energy_ : protocols::simple_filters::ResidueIEFilter
• report_every_ : protocols::simple_moves::PeriodicBoxMover
• report_filter_at_end_ : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• report_filter_name_ : protocols::simple_filters::ReportFilter
• report_format_ : protocols::analysis::PeptideDeriverFilter
• report_gdt_components_ : protocols::comparative_modeling::Align_RmsdEvaluator , protocols::simple_filters::RmsdEvaluator
• report_grads_ : protocols::cryst::TagPoseWithRefinementStatsMover
• report_per_residue_sasa_ : protocols::simple_filters::TotalSasaFilter
• report_residue_pair_energies_ : protocols::simple_filters::ScoreCutoffFilter
• report_scorecomp_ : protocols::md::MDBase
• report_scorefile_ : protocols::simple_moves::PeriodicBoxMover
• report_sequence_ : protocols::helical_bundle::BundleReporterFilter
• report_silent_ : protocols::simple_moves::PeriodicBoxMover
• report_string_ : protocols::simple_filters::ReportFilter
• report_subvalues_ : protocols::simple_filters::Operator
• report_thermodynamics_ : protocols::simple_moves::PeriodicBoxMover
• report_this_as_effective_sequence_separation_ : core::scoring::constraints::MultiConstraint
• report_three_letter_codes_ : protocols::helical_bundle::BundleReporterFilter
• report_to_db_ : protocols::rotamer_recovery::RRReporterSQLite
• report_type_ : protocols::fldsgn::filters::NcontactsFilter
• report_water_ : protocols::simple_moves::PeriodicBoxMover
• reporter_ : protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::features::RotamerRecoveryFeatures , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::TopNByProperty , protocols::rosetta_scripts::PoseSelector , protocols::rotamer_recovery::RotamerRecovery
• reporter_creator_map_ : protocols::rosetta_scripts::PosePropertyReporterFactory
• reporter_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• reporters_ : protocols::features::Report
• reporting_ : protocols::docking::DockingProtocol
• reprepare_ : protocols::abinitio::abscript::ConstraintPreparer
• representative_downstream_algorithm_ : protocols::match::Matcher
• representative_dspos_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• representative_group_matches_ : protocols::match::output::CloudPDBWriter
• representative_seqpos_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• 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::antibody::RefineBetaBarrel
• repW : protocols::pockets::PocketExemplarMultifunc
• req_residue_str_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• reqfile_name_ : protocols::enzdes::EnzdesScorefileFilter
• requested_level_ : protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest
• 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
• required_resnums_ : protocols::sewing::sampling::requirements::ResidueRetentionRequirement
• requirement_factory_ : protocols::sewing::AssemblyMover
• requirement_set_ : protocols::sewing::AssemblyMover
• rerelax_type : protocols::mpi_refinement::MethodParams
• rerun_motifsearch_ : protocols::motifs::MotifSearch
• res : core::scoring::packstat::SimplePDB_Atom , protocols::cartesian::CartesianAtom
• res1 : protocols::denovo_design::components::BondInfo
• res1_ : core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::fldsgn::topology::DimerPairing , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::stepwise::screener::StepWiseResiduePairScreener
• 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 > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >
• res1_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res1_cp_data_ : core::scoring::vdwaals::VDWTrieCountPair1B
• res1_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res1_dat_ : core::scoring::hbonds::HBondResPairMinData
• res1_data_ : core::scoring::lkball::LKB_ResPairMinData , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::VdWTinkerResPairMinData
• res1_inds_ : core::scoring::disulfides::DisulfMinData
• res1_nb_ : core::scoring::hbonds::HBondEnergy
• res1_pbconn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2 : protocols::denovo_design::components::BondInfo
• res2_ : core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::fldsgn::topology::DimerPairing , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::stepwise::screener::StepWiseResiduePairScreener
• 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 > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >
• res2_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2_cp_data_ : core::scoring::vdwaals::VDWTrieCountPair1B
• res2_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res2_dat_ : core::scoring::hbonds::HBondResPairMinData
• res2_data_ : core::scoring::lkball::LKB_ResPairMinData , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::VdWTinkerResPairMinData
• 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 , protocols::cyclic_peptide::CreateTorsionConstraint
• res4_ : protocols::cyclic_peptide::CreateTorsionConstraint
• 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_center_ : protocols::cyclic_peptide::CreateAngleConstraint
• res_check_task_factory_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• res_collections_ : core::pack::scmin::AtomTreeCollection
• res_cutoff_high : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions
• res_cutoff_low : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions
• res_energy1_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_energy2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_first : protocols::rbsegment_relax::RBResidueRange
• res_high_ : protocols::cryst::SetRefinementOptionsMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• res_id_ : core::chemical::ResConnID
• res_identities_i_ : core::scoring::bin_transitions::BinTransitionData
• res_identities_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• 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_is_mirrored_ : core::conformation::symmetry::MirrorSymmetricConformation
• res_it_ : protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T >
• res_labels_ : core::scoring::packstat::SimplePDB
• res_last : protocols::rbsegment_relax::RBResidueRange
• res_links_ : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• res_list_ : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::SubMotifInfo , core::scoring::methods::ReferenceEnergyNoncanonical , protocols::noesy_assign::FloatingResonance
• res_low_ : protocols::cryst::SetRefinementOptionsMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• res_map_ : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::farna::libraries::ChunkSet , protocols::simple_moves::CopyDofMover , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• res_min_data_ : core::scoring::MinimizationNode
• res_name1_ : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences
• res_name2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_name3_str_ : core::select::residue_selector::ResidueNameSelector
• res_name_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , protocols::simple_moves::MutateResidue
• res_name_str_ : core::select::residue_selector::ResidueNameSelector
• 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_add_in_full_model_numbering_ : protocols::stepwise::monte_carlo::mover::AddMover
• res_to_average_hASA_ : core::pack::interaction_graph::SurfacePotential
• res_to_build_off_in_full_model_numbering_ : protocols::stepwise::monte_carlo::mover::AddMover
• res_to_superimpose_ : protocols::enzdes::EnzdesBaseProtocol
• res_type_linking_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• res_type_set_ : protocols::sewing::scoring::MotifScorer
• res_type_set_name_ : core::chemical::Patch
• res_types_ : protocols::simple_filters::ResidueCountFilter
• resA_ : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resA_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• resA_basename_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resAdjustmentAfterLoop_ : protocols::pose_length_moves::PossibleLoop
• resAdjustmentBeforeLoop_ : protocols::pose_length_moves::PossibleLoop
• resAdjustmentStartHigh_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStartHigh_sheet_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStartLow_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStartLow_sheet_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStopHigh_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStopHigh_sheet_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStopLow_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAdjustmentStopLow_sheet_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• resAfterLoop_ : protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_length_moves::PossibleLoop
• resample_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• 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_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resBeforeLoop_ : protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_length_moves::PossibleLoop
• rescore_only_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• rescover : core::scoring::motif::MotifHits
• reserve_size_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• reset_ : protocols::cyclic_peptide::PeptideStubMover
• reset_baselines_ : protocols::simple_moves::GenericMonteCarloMover
• reset_count_ : protocols::contact_map::ContactMap
• reset_delta_filters_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• reset_filters_ : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter
• reset_grid_bb_ : protocols::match::downstream::ActiveSiteGrid
• reset_mode_ : protocols::helical_bundle::BundleGridSampler
• reset_pose_ : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix
• reset_slide_ : protocols::simple_moves::symmetry::SymmetrySlider
• resfile_ : protocols::docking::DockTaskFactory , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::forge::components::BDR , protocols::ligand_docking::HighResDocker , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• resfile_1_ : protocols::anchored_design::AnchorMoversData
• resfile_2_ : protocols::anchored_design::AnchorMoversData
• resfile_cache_ : core::pack::task::operation::ReadResfile
• resfile_filename_ : core::pack::task::operation::ReadResfile
• resfile_general_property_ : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_name_ : protocols::pack_daemon::StructureFileNames , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_prefix_ : protocols::simple_filters::SaveResfileToDiskFilter
• resfile_suffix_ : protocols::simple_filters::SaveResfileToDiskFilter
• resfilename_ : protocols::enzdes::DetectProteinLigandInterface
• resfiles_ : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• reshash_ : protocols::sic_dock::scores::MotifHashRigidScore
• resi : protocols::toolbox::Node
• resi1_ : core::scoring::motif::ResPairMotif
• resi2_ : core::scoring::motif::ResPairMotif
• resi_ : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• resID : protocols::sparta::RingData
• resID1 : core::io::LinkInformation , core::io::SSBondInformation
• resid1_ : protocols::enzdes::DiffAtomSasaFilter
• resID2 : core::io::LinkInformation , core::io::SSBondInformation
• resid2_ : protocols::enzdes::DiffAtomSasaFilter
• resid_ : core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RotamerExplosion , protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::ResidueTorsionRestraints , protocols::moves::ResId , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• 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_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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
• residual_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• residue : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::Atom
• residue1 : core::scoring::motif::MotifHit
• residue1_ : protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter
• residue2 : core::scoring::motif::MotifHit
• residue2_ : protocols::simple_filters::AtomicDistanceFilter
• residue_ : core::conformation::UltraLightResidue , protocols::hotspot_hashing::HotspotStub , protocols::ncbb::SecStructFinder , protocols::pose_length_moves::InsertResMover , protocols::qsar::qsarMap , protocols::qsar::qsarPoint , protocols::simple_filters::ResidueBurialFilter
• residue_alternative_rotamer_list_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• residue_alternative_rotamer_map_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• residue_alternative_sets_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler
• residue_alternatives_rotamer_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• 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_covered_by_template_ : protocols::hybridization::ChunkTrialMover
• residue_dbio_ : protocols::features::ResidueTypesFeatures
• residue_decomposition_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_dEdN_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• residue_E_ : core::scoring::membrane::FaMPEnvSmoothEnergy , 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::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_group_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• residue_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_hsasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_id_ : core::conformation::AtomGraphVertexData
• residue_index_ : protocols::ligand_docking::AddHydrogen
• residue_indices_ : core::pack::task::operation::OperateOnCertainResidues , protocols::helical_bundle::BackboneGridSamplerHelper
• residue_info_ : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::MultipoleElecRotamerSetInfo , core::scoring::VdWTinkerPoseInfo , core::scoring::VdWTinkerRotamerSetInfo
• residue_level_tasks_for_placed_hotspots_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• residue_list_ : core::conformation::parametric::Parameters , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::simple_moves::RingConformationMover , protocols::simple_moves::Tumble
• residue_map_ : core::pose::reference_pose::ReferencePose
• residue_max_registry_shift_ : protocols::hybridization::HybridizeProtocol
• residue_N_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_name_ : protocols::helical_bundle::MakeBundleHelix , 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 , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• residue_numbers_ : core::io::silent::SilentStruct , 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_rel_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_sample_abinitio_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• residue_sample_template_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• residue_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy
• residue_sasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_score_term_weights_ : core::scoring::SplitUnfoldedTwoBodyPotential
• 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_selector_ : core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::ReadResfile
• residue_semiexpl_score_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• 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_two_body_energies_ : core::scoring::SplitUnfoldedTwoBodyPotential
• residue_type_ : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::rna::RNA_ResidueType , protocols::sewing::SewResidue , protocols::simple_moves::MinimalRotamer
• residue_type_base_name_ : core::chemical::ResidueTypeFinder
• residue_type_base_names_ : core::io::StructFileRep
• 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::chemical::ResidueTypeFinder , core::import_pose::ImportPoseOptions , core::io::pose_from_sfr::PoseFromSFRBuilder , protocols::simple_moves::ExtendedPoseMover
• residue_type_set_tag_ : core::chemical::ResidueLoaderOptions
• residue_type_sets_ : core::chemical::ChemicalManager
• residue_types_ : core::io::pose_from_sfr::PoseFromSFRBuilder , core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos , protocols::simple_filters::NeighborTypeFilter
• residue_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• residue_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_variants_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• residue_was_recognized_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• ResiduePairJumps_ : protocols::jumping::ResiduePairJumpSetup
• residues : protocols::forge::remodel::Segment , protocols::ligand_docking::Ligand_info , protocols::pockets::PocketExemplarMultifunc
• residues1_ : protocols::simple_filters::ShapeComplementarityFilter
• residues2_ : protocols::simple_filters::ShapeComplementarityFilter
• residues_ : core::conformation::Conformation , core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::scoring::packing::HolesParamsRes , protocols::frag_picker::VallChunk , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::jumping::ResiduePairJump , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::pockets::PocketConstraint , protocols::pose_reporters::RMSDReporter , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::sewing::SewSegment , protocols::simple_moves::SetTorsion , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::viewer::ConformationViewer
• residues_considered_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• residues_contact_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• residues_for_atom_name_remapping_ : core::io::StructFileRepOptions
• residues_for_each_type_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• residues_in_interface_threshold_ : protocols::simple_filters::ResiduesInInterfaceFilter
• residues_info_ : core::scoring::lkball::LKB_ResiduesInfo
• residues_per_repeat_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::helical_bundle::parameters::BundleParameters
• residues_to_exclude_ : protocols::hybridization::CartesianSampler
• residues_to_include_ : protocols::hybridization::CartesianSampler
• 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_ : core::pose::ResidueIndexDescription
• resize_vol_every_ : protocols::simple_moves::PeriodicBoxMover
• resl_params_ : core::scoring::packing::HolesEnergy
• resl_score : core::scoring::packing::HolesResult
• reslist_ : protocols::sic_dock::scores::MotifHashRigidScore
• resmap1_ : core::scoring::motif::MotifHits
• resmap2_ : core::scoring::motif::MotifHits
• resn_ : protocols::membrane::MPMutateRelaxMover
• resName : core::io::AtomInformation , core::io::ModifiedResidueInformation
• resname : protocols::forge::remodel::LineObject
• resName : protocols::sparta::CORdata , protocols::sparta::RingData
• resName1 : core::io::LinkInformation , core::io::SSBondInformation
• resName2 : core::io::LinkInformation , core::io::SSBondInformation
• resName_ : core::io::ResidueInformation
• resname_ : protocols::contact_map::ContactPartner , protocols::helical_bundle::BackboneGridSampler , protocols::jd2::parser::BluePrint , protocols::metal_interface::MetalSiteResidue , protocols::simple_moves::IonizableResidue
• resnames_ : protocols::protein_interface_design::movers::HotspotHasherMover
• resno_ : protocols::scoring::ImplicitFastClashCheck
• resnum : core::scoring::packstat::SimplePDB_Atom , protocols::antibody::design::PDBNumbering , protocols::sewing::Basis , protocols::sewing::HashValue
• resNum : protocols::sparta::CORdata
• resnum_ : core::pack::task::operation::AppendResidueRotamerSet , protocols::antibody::PDBLandmark , protocols::comparative_modeling::features::ResidueFeature , protocols::enzdes::EnzScoreFilter , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::jd2::parser::BluePrint , protocols::protein_interface_design::filters::HbondsToAtomFilter , 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::SetAtomTree , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::TryRotamers , protocols::sewing::SewResidue , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::SetChiMover
• resnum_map_ : protocols::jd2::parser::BluePrint
• resnum_str_ : protocols::simple_filters::ResidueIEFilter
• resnums_allow_design_ : protocols::toolbox::task_operations::DesignAroundOperation
• reso : core::scoring::electron_density::ElectronDensity
• resolution : protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence
• resolution_ : protocols::qsar::scoring_grid::GridManager
• 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
• respair_evaluators_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respos_from_external_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• resSeq : core::io::AtomInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• resSeq1 : core::io::LinkInformation , core::io::SSBondInformation
• resSeq2 : core::io::LinkInformation , core::io::SSBondInformation
• resSeq_ : core::io::ResidueInformation
• ResSurfaceFullList : protocols::sparta::PDB
• ResSurfacePartList : protocols::sparta::PDB
• restart_mode_ : protocols::forge::components::VarLengthBuild
• restore_ : protocols::rbsegment_relax::MakeStarTopologyMover
• restore_csts_ : protocols::hybridization::CartesianSampler
• restore_pose_ : protocols::rosetta_scripts::SavePoseMover
• restraints_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• restrict_design_operation_ : protocols::antibody::design::GeneralAntibodyModeler
• restrict_identities_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_only_design_ : protocols::toolbox::task_operations::RestrictToLoops
• restrict_partners_to_chains_ : protocols::analysis::PeptideDeriverFilter
• restrict_receptors_to_chains_ : protocols::analysis::PeptideDeriverFilter
• restrict_restypes_ : protocols::flxbb::LayerDesignOperation
• restrict_to_aligned_segments_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_interface_ : protocols::docking::DockTaskFactory
• restrict_to_nbrhood_ : protocols::ddg::ddGMover
• restrict_to_repacking_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_wt_ : protocols::motifs::MotifSearch
• restricted_aatypes_for_selection_ : core::select::util::SelectResiduesByLayer
• restrictSize_ : protocols::pockets::PocketGrid
• restype2_ : core::chemical::AutomorphismIterator
• restype_ : core::chemical::AutomorphismIterator , core::chemical::orbitals::AssignOrbitals , core::chemical::RerootEdgeSorter , core::chemical::RerootRestypeVisitor , core::chemical::RigidDistanceVisitor , core::pack::dunbrack::RotamerConstraint , protocols::enzdes::ResidueConformerFilter , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::upstream::BuildSet
• resType_ : protocols::pose_length_moves::InsertResMover
• restype_ : 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::enzdes::EnzdesBaseProtocol , protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• resTypeAfterLoop_ : protocols::pose_length_moves::PossibleLoop
• resTypeBeforeLoop_ : protocols::pose_length_moves::PossibleLoop
• restypegroup_adjacency_ : core::pack::interaction_graph::SymmOnTheFlyEdge
• restypeinfo_ : core::scoring::FACTSResidueInfo
• result : core::scoring::APBSWrapper
• result_ : protocols::environment::EnvClaimBroker
• result_hack_awful_1 : protocols::sic_dock::NoPoseXYX_Func
• result_hack_awful_2 : protocols::sic_dock::NoPoseXYX_Func
• result_query_string_ : protocols::wum::DatabaseEntryWorkUnit
• results : core::scoring::sc::MolecularSurfaceCalculator
• resume_support_ : protocols::rosetta_scripts::ParsedProtocol
• retrieve_index : protocols::loophash::FilterBucket
• retry_count_ : protocols::jd2::FileSystemJobDistributor
• return_centroid_ : protocols::abinitio::Protocol
• return_pseudo_hits_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_single_random_match_ : protocols::match::MatcherMover
• return_val_ : core::scoring::func::ConstantFunc
• reverse_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• reverse_connections_ : protocols::sewing::SegmentGraph
• reverse_mapping_ : protocols::abinitio::Template
• reversion_scan_ : protocols::dna::DnaInterfacePacker
• revert_to_template_ : protocols::toolbox::task_operations::DatabaseThread
• revision_id_ : core::scoring::constraints::ConstraintSet , protocols::match::OccupiedSpaceHash
• revision_id_current_ : core::scoring::constraints::ConstraintSet
• REWARD : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• reweight_ : core::scoring::methods::D2H_SA_Energy
• reweight_stride_ : protocols::canonical_sampling::SimulatedTempering
• reweight_symm_interactions_ : core::conformation::symmetry::SymmetryInfo
• rg : core::scoring::methods::RG_MinData
• rg_ : core::scoring::rna::RG_Energy_RNA
• rg_atom1_ : protocols::simple_moves::PeriodicBoxMover
• rg_atom2_ : protocols::simple_moves::PeriodicBoxMover
• RGF_ : protocols::forge::remodel::RemodelLoopMover
• rgstr_shift_ : protocols::fldsgn::topology::StrandPairing
• rh_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• rho : protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum
• rho_ : core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore
• rho_cylindrical_ : core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• rhoC_ : protocols::electron_density::BfactorMultifunc , protocols::electron_density::VoxelSpacingMultifunc
• rhoMask_ : protocols::electron_density::BfactorMultifunc
• 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::claims::DofClaim
• right_cdf_ : core::scoring::Ramachandran2B
• right_cdf_by_torsion_bin_ : core::scoring::Ramachandran2B
• right_position_ : protocols::forge::build::ConnectRight
• right_ram_probabil_ : core::scoring::Ramachandran2B
• right_stub_atoms_ : protocols::forge::build::ConnectRight
• rigid_ : protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• 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::DockingInitialPerturbation , protocols::docking::DockSetupMover
• rigid_body_modeler_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rigid_body_mover_ : protocols::farna::RNA_FragmentMonteCarlo , protocols::simple_moves::CoupledMover
• rigid_body_rotamer_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• 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
• rinfo_ : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback
• rinfos_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• ring_ : core::chemical::Bond
• ring_affixes_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• ring_atoms_ : core::chemical::ResidueType
• ring_atoms_indices_ : core::chemical::ResidueType
• 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 , core::chemical::rings::RingConformerSet
• ring_size_to_morphemes_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• ring_sizes_ : core::chemical::ResidueType
• ringFact : protocols::sparta::RingData
• RingNo : protocols::sparta::PDB
• Rings : protocols::sparta::PDB
• rings_and_their_edges_ : core::chemical::ResidueType
• rise_ : protocols::dna::DNABasestep , protocols::forge::remodel::RemodelGlobalFrame
• rKirkwood_ : core::scoring::MultipoleElecResidueInfo
• rltoc_map_ : core::pack::task::operation::ResLvlTaskOperationFactory
• rm_virt_phosphate_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• Rmax : core::scoring::fiber_diffraction::FiberDiffraction
• rmax_ : core::scoring::func::MixtureFunc , protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• rmdl_attempts_ : protocols::fldsgn::BluePrintBDR
• rms : core::scoring::motif::MotifHit
• rms_ : protocols::optimize_weights::SingleStructureData , protocols::seeded_abinitio::SegmentHybridizer
• rms_all_rpked_ : protocols::enzdes::RepackWithoutLigandFilter
• rms_cutoff_ : protocols::hybridization::CartesianSampler
• rms_group_cutoff_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• rms_limit_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• rms_offset_ : protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixMultiFunc
• rms_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• rms_target_ : core::scoring::methods::RMS_Energy
• rms_threshold_ : protocols::enzdes::RepackWithoutLigandFilter
• rmsd : protocols::ligand_docking::Transform_info
• RMSD : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• rmsd : protocols::pockets::SmallMol , protocols::simple_moves::LookupResultPlus
• RMSD : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• rmsd : protocols::stepwise::modeler::rna::output_data_struct
• rmsd_ : core::scoring::ResidualDipolarCoupling , protocols::anchored_design::AnchoredDesignMover , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWisePoseAligner
• rmsd_ca_list_ : protocols::toolbox::KClusterData
• rmsd_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• rmsd_cutoff_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::screener::AlignRMSD_Screener
• rmsd_cutoff_1_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_cutoff_2_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_cutoff_goodfrag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• rmsd_lookup_thresh_ : protocols::simple_filters::LeastNativeLike9merFilter
• rmsd_max_cutoff_ : protocols::farna::movers::RNA_Relaxer
• rmsd_min_cutoff_ : protocols::farna::movers::RNA_Relaxer
• rmsd_norm : protocols::simple_moves::LookupResultPlus
• 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::ChiWellRmsdEvaluator , protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::SymmetricRmsdEvaluator
• rmsd_res_in_pose_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• rmsd_screen_ : protocols::stepwise::options::StepWiseBasicOptions
• 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::stepwise::modeler::rna::output_data_struct
• rmsd_wrt_minimized : protocols::stepwise::modeler::rna::output_data_struct
• rmsd_wt_ : protocols::simple_filters::SymmetricMotifFilter
• rmsdcut_ : protocols::simple_moves::CombinePoseMover
• rmsThreshold_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::simple_moves::StructProfileMover
• rN : protocols::sparta::PDB , protocols::sparta::Sparta::SpartaLib
• rna_add_mover_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• rna_add_or_delete_mover_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• rna_atom_vdw_ : core::scoring::rna::RNA_VDW_Energy , core::scoring::ScoringManager
• rna_atr_rep_checker_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• 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_base_pair_handler_ : protocols::farna::RNA_FragmentMonteCarlo
• 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_bulge_bonus_once_per_loop_ : core::scoring::rna::RNA_BulgeEnergy
• rna_centroid_info_ : core::scoring::rna::RNA_ScoringInfo , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• rna_ch_o_bond_distance_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_chain_break_gap_sizes_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_chain_closable_geometry_checkers_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_chain_closure_checkers_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_chemical_shift_potential_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::ScoringManager
• rna_chunk_library_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo
• 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_cutpoints_closed_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_data_ : core::scoring::rna::data::RNA_DataInfo
• rna_data_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_data_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_data_info_with_conventional_numbering_ : core::io::rna::RNA_DataReader
• rna_data_reader_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_de_novo_pose_setup_ : protocols::farna::RNA_FragmentMonteCarlo
• rna_delete_mover_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• rna_dms_low_resolution_potential_ : core::scoring::ScoringManager
• rna_dms_potential_ : core::scoring::ScoringManager
• rna_filtered_base_base_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_fitted_torsion_info_ : core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionPotential , protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• rna_five_prime_chain_breaks_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_fragment_libraries_ : protocols::farna::libraries::RNA_LibraryManager
• rna_fragment_monte_carlo_ : protocols::farna::FARNA_Optimizer , protocols::farna::RNA_DeNovoProtocol
• rna_fragment_mover_ : protocols::farna::movers::RNA_Relaxer , protocols::farna::RNA_FragmentMonteCarlo
• rna_fragments_ : protocols::farna::movers::RNA_FragmentMover
• rna_from_scratch_mover_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• rna_gaussian_variance_per_residue_ : core::scoring::loop_graph::LoopGraph
• rna_jump_libraries_ : protocols::farna::libraries::RNA_LibraryManager
• rna_jump_library_ : protocols::farna::movers::RNA_JumpMover
• rna_jump_mover_ : protocols::farna::RNA_FragmentMonteCarlo
• rna_legacy_output_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• rna_loop_closer_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::MultipleDomainMover , protocols::farna::RNA_FragmentMonteCarlo
• rna_low_resolution_potential_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::ScoringManager
• rna_mg_knowledge_based_potential_ : core::scoring::magnesium::RNA_MgPointEnergy
• rna_minimizer_ : protocols::farna::movers::RNA_Relaxer , protocols::farna::RNA_FragmentMonteCarlo
• rna_o2prime_mover_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• rna_options_ : core::scoring::methods::EnergyMethodOptions
• rna_pairing_list_ : protocols::farna::base_pairs::RNA_BasePairHandler , protocols::farna::movers::RNA_JumpMover , protocols::farna::setup::RNA_DeNovoParameters
• rna_pairing_template_map_ : protocols::farna::libraries::RNA_JumpLibrary
• rna_params_ : protocols::farna::setup::RNA_DeNovoPoseSetup
• rna_params_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• rna_raw_base_base_info_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_ScoringInfo
• rna_reactivities_ : core::scoring::rna::data::RNA_DataInfo
• rna_relaxer_ : protocols::farna::RNA_FragmentMonteCarlo
• 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_residue_type_ : core::chemical::ResidueType
• rna_secstruct_ : protocols::farna::secstruct::RNA_SecStructInfo , protocols::farna::setup::RNA_DeNovoParameters
• rna_stagger_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_structure_parameters_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• rna_sugar_close_constraints_ : core::scoring::rna::RNA_SugarCloseEnergy
• rna_suite_name_ : core::scoring::rna::RNA_SuitePotential
• rna_suite_potential_ : core::scoring::rna::RNA_SuiteEnergy
• rna_suite_potential_for_suiteness_bonus_ : core::scoring::rna::RNA_SuiteEnergy
• rna_task_ : core::pack::task::ResidueLevelTask_
• rna_three_prime_chain_breaks_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_tight_torsions_ : core::chemical::rna::RNA_FittedTorsionInfo
• rna_torsion_mover_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• rna_torsion_potential_ : core::scoring::rna::RNA_TorsionEnergy
• rna_vdw_atom_ : core::scoring::rna::RNA_AtomVDW
• rna_vdw_parameter_ : core::scoring::rna::RNA_AtomVDW
• rna_verbose_ : core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_LowResolutionPotential
• rna_virt_sugar_atr_rep_checker_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rnl_pose_ : protocols::enzdes::EnzdesScorefileFilter
• roll_ : protocols::dna::DNABasestep
• root_ : core::chemical::RerootRestypeVisitor , core::conformation::symmetry::SymmData , core::kinematics::AtomTree , protocols::jumping::ResiduePairJumpSetup , protocols::topology_broker::CoordConstraintClaimer
• root_at_first_rigid_body_ : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::setup::RNA_DeNovoPoseSetup
• root_atom_ : core::chemical::ResidueType , core::scoring::methods::GoapRsdType
• root_expression_ : protocols::pack_daemon::SurrogateVariableExpression
• root_from_label_ : protocols::topology_broker::CoordConstraintClaimer
• root_partition_res_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• rooted_chunk_indices_ : protocols::hybridization::HybridizeFoldtreeDynamic
• rosetta2methyl_ : protocols::noesy_assign::MethylNames
• rosetta2nmr_ : protocols::noesy_assign::MethylNames
• rosetta_atom_name_ : core::chemical::AddAtomAlias
• rosetta_res_type_ : core::scoring::MultipoleElecResidueInfo
• rosetta_residue_name3s_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• ROSETTA_SASA_radii_ : core::pack::interaction_graph::RotamerDotsRadiusData
• rosetta_script_file_ : protocols::jd2::archive::Batch
• rosetta_scripts_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_build_disulfide_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_bypass_fragments_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_fast_disulfide_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_include_current_ds_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_keep_current_ds_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_match_rt_limit_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_max_disulfides_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_min_disulfides_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_min_loop_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_quick_and_dirty_ : protocols::forge::remodel::RemodelMover
• rosetta_scripts_tag_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover
• rosettascripts_filter_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• rosettascripts_filter_exists_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• rot : core::pack::dunbrack::ChiSet
• rot_bin_ : core::pack::dunbrack::DunbrackConstraint
• rot_center_ : protocols::membrane::RotationMover , 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::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::cryst::DockLatticeMover , protocols::farna::MultipleDomainMover , protocols::membrane::RandomPositionRotationMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• rot_mag_in_ : protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::topology_broker::RigidBodyRandomTMHMover
• rot_mag_smooth_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover
• rot_magnitude_ : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• rot_mat_ : protocols::pockets::PocketGrid
• rot_num : protocols::make_rot_lib::CentroidRotNum
• rot_number_ : protocols::optimize_weights::PNatAAOptERotamerData
• rot_prob_accumulation_limit_ : protocols::match::upstream::BuildSet
• rot_sets_ : protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• rot_step_ : protocols::simple_moves::PeriodicBoxMover
• 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::dunbrack::RotamericData< T, N > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots
• rotamer_aa_ : core::chemical::ResidueType
• rotamer_boltzmann_weight_ : protocols::features::RotamerBoltzmannWeightFeatures
• rotamer_combo_indexer_ : protocols::match::output::SameRotamerComboGrouper
• rotamer_couplings_ : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::task::operation::SetRotamerCouplings , core::pack::task::PackerTask_
• rotamer_energies_ : core::pack::interaction_graph::DoubleDensePDNode
• 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
• rotamer_library_specification_ : core::chemical::ResidueType
• rotamer_links_ : core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::task::operation::SetRotamerLinks , core::pack::task::PackerTask_
• rotamer_list_ : protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• 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, N, 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::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• rotamer_set_operation_ : core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamerSet
• rotamer_sets_ : core::pack::annealer::FASTERAnnealer , core::pack::annealer::RotamerAssigningAnnealer , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::rotamer_set::ContinuousRotamerSets , protocols::motifs::IRCollection , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• rotamer_well_counts_ : protocols::optimize_weights::PNatRotOptEPositionData
• rotamerid : core::pack::annealer::RotSub
• rotamers_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::make_rot_lib::MakeRotLibMover
• rotamers_in_subtree_ : core::scoring::trie::TrieNode< AT, CPDATA >
• rotamers_recovered_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• rotamers_vector_ : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• rotamersets_p_ : protocols::multistate_design::PackingState
• rotate_anchor_to_x_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover
• 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_ : protocols::electron_density::RBfitResult
• rotation_axes_ : protocols::matdes::SymDofMover
• rotation_mag_ : protocols::rigid::MembraneNormalPerturbationMover , protocols::rigid::UniformRigidBodyMover , protocols::topology_broker::TMHTopologySamplerClaimer
• rotation_magnitude_ : protocols::simple_moves::CoupledMover
• rotation_matrices_ : core::conformation::symmetry::SymmData
• rotation_matrix_ : protocols::rigid::RigidBodyRandomizeMover
• rotation_std_dev_ : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• rotlib_ : core::pack::dunbrack::RotamerConstraint
• RotM : protocols::motif_grafting::movers::motif2scaffold_data
• rotno_2_packed_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• rots2add_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rots_for_nodes_ : core::pack::annealer::RotamerAssigningAnnealer
• rotset_ : protocols::protein_interface_design::movers::TryRotamers , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• rotsetops_ : core::pack::task::ResidueLevelTask_
• rotsets_ : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::jumping::ResiduePairJump
• rottrials_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• rotwell_ : core::pack::dunbrack::DunbrackRotamer< S, N, P > , core::pack::dunbrack::RotamerLibraryScratchSpace
• rotwell_exists_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• rotx : protocols::loophash::LegacyLeapIndex
• roty : protocols::loophash::LegacyLeapIndex
• rotz : protocols::loophash::LegacyLeapIndex
• rounds_ : protocols::carbohydrates::GlycanRelaxMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::RNA_FragmentMonteCarlo , protocols::relax::CentroidRelax
• roundtype : protocols::mpi_refinement::MethodParams
• row_format_ : protocols::contact_map::ContactMap
• row_map_ : protocols::wum::DatabaseEntryWorkUnit
• row_names_ : protocols::contact_map::ContactMap
• rp : core::scoring::fiber_diffraction::Hankel , core::scoring::sc::MolecularSurfaceCalculator
• rp0 : core::scoring::fiber_diffraction::Hankel
• rp_ : protocols::forge::build::RelativeConnectRight
• rsa_class_pred_ : core::scoring::methods::ProQ_Energy
• rsa_index_end_ : core::scoring::methods::D2H_SA_Energy
• rsa_index_start_ : core::scoring::methods::D2H_SA_Energy
• rsa_pred_ : core::scoring::methods::ProQ_Energy
• Rscale_factor : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• rsd1_ : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::scoring::func::ResiduePairXYZ
• rsd1_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd2_ : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::scoring::func::ResiduePairXYZ
• rsd2_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd_ : core::chemical::GraphvizPropertyWriter , core::id::AtomID , core::id::NamedAtomID , core::id::TorsionID , core::scoring::AtomNeighbor , core::scoring::func::ResidueXYZ , protocols::kinmatch::FunGroupTK , protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• rsd_hsasa_ : core::scoring::sasa::SasaCalc
• rsd_hsasa_sc_ : core::scoring::sasa::SasaCalc
• rsd_id_ : core::optimization::SingleResidueMultifunc , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• rsd_layer_ : core::select::util::SelectResiduesByLayer
• rsd_neighbor_denominator_ : core::select::util::SelectResiduesByLayer
• RSD_OMG_INDEX : core::pack::rotamers::SingleResiduePeptoidLibrary
• RSD_PHI_INDEX : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• RSD_PSI_INDEX : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• rsd_sasa_ : core::scoring::sasa::SasaCalc , core::select::util::SelectResiduesByLayer
• rsd_sasa_sc_ : core::scoring::sasa::SasaCalc
• rsd_set_ : protocols::jd2::PoseInputStreamJobInputter , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• rsd_type_ : core::conformation::Residue , core::scoring::lkball::LKB_ResidueInfo
• rsd_type_name3_ : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint
• rsd_type_name_ : core::pack::dunbrack::RotamerConstraint
• rsd_type_ptr_ : core::conformation::Residue
• rsd_type_set_ : core::chemical::ResidueTypeSetCache , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::topology_broker::SequenceClaimer
• rsd_wdw_size_ : protocols::hybridization::FragmentBiasAssigner
• rsd_wdw_to_refine_ : protocols::hybridization::CartesianSampler
• rsdgrps_ : core::scoring::elec::GroupElec
• rsdtype_ : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent
• rsdtypemap_ : core::scoring::methods::GoapEnergy
• rsigma_dot_ : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rsigma_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• rsrfilename_ : protocols::md::MDBase
• Rsum_obs : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• rswitch_ : core::scoring::constraints::BoundFunc
• RT : core::scoring::dna::DirectReadoutPotential
• rt6_ : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfrag
• rt_ : core::fragment::DownJumpSRFD , core::kinematics::Jump , protocols::forge::build::ConnectRight , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• rt_min_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol
• rtmin_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockMCMCycle , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::RelativePoseFilter , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• rtmin_mover_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• rts_ : protocols::forge::build::BuildInstruction
• run_ : core::scoring::sc::MolecularSurfaceCalculator , protocols::abinitio::FoldConstraints
• run_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• run_graft_designer_ : protocols::antibody::design::AntibodyDesignProtocol
• run_kic_ : protocols::cyclic_peptide::DeclareBond
• run_motifs_ : protocols::motifs::MotifDnaPacker
• run_relax_ : protocols::antibody::design::AntibodyDesignProtocol
• run_snugdock_ : protocols::antibody::design::AntibodyDesignProtocol
• RV : core::scoring::electron_density::ElectronDensity
• rv_infos_ : protocols::forge::remodel::ResidueVicinityRCG
• rvjump_pose : protocols::forge::remodel::RemodelWorkingSet