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

- r -

• r0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• r0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• r1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::hybridization::TMalign , protocols::sparta::PDB , protocols::sparta::Sparta::SpartaLib
• r1_ : protocols::helical_bundle::parameters::BundleParameters
• r1_initial_ : protocols::helical_bundle::FitSimpleHelix
• r1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• r1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• r2 : protocols::hybridization::TMalign
• r21 : protocols::normalmode::ContactStruct
• r_handed_ : protocols::simple_filters::RepeatParameterFilter
• r_ids_ : protocols::scoring::methods::saxs::PDDFEnergy
• r_ik : protocols::cluster::Exemplar
• r_kk : protocols::cluster::DataPoint
• r_pose_ : protocols::simple_filters::MultipleSigmoids
• rad : protocols::sparta::RingData
• radial_count() : protocols::loophash::LoopHashMap
• radial_disp() : protocols::matdes::GetRBDOFValues
• 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_lookup() : protocols::loophash::LoopHashMap
• radial_lookup_withkey() : protocols::loophash::LoopHashMap
• radial_offsets_ : protocols::matdes::SymDofMover
• radii_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• radius() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• radius_ : 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
• RadiusOfGyrationFeatures() : protocols::features::RadiusOfGyrationFeatures
• RadiusOfGyrationFeaturesCreator() : protocols::features::RadiusOfGyrationFeaturesCreator
• rama() : protocols::hybridization::FragmentBiasAssigner , protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• rama_ : 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_delta() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• rama_params : protocols::relax::CentroidRelax::parameters
• rama_type_ : protocols::relax::CentroidRelax
• ramachandran_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• RamaCheck1B() : protocols::loops::loop_closure::ccd::RamaCheck1B
• RamaCheck2B() : protocols::loops::loop_closure::ccd::RamaCheck2B
• RamaCheckBase() : protocols::loops::loop_closure::ccd::RamaCheckBase
• 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
• RamaScore() : protocols::frag_picker::scores::RamaScore
• RamaScoreVector : protocols::loops::loop_closure::ccd::RamaCheckBase
• ramp_ : protocols::abinitio::CoordinateConstraintKC
• ramp_chainbreak() : protocols::loops::loop_closure::ccd::LoopClosure
• ramp_cst_cycles_ : protocols::abinitio::FoldConstraints
• ramp_down_constraints() : protocols::relax::RelaxProtocolBase
• ramp_down_constraints_ : protocols::relax::RelaxProtocolBase
• ramp_fa_rep : protocols::flexpep_docking::FlexPepDockingFlags , protocols::simple_moves::ShakeStructureMover
• ramp_iterations_ : protocols::abinitio::FoldConstraints
• ramp_minpack_loop2() : protocols::mpi_refinement::WorkUnit_Sampler
• ramp_one_weight_ : protocols::moves::RampingMover
• ramp_rama : protocols::flexpep_docking::FlexPepDockingFlags
• ramp_rama_ : protocols::relax::CentroidRelax
• ramp_score_function() : protocols::loop_modeling::LoopProtocol
• ramp_sfxn_rama_ : protocols::loop_modeling::LoopProtocol
• ramp_sfxn_rep_ : protocols::loop_modeling::LoopProtocol
• ramp_temp_ : protocols::loop_modeling::LoopProtocol
• ramp_temperature() : protocols::loop_modeling::LoopProtocol
• ramp_temperature_ : protocols::canonical_sampling::CanonicalSamplingMover
• ramp_vdw_ : protocols::relax::CentroidRelax
• ramp_weight : protocols::moves::TrialMover
• ramping_funcs_for_weights_ : protocols::moves::RampingMover
• ramping_scorefxn() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• ramping_scorefxn_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• RampingMover() : protocols::moves::RampingMover
• rand_ : protocols::rbsegment_relax::RBSegmentRelax
• rand_drop_rate_ : protocols::abinitio::abscript::ConstraintPreparer
• randfragprob_ : protocols::hybridization::CartesianHybridize
• randfragprob_stage2_ : protocols::hybridization::HybridizeProtocol
• randmove_ : protocols::canonical_sampling::CanonicalSamplingMover
• random() : protocols::stepwise::sampler::StepWiseSamplerBase
• random_ : protocols::stepwise::sampler::StepWiseSamplerBase
• random_access() : protocols::simple_moves::AddChainMover
• random_access_ : protocols::simple_moves::AddChainMover
• random_angle() : protocols::backrub::BackrubMover
• random_basepair() : protocols::dna::DNAParameters
• random_basestep() : protocols::dna::DNAParameters
• random_chain_closed_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• random_chunk() : protocols::nonlocal::SingleFragmentMover
• random_chunk_insertion() : protocols::farna::RNA_ChunkLibrary
• random_chunk_trial() : protocols::farna::RNA_DeNovoProtocol
• random_conformer() : protocols::ligand_docking::LigandDockProtocol
• random_conformer_ : protocols::docking::ConformerSwitchMover
• random_counter_ : protocols::jobdist::BaseJobDistributor
• random_domain_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• random_drop_rate() : protocols::abinitio::abscript::ConstraintPreparer
• random_entity() : protocols::genetic_algorithm::EntityRandomizer
• random_entry() : protocols::protein_interface_design::PatchdockReader
• random_entry_ : protocols::protein_interface_design::PatchdockReader
• random_flush_frequency_ : protocols::jd2::SilentFileJobOutputter
• random_fragment_insertion() : protocols::farna::RNA_FragmentMover
• random_fragment_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• random_grow_loops_by_ : protocols::topology_broker::RigidChunkClaimer
• random_jump_change() : protocols::farna::RNA_StructureParameters
• random_jump_trial() : protocols::farna::RNA_DeNovoProtocol
• random_limit_groupsize() : protocols::cluster::ClusterBase
• random_loop_flag_ : protocols::LoopRebuild
• random_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• random_mover_ : protocols::abinitio::abscript::AbscriptStageMover
• random_order_ : protocols::loops::loop_mover::IndependentLoopMover
• random_order_protocol() : protocols::rosetta_scripts::ParsedProtocol
• random_peptide_phi_psi_perturbation() : protocols::flexpep_docking::FlexPepDockingProtocol
• random_perturbation() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• 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_position() : protocols::nonlocal::BiasedFragmentMover
• random_rb_pert() : protocols::flexpep_docking::FlexPepDockingProtocol
• random_set_ : protocols::simple_moves::SetTorsion
• random_sheets_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• random_single_protocol() : protocols::rosetta_scripts::ParsedProtocol
• random_step_ : protocols::rigid::UniformSphereTransMover
• random_store_ : protocols::jobdist::BaseJobDistributor
• random_stub() : protocols::hotspot_hashing::HotspotStubSet
• random_template_ : protocols::hybridization::ChunkTrialMover
• random_torsion_move() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• random_torsion_strings_ : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• randomAngle() : protocols::pockets::PocketGrid
• RandomConformerMover() : protocols::ligand_docking::RandomConformerMover
• RandomConformers() : protocols::ligand_docking::RandomConformers
• randomize1_ : protocols::docking::DockingInitialPerturbation
• randomize2_ : protocols::docking::DockingInitialPerturbation
• randomize_bs() : protocols::cryst::FitBfactorsMover
• randomize_equiv_frag_ : protocols::forge::remodel::RemodelMover::instruction_flags
• randomize_input_ : protocols::jd2::MSDJobDistributor
• randomize_input_sequence() : protocols::anchored_design::AnchoredDesignMover
• randomize_input_sequence_ : protocols::anchored_design::AnchoredDesignMover
• randomize_loop() : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• 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_loop_coords_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• randomize_loops() : protocols::forge::remodel::RemodelLoopMover
• randomize_loops_ : protocols::forge::remodel::RemodelLoopMover
• randomize_order_ : protocols::ligand_docking::CompoundTranslate
• randomize_orientations() : protocols::farna::MultipleDomainMover
• randomize_pose_rigid_bodies() : protocols::farna::MultipleDomainMover
• randomize_resnum_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• randomize_rigid_body_orientations() : protocols::farna::RNA_DeNovoProtocol
• randomize_stage() : protocols::forge::remodel::RemodelLoopMover
• randomlySlidePeptideJump() : protocols::flexpep_docking::FlexPepDockingProtocol
• RandomMover() : protocols::moves::RandomMover
• RandomMutation() : protocols::protein_interface_design::movers::RandomMutation
• randomness_ : protocols::rbsegment_relax::RBSegmentRelax
• RandomOmegaFlipMover() : protocols::simple_moves::RandomOmegaFlipMover
• RandomPositionRotationMover() : protocols::membrane::RandomPositionRotationMover
• RandomPositionTranslationMover() : protocols::membrane::RandomPositionTranslationMover
• randomRBstart : protocols::flexpep_docking::FlexPepDockingFlags
• RandomSheetBuilder() : protocols::jumping::RandomSheetBuilder
• RandomSymmetrySlider() : protocols::simple_moves::symmetry::RandomSymmetrySlider
• RandomTorsionMover() : protocols::simple_moves::RandomTorsionMover
• range() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::simple_filters::DeltaFilter
• range1_ : protocols::simple_filters::AtomicContactFilter
• range_ : protocols::simple_filters::DeltaFilter
• range_squared_ : protocols::ligand_docking::ComputeLigandRDF
• RangeFilter() : protocols::simple_filters::RangeFilter
• rank() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering , protocols::jd2::MPIFileBufJobDistributor , protocols::wum2::StatusRequest , protocols::wum2::StatusResponse
• 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
• ranked_model() : protocols::abinitio::PairingStatistics
• ranking_cenfilter() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ranking_cenfilter_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ranking_fafilter() : protocols::loophash::LoopHashMoverWrapper
• ranking_fafilter_ : protocols::loophash::LoopHashMoverWrapper
• rate_threshold() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• rate_threshold_ : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• ratio_cutoff() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• ratio_cutoff_goodfrag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• RationalMonteCarlo() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• ratios_ : protocols::frag_picker::scores::ABEGO_SS_Score
• Rattle() : protocols::md::Rattle
• raw_data_dump() : protocols::wum::WorkUnitBase
• raw_data_load() : protocols::wum::WorkUnitBase
• raw_data_size() : protocols::wum::WorkUnitBase
• raw_probs_ : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• rawfile_name_ : protocols::jobdist::PlainRawJobDistributor
• rb_chunks_ : protocols::rbsegment_relax::AutoRBMover
• rb_delta_ : protocols::rigid::RigidBodyPerturbMover
• rb_jump() : protocols::rigid::RigidBodyMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ddG , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::task_operations::RestrictToInterface
• 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_jumps_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzRepackMinimize
• rb_min_post_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• rb_minimizable() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• rb_minimizable_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• rb_minimize_all_confs() : protocols::enzdes::MinimizeStoredRBConfs
• 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
• RBConfLists : protocols::enzdes::ModifyStoredRBConfs
• rbMCM : protocols::flexpep_docking::FlexPepDockingFlags
• RBResidueRange() : protocols::rbsegment_relax::RBResidueRange
• RBSegment() : protocols::rbsegment_relax::RBSegment
• RBSegmentMover() : protocols::rbsegment_relax::RBSegmentMover
• RBSegmentRelax() : protocols::rbsegment_relax::RBSegmentRelax
• RBSegmentRelaxImpl() : protocols::RBSegmentRelaxImpl
• 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
• rcFileName : protocols::sparta::Sparta::SpartaLib
• rcgs_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• RCR : protocols::sic_dock::Rose
• rd1_model : protocols::ss_prediction::SS_predictor
• rd2_model : protocols::ss_prediction::SS_predictor
• rdc_data_ : protocols::abinitio::IterativeBase , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::SelectRDC_Evaluator
• RDC_Evaluator() : protocols::simple_filters::RDC_Evaluator
• rdc_file_ : protocols::frag_picker::scores::RDCScore , protocols::simple_filters::SelectRDC_Evaluator
• RDC_lines : protocols::scoring::ResidualDipolarCouplingRigidSegments
• rdc_raw_data_ : protocols::frag_picker::scores::RDCScore
• RDC_Segments : protocols::scoring::ResidualDipolarCouplingRigidSegments
• rdc_segments_ : protocols::scoring::ResidualDipolarCouplingRigidSegments
• rdc_segments_from_pose() : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• RdcEvaluatorCreator() : protocols::simple_filters::RdcEvaluatorCreator
• rdcs_ : protocols::simple_filters::TruncatedScoreEvaluator
• RDCScore() : protocols::frag_picker::scores::RDCScore
• RdcSelectEvaluatorCreator() : protocols::simple_filters::RdcSelectEvaluatorCreator
• RdcTargetEvaluatorCreator() : protocols::simple_filters::RdcTargetEvaluatorCreator
• rdf_functions_ : protocols::ligand_docking::ComputeLigandRDF
• RDFBase() : protocols::ligand_docking::rdf::RDFBase
• RDFBinaryHbondFunction() : protocols::ligand_docking::rdf::RDFBinaryHbondFunction
• RDFBinaryOrbitalFunction() : protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction
• RDFChargeFunction() : protocols::ligand_docking::rdf::RDFChargeFunction
• RDFElecFunction() : protocols::ligand_docking::rdf::RDFElecFunction
• RDFEtableFunction() : protocols::ligand_docking::rdf::RDFEtableFunction
• RDFFunctionCreator() : protocols::ligand_docking::rdf::RDFFunctionCreator
• RDFFunctionCreatorMap : protocols::ligand_docking::rdf::RDFFunctionFactory
• RDFFunctionFactory() : protocols::ligand_docking::rdf::RDFFunctionFactory
• RDFFunctionRegistrator() : protocols::ligand_docking::rdf::RDFFunctionRegistrator< T >
• RDFHbondFunction() : protocols::ligand_docking::rdf::RDFHbondFunction
• RDFOrbitalFunction() : protocols::ligand_docking::rdf::RDFOrbitalFunction
• Rdimers : protocols::simple_filters::SymmetricMotifFilter
• re_init() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager , protocols::scoring::methods::pcs2::PcsInputCenterManager
• read() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::JCouplingIO , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::TorsionBinIO , protocols::toolbox::ClusterBase , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::TopologyClaimer
• read_adjust_table() : protocols::frag_picker::CS2ndShift
• read_all_variables_from_input_file() : protocols::pack_daemon::DynamicAggregateFunction
• read_anchorfile() : protocols::anchored_design::Anchor
• read_and_set_project_prefs() : protocols::boinc::Boinc
• read_and_store_fragments() : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::AntibodyModeler
• read_assignments() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_batch() : protocols::jd2::BatchJobInputter
• read_blueprint() : protocols::jd2::parser::BluePrint
• read_BooleanOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_BooleanVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_cdr_definition_file() : protocols::antibody::AntibodyNumberingParser
• read_cdr_definition_numbering_line() : protocols::antibody::AntibodyNumberingParser
• read_cdr_definition_transform_line() : protocols::antibody::AntibodyNumberingParser
• read_chain_connection() : protocols::farna::RNA_StructureParameters
• read_checkpoint() : protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::SingleStateEntityData
• read_checkpoint_file() : protocols::frag_picker::nonlocal::NonlocalFrags
• read_cmd() : protocols::mpi_refinement::Scheduler
• read_cmd_line_options() : protocols::antibody::design::AntibodyDesignMover
• read_coef1() : protocols::branch_angle::BranchAngleOptimizer
• read_coef1_default() : protocols::branch_angle::BranchAngleOptimizer
• read_coef1_user() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2_default() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2_user() : protocols::branch_angle::BranchAngleOptimizer
• read_command_line_options() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator
• read_config_file() : protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• read_constraints() : protocols::abinitio::Template , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore
• read_constraints_from_file() : protocols::topology_broker::CoordConstraintClaimer
• read_cst_pose() : protocols::topology_broker::CoordConstraintClaimer
• read_data() : protocols::hotspot_hashing::HotspotStubSet , protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList , protocols::toolbox::match_enzdes_util::ResInteractions
• read_Data_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_database() : protocols::branch_angle::BranchAngleOptimizer
• read_db() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_def() : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• read_default_parameters() : protocols::relax::CentroidRelax
• read_depth() : protocols::frag_picker::FragmentPicker
• read_done_jobs() : protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• read_eigvec_file() : protocols::evaluation::PCA
• read_entities_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• read_enzyme_cstfile() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• read_existing_batches() : protocols::jd2::archive::ArchiveManager
• read_exp_data() : protocols::ddG::ddGData
• read_fasta_file() : protocols::topology_broker::SequenceClaimer
• read_file() : protocols::frags::RMSVallData , protocols::frags::TorsionFragmentLibrary , protocols::frags::VallData , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup
• read_FileOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_FileVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_fragfiles_ : protocols::forge::remodel::RemodelMover::instruction_flags
• read_from_binary_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• read_from_cmd_line() : protocols::wum::SilentStructStore
• read_from_file() : protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary , protocols::noesy_assign::FragsToAtomDist , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::wum::SilentStructStore
• read_from_file_no_filters() : protocols::jumping::PairingLibrary
• read_from_pose() : protocols::loophash::BackboneSegment
• read_from_stream() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::ResonanceList , protocols::wum::SilentStructStore
• read_from_string() : protocols::wum::SilentStructStore
• read_generations_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• read_gridlig_file_ : protocols::match::Matcher
• read_H3_cter_fragment() : protocols::antibody::H3CterInsert
• read_header() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_homologs() : protocols::loophash::BackboneDB
• read_in_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• read_in_structures() : protocols::pmut_scan::PointMutScanDriver
• read_info_file() : protocols::jd2::archive::Batch
• read_input_files() : protocols::noesy_assign::NoesyModule
• read_input_pose_and_copy_dofs() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• read_IntegerOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_IntegerVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_jumps_from_file() : protocols::farna::RNA_JumpLibrary
• read_legacydb() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_ligand_superposition_file() : protocols::enzdes::EnzdesBaseProtocol
• read_loop_file() : protocols::loops::JSONFormattedLoopsFileReader , protocols::loops::Loops , protocols::loops::LoopsFileIO
• read_loop_file_stream() : protocols::loops::LoopsFileIO
• read_loops_file() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• read_loops_file_block() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• read_loops_options() : protocols::loops::Loops
• read_mover_weight() : protocols::topology_broker::TopologyClaimer
• read_mut_data() : protocols::ddG::ddGData
• read_mutants_list_file() : protocols::pmut_scan::PointMutScanDriver
• read_numbering_scheme_file() : protocols::antibody::AntibodyNumberingParser
• read_Option_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_options() : protocols::anchored_design::Anchor , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::anchored_design::AnchorMoversData , protocols::flxbb::FlxbbDesign , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::ConstraintSetMover
• read_pairings() : protocols::abinitio::Templates
• read_parameters_from_file() : protocols::farna::RNA_StructureParameters
• read_params() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• read_patchdock() : protocols::protein_interface_design::PatchdockReader
• read_patchdock_entry() : protocols::protein_interface_design::PatchdockReader
• read_PathOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_PathVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_PCS_file() : protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• read_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• read_peak() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_pose() : protocols::hybridization::TMalign
• read_pose_numbered_loops_file() : protocols::loops::PoseNumberedLoopFileReader
• read_poses() : protocols::docking::membrane::MPDockingSetupMover , protocols::protein_interface_design::PatchdockReader
• read_psipred_ss2() : protocols::frag_picker::FragmentPicker
• read_queue() : protocols::wum::WorkUnitManager
• read_queues_from_file() : protocols::wum::WorkUnitManager
• read_RDC_segment_file() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• read_RDC_segment_file_from_cmdline() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• read_RDCs_from_cmdline() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• read_RealOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_RealVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_reference_energies_from_file() : protocols::optimize_weights::IterativeOptEDriver
• read_ResidueType_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_resonances() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_resource_locator_items() : protocols::jd2::JD2ResourceManager
• read_resource_locators_tags() : protocols::jd2::JD2ResourceManager
• read_resource_option_item() : protocols::jd2::JD2ResourceManager
• read_resource_options_table_tag() : protocols::jd2::JD2ResourceManager
• read_resource_options_tag_item() : protocols::jd2::JD2ResourceManager
• read_resource_options_tags() : protocols::jd2::JD2ResourceManager
• read_resource_table_tag() : protocols::jd2::JD2ResourceManager
• read_resource_tag_item() : protocols::jd2::JD2ResourceManager
• read_resources_tags() : protocols::jd2::JD2ResourceManager
• read_returning_decoys() : protocols::jd2::archive::BaseArchiveManager
• read_scheme_defines_line() : protocols::antibody::AntibodyNumberingParser
• read_scheme_numbering_line() : protocols::antibody::AntibodyNumberingParser
• read_script_file() : protocols::relax::FastRelax
• read_secstruct_from_file() : protocols::farna::RNA_StructureParameters
• read_spanfiles() : protocols::docking::membrane::MPDockingSetupMover
• read_spine_x() : protocols::frag_picker::FragmentPicker
• read_ss_file() : protocols::frag_picker::FragmentPicker
• read_ss_files() : protocols::frag_picker::FragmentPicker
• read_sslimit_table() : protocols::frag_picker::CS2ndShift
• read_state_vector_file() : protocols::pack_daemon::DynamicAggregateFunction
• read_strength() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_StringOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_StringVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_structure() : protocols::evaluation::PCA
• read_structures() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive
• read_tag() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• read_tagfile_to_taskfactory() : protocols::optimize_weights::IterativeOptEDriver
• read_talos_phi_psi() : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::PhiPsiRmsd
• read_talos_ss() : protocols::frag_picker::FragmentPicker
• read_topol_file() : protocols::topology_broker::TemplateJumpClaimer
• read_type_ : protocols::jd2::parser::FragmentReader
• read_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• read_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• read_vall() : protocols::frag_picker::FragmentPicker
• read_vall_torsions() : protocols::farna::FullAtomRNA_Fragments
• read_work_unit() : protocols::wum::WorkUnitManager
• read_wt_data() : protocols::ddG::ddGData
• ReadResfileFromDB() : protocols::toolbox::task_operations::ReadResfileFromDB
• ready() : protocols::forge::build::BuildInstruction
• ready_for_batch() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom
• ready_for_exchange_ : protocols::canonical_sampling::AsyncMPITemperingBase
• ready_to_align() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• ready_to_align_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• Real : protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::enzdes::ModifyStoredRBConfs , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairing , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frag_picker::VallResidue , protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragment , protocols::frags::TorsionFragmentLibrary , protocols::frags::TorsionFragmentMover , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jd2::parser::BluePrint , protocols::loophash::FastGapMover , protocols::match::Bool3DGrid , protocols::match::Bool3DGridKinemageWriter , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherMover , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::output::BestMatchesCollection , protocols::match::output::MatchCollisionFilter , protocols::match::output::MatchConsolidator , protocols::match::output::MatchEvaluator , protocols::match::output::MatchGrouper , protocols::match::output::ProcessorFactory , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::SampleStrategyData , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::matdes::SymUnsatHbondFilter , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::MonteCarlo , protocols::moves::RampingFunc , protocols::moves::TrialMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::Transformation , protocols::rosetta_scripts::ParsedProtocol , protocols::scoring::Interface , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ddG , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::MinMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , Transformation
• Real3 : protocols::match::HitHasher , protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• Real6 : protocols::match::OccupiedSpaceHash , protocols::toolbox::match_enzdes_util::LigandConformer
• real_dof_deriviative_expressions_ : protocols::optimize_weights::WrapperOptEMultifunc
• real_value : protocols::simple_moves::AddJobPairData
• real_value_ : protocols::simple_moves::AddJobPairData
• realign_domains_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• realign_domains_stage2_ : protocols::hybridization::HybridizeProtocol
• Reals : protocols::sic_dock::RigidScore
• reassign_noesy_data() : protocols::abinitio::IterativeBase
• rebuild_atoms() : protocols::cyclic_peptide::PeptideStubMover
• rebuild_bulge_mode() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• rebuild_bulge_mode_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• rebuild_conformation() : protocols::helical_bundle::PerturbBundle
• rebuild_cycles_ : protocols::rbsegment_relax::OptimizeThreadingMover
• rebuild_filter() : protocols::comparative_modeling::LoopRelaxMover
• rebuild_filter_ : protocols::comparative_modeling::LoopRelaxMover
• rebuild_fold_tree_ : protocols::cyclic_peptide::DeclareBond
• rebuild_polymer_bond_dependent_atoms() : protocols::environment::ProtectedConformation
• rebuild_unaligned() : protocols::rbsegment_relax::OptimizeThreadingMover
• recal_foldtree : protocols::flexpep_docking::FlexPepDockingFlags
• recalculate_rmsd_and_output_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• recalculate_z_coordinate() : protocols::docking::EllipsoidalRandomizationMover
• receive_and_output_structures() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• receive_batch() : protocols::jd2::archive::MPIArchiveJobDistributor
• receive_exchange_requests() : protocols::canonical_sampling::AsyncMPITemperingBase
• receive_is_accepted() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• receive_message() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• receive_MPI_workunit() : protocols::wum::MPI_WorkUnitManager
• receive_newest_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• receive_silent_struct_any_source() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• receive_str() : protocols::jd2::MpiFileBuffer
• receive_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• received() : protocols::topology_broker::ClaimerMessage
• received_by_ : protocols::topology_broker::ClaimerMessage
• received_by_me() : protocols::topology_broker::ClaimerMessage
• recent_quota_score_ : protocols::frag_picker::scores::FragmentScoreMap
• recent_score() : protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter
• recent_total_ : protocols::frag_picker::scores::FragmentScoreMap
• recenter() : protocols::pockets::PocketGrid
• receptor_anchor_pos : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• recieve_daemon_inds_requiring_pose_creation() : protocols::pack_daemon::DaemonSet
• recieve_entity() : protocols::pack_daemon::DaemonSet
• recluster_current_pose_list() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• recompute() : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• recompute_and_print() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• RecomputeDensityMapMover() : protocols::cryst::RecomputeDensityMapMover
• reconstruct_dependencies() : protocols::forge::build::BuildManager
• record() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• record_chi() : protocols::simple_moves::MinimalRotamer
• record_helix_sasas() : protocols::features::helixAssembly::HelixBundleFeatures
• record_histograms() : protocols::backrub::BackrubSidechainMover
• record_internal_geometry() : protocols::simple_moves::MinimalRotamer
• record_inv6() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• record_job() : protocols::jd2::JD2ResourceManagerJobInputter
• record_match() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• record_statistics() : protocols::backrub::BackrubSidechainMover
• record_statistics_ : protocols::backrub::BackrubSidechainMover
• recorder_stream_ : protocols::canonical_sampling::MetricRecorder
• recover_checkpoint() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer , protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::nonlocal::NonlocalFrags
• recover_conformer_sidechains() : protocols::docking::DockingEnsemble
• recover_hit() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• recover_hits() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• recover_loops_from_file() : protocols::enzdes::EnzdesFlexBBProtocol
• recover_low() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::ligand_docking::RigidSearchMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_original_on_failure_ : protocols::forge::components::VarLengthBuild
• recover_poses_from_states() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• recover_relevant_poses_for_entity() : protocols::pack_daemon::MultistateFitnessFunction
• recover_sidechains() : protocols::symmetric_docking::SymDockProtocol
• recover_sidechains_ : protocols::docking::DockingProtocol
• recover_sidechains_filename_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• RecoverSideChainsMover() : protocols::comparative_modeling::RecoverSideChainsMover
• recovery_rate() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• 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
• recreate_pose_for_entity() : protocols::pack_daemon::PackDaemon
• recursive_multiple_disulfide_former() : protocols::denovo_design::DisulfidizeMover
• 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
• redefine_begin_end() : protocols::fldsgn::topology::StrandPairing
• 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
• redesign_loop_neighborhood_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• redo() : protocols::jumping::SameStrand
• reduce_fa_rep() : protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• reduce_task() : protocols::forge::remodel::RemodelDesignMover
• reduced_IG_as_L_ : protocols::moves::DsspMover
• reduced_scofx_ : protocols::enzdes::SecondaryMatchProtocol
• reduced_scorefxn() : protocols::enzdes::EnzdesBaseProtocol
• reduced_sfxn_ : protocols::enzdes::EnzdesBaseProtocol
• ref_baseline() : protocols::simple_filters::DeltaFilter
• 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_gunn_data_ : protocols::frag_picker::scores::GunnCostScore
• ref_model_ : protocols::hybridization::CartesianSampler
• ref_motifs_ : protocols::simple_filters::SymmetricMotifFilter
• ref_pKa() : protocols::simple_moves::IonizableResidue
• ref_pKa_ : protocols::simple_moves::IonizableResidue
• ref_pose() : protocols::toolbox::DecoySetEvaluation
• ref_pose_ : 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_profile_ : protocols::simple_moves::FavorSequenceProfile
• ref_residue_total_energies_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• ref_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::simple_moves::SuperimposeMover
• ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• ref_start_struct_ : protocols::flexpep_docking::FlexPepDockingFlags
• ref_structure_ : protocols::toolbox::DecoySetEvaluation
• ref_xyz_ : protocols::md::MDBase
• refCSFileName : protocols::sparta::Sparta
• reference : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• 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_energies_inner_loop_ : protocols::optimize_weights::IterativeOptEDriver
• reference_moltenres_2_resid_ : protocols::simple_moves::GreenPacker
• reference_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• reference_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• reference_pose() : protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• reference_pose_ : protocols::abinitio::IterativeBase , 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_from_options() : protocols::features::ProteinRMSDNoSuperpositionFeatures
• reference_pose_local_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• reference_res : protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• 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_types_ : protocols::dna::DnaInterfacePacker
• reference_residues_indexes_ : protocols::fldsgn::MatchResidues
• reference_rotamer_sets_ : protocols::simple_moves::GreenPacker
• reference_structure() : protocols::rotamer_recovery::RRProtocolReferenceStructure
• reference_stub() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• 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
• reference_xyz_consistency_check() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• refill_torsion_string_vector() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• refine() : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• refine_ : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• refine_CCD_off_ : protocols::anchored_design::AnchoredRefineMover
• refine_cycles_ : protocols::anchored_design::AnchoredRefineMover
• refine_from_silent_ : protocols::farna::RNA_DeNovoProtocol
• refine_grid_and_subsample_for_hit_subsets() : protocols::match::Matcher
• 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::RNA_DeNovoProtocol
• refine_pose_list_ : protocols::farna::RNA_DeNovoProtocol
• refine_repack_cycles_ : protocols::anchored_design::AnchoredRefineMover
• refine_temp_ : protocols::anchored_design::AnchoredRefineMover
• RefineBetaBarrel() : protocols::antibody::RefineBetaBarrel
• refinement_angle_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• refinement_cycle() : protocols::surface_docking::FullatomRelaxMover
• 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
• RefineOneCDRLoop() : protocols::antibody::RefineOneCDRLoop
• RefineOneCDRLoopCentroid() : protocols::antibody::RefineOneCDRLoopCentroid
• refiners_ : protocols::loop_modeling::LoopProtocol
• reformat() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• refpose_ : protocols::relax::AtomCoordinateCstMover
• refresh() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid
• refresh_bbstub_constraints() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• refresh_coordinate_constraints() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• refresh_normalmode() : protocols::normalmode::NormalModeRelaxMover
• refresh_normalmode_ : protocols::normalmode::NormalModeRelaxMover
• refx() : protocols::simple_filters::AngleToVector
• refx_ : protocols::simple_filters::AngleToVector
• refy() : protocols::simple_filters::AngleToVector
• refy_ : protocols::simple_filters::AngleToVector
• refz() : protocols::simple_filters::AngleToVector
• refz_ : protocols::simple_filters::AngleToVector
• reg_only_movers_ : protocols::environment::EnvMover
• regenerate_round1_hits() : protocols::match::Matcher
• region() : protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover
• Region() : protocols::nonlocal::Region
• region1() : protocols::simple_filters::RegionalConnections
• region1_ : protocols::simple_filters::RegionalConnections
• region1_region2_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• region2() : protocols::simple_filters::RegionalConnections
• region2_ : protocols::simple_filters::RegionalConnections
• region_ : 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
• RegionalConnections() : protocols::simple_filters::RegionalConnections
• register_batch() : protocols::jd2::archive::ArchiveManager
• register_calculators() : protocols::analysis::InterfaceAnalyzerMover
• register_factory_prototypes() : protocols::rosetta_scripts::RosettaScriptsParser
• register_intergroup_calculator() : protocols::analysis::InterfaceAnalyzerMover
• register_label_offset() : protocols::topology_broker::SequenceNumberResolver
• register_mover() : protocols::environment::Environment , protocols::wum::MoverList
• register_movers() : protocols::environment::Environment
• register_options() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::PairingStatistics , protocols::abinitio::Protocol , protocols::abinitio::Template , protocols::abinitio::Templates , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory , protocols::docking::membrane::MPDockingMover , protocols::docking::TemperedDocking , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::features::ReportToDB , protocols::flxbb::FlxbbDesign , protocols::forge::remodel::RemodelLoopMover , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::RotationMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::moves::Mover , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::PeakFileFormat , protocols::relax::ClassicRelax , protocols::relax::RelaxProtocolBase , protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::ScoreMover , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::sparta::Sparta , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::DecoySetEvaluation , protocols::topology_broker::ConstraintEvaluatorWrapperCreator , protocols::topology_broker::TMHTopologySamplerClaimer
• register_preparer() : protocols::abinitio::abscript::AbscriptMover
• register_score_maker() : protocols::frag_picker::scores::FragmentScoreManager
• register_submover() : protocols::abinitio::abscript::AbscriptMover
• register_user_options() : protocols::forge::remodel::RemodelMover
• register_variable_expression() : protocols::optimize_weights::WrapperOptEMultifunc
• register_work_unit() : protocols::wum::WorkUnitList
• register_work_units() : protocols::wum::WorkUnitManager
• registered_makers_ : protocols::frag_picker::scores::FragmentScoreManager
• registered_movers_ : protocols::environment::Environment
• registry_shift_ : protocols::hybridization::InsertChunkMover
• regularize_angle() : protocols::stepwise::sampler::MC_OneTorsion
• reindex_AtomIDs() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• reinitialize() : protocols::cluster::APCluster , protocols::stepwise::modeler::StepWiseModeler
• reinitialize_CCD_torsions() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• reinitialize_CCD_torsions_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• reinitialize_for_each_job() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::floppy_tail::FloppyTailMover , protocols::ligand_docking::LigandDockMain , protocols::moves::Mover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• reinitialize_for_new_input() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::docking::DockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::ligand_docking::LigandDockMain , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::moves::Mover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• reinstantiate_backbone_at_moving_res() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• reinstantiate_distal_partition() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• reinstate_original_constraints() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• reinstate_pose() : protocols::enzdes::PredesignPerturbMover
• reinstate_side_chain_angles() : protocols::stepwise::modeler::packer::StepWisePacker
• reject_mutant() : protocols::pmut_scan::AlterSpecDisruptionDriver , protocols::pmut_scan::PointMutScanDriver
• reject_on_chains() : protocols::pmut_scan::AlterSpecDisruptionDriver
• reject_on_interface() : protocols::pmut_scan::AlterSpecDisruptionDriver
• REJECTED : protocols::topology_broker::claims::DofClaim
• rejected_ : protocols::moves::MoverStatistics
• relative() : protocols::environment::claims::XYZClaim
• relative_pose_filter() : protocols::simple_filters::MultipleSigmoids
• relative_pose_names() : protocols::simple_filters::Operator
• relative_pose_names_ : protocols::simple_filters::Operator
• RelativeConnectRight() : protocols::forge::build::RelativeConnectRight
• RelativePoseFilter() : protocols::simple_filters::RelativePoseFilter
• RelativeSegmentFilter() : protocols::protein_interface_design::filters::RelativeSegmentFilter
• relax() : protocols::abinitio::AbrelaxApplication , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• relax_ : protocols::comparative_modeling::LoopRelaxMover , 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_bound_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• relax_cdrs() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody_legacy::AntibodyModeler
• relax_constraint_to_design_ : protocols::flxbb::FlxbbDesign
• relax_cycles_ : protocols::farna::RNA_Relaxer , protocols::hybridization::MRMover
• relax_favorable_poses() : protocols::vip::VIP_Mover
• 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_interface() : protocols::antibody::design::AntibodyDesignModeler
• relax_max_iter_ : protocols::hybridization::MRMover
• relax_mover() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::loophash::LoopHashMoverWrapper , 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_mover_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , 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_optimized_CDR_grafts() : protocols::antibody_legacy::GraftMover
• relax_protocol() : protocols::abinitio::AbrelaxMover
• relax_protocol_ : protocols::abinitio::AbrelaxMover , protocols::relax::membrane::MPFastRelaxMover
• relax_repeats_ : protocols::hybridization::HybridizeProtocol
• relax_structure_ : protocols::farna::RNA_DeNovoProtocol
• relax_type : protocols::mpi_refinement::MethodParams
• relax_unbound() : protocols::simple_filters::DeltaFilter
• relax_unbound_ : protocols::simple_filters::DeltaFilter
• relax_wildtype_structure() : protocols::ddg::ddGMover
• relaxmode() : protocols::normalmode::NormalModeRelaxMover
• relaxmode_ : protocols::normalmode::NormalModeRelaxMover
• RelaxProtocolBase() : protocols::relax::RelaxProtocolBase
• RelaxScriptCommand() : protocols::relax::RelaxScriptCommand
• relay_message() : protocols::topology_broker::TopologyBroker
• release() : protocols::ligand_docking::TetherLigand
• release_file() : protocols::jd2::MpiFileBuffer
• 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::MatcherTask
• 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() : protocols::comparative_modeling::features::ResidueFeature , protocols::rbsegment_relax::RBSegment
• remap_atomid_vector() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms
• remap_resid() : protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesFlexibleRegion , 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::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• remap_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• remapped_clone() : protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet
• remark() : protocols::motifs::Motif
• remark_ : protocols::motifs::Motif
• REMARKS : protocols::sparta::GDB
• remembered_pose_ : protocols::simple_moves::ReturnSidechainMover
• remodel() : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• remodel_ : protocols::antibody::ModelCDRH3 , protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• remodel_data_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::forge::remodel::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_max_length_ : protocols::enzdes::EnzdesFlexibleRegion
• remodel_min_length() : protocols::enzdes::EnzdesFlexibleRegion
• remodel_min_length_ : protocols::enzdes::EnzdesFlexibleRegion
• remodel_mover_ : protocols::antibody::ModelCDRH3
• remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• remodelable_ : protocols::enzdes::EnzdesFlexibleRegion
• RemodelAccumulator() : protocols::forge::remodel::RemodelAccumulator
• RemodelConstraintGenerator() : protocols::forge::remodel::RemodelConstraintGenerator
• RemodelConstraintGeneratorOP : protocols::forge::components::VarLengthBuild
• RemodelData : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame
• remodelData() : protocols::forge::remodel::RemodelLoopMover
• RemodelData : protocols::forge::remodel::RemodelMover
• RemodelDesignMover() : protocols::forge::remodel::RemodelDesignMover
• RemodelEnzdesCstModule() : protocols::forge::remodel::RemodelEnzdesCstModule
• remodeler_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• RemodelGlobalFrame() : protocols::forge::remodel::RemodelGlobalFrame
• RemodelLoopMover() : protocols::forge::remodel::RemodelLoopMover
• RemodelMover() : protocols::forge::remodel::RemodelMover
• RemodelRotamerLinks() : protocols::forge::remodel::RemodelRotamerLinks
• RemodelWorkingSet : protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelWorkingSet
• remote_close_file() : protocols::jd2::MpiFileBuffer
• removable_ : protocols::simple_moves::VirtualRootMover
• remove() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::protein_interface_design::movers::AddChainBreak , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim
• remove_ : protocols::protein_interface_design::movers::AddChainBreak , protocols::simple_moves::VirtualRootMover
• remove_all_hotspot_constraints() : protocols::hotspot_hashing::HotspotStubSet
• remove_bad_inputs_from_job_list() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• remove_chainbreak_variants() : protocols::environment::Environment
• remove_chainbreaks() : protocols::jumping::JumpSample
• remove_child() : protocols::loop_modeling::LoopMover
• remove_conservative_design_residues_from_prob_set() : protocols::antibody::design::AntibodySeqDesignTFCreator
• remove_constraints_from_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_constraints_from_pose_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_covalent_connection_from_pose() : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• remove_covalent_connections_from_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• remove_cterminus_variant_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• remove_cut() : protocols::hybridization::HybridizeFoldtreeDynamic
• remove_cycles_from_request_list() : protocols::canonical_sampling::AsyncMPITemperingBase
• remove_downstream_object_from_upstream_pose() : protocols::match::MatcherTask
• remove_duplicate_phi_psi() : protocols::pockets::NonPlaidFingerprint
• remove_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• remove_evaluation() : protocols::jd2::archive::EvaluatedArchive
• remove_favor_native_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• remove_first_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• remove_from_consideration_first_multi_residue_move_element() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• remove_highest_energy_member_of_each_group() : protocols::cluster::ClusterBase
• remove_info() : protocols::dna::PDBOutput
• remove_invrots_clashing_with_parent_res() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• remove_last_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• remove_last_filter() : protocols::filters::FilterCollection
• remove_ligand_tethers() : protocols::ligand_docking::HighResDocker
• remove_member() : protocols::cluster::Cluster
• remove_nonpermenant_features() : protocols::environment::Environment
• 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_output_observer() : protocols::jd2::Job
• remove_pending_decoys() : protocols::abinitio::HedgeArchive
• remove_position_from_template_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_position_from_template_res_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_random_stubs_from_set() : protocols::hotspot_hashing::HotspotStubSet
• remove_remodel_constraints() : protocols::forge::components::VarLengthBuild
• remove_remodel_constraints_from_pose() : protocols::forge::remodel::RemodelConstraintGenerator
• remove_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• remove_seqpos() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• remove_seqpos_from_template_res() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• remove_shove_variant_ : protocols::protein_interface_design::movers::ShoveResidueMover
• remove_singletons() : protocols::cluster::ClusterBase
• remove_singletons_ : protocols::pose_selectors::ClusterPoseSelector
• remove_singletons_and_update_pose_focus() : protocols::stepwise::monte_carlo::mover::DeleteMover
• remove_stub() : protocols::hotspot_hashing::HotspotStubSet
• remove_stubs_from_set() : protocols::hotspot_hashing::HotspotStubSet
• remove_system_signal_handler() : protocols::jd2::JobDistributor
• remove_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• remove_terminal_loops() : protocols::loops::Loops
• remove_trigger() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• remove_variants_at_extra_cutpoints() : protocols::farna::RNA_LoopCloser
• remove_vector_exclude_residues() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• remove_xray_virt_ : protocols::features::ReportToDB
• RemoveCsts() : protocols::forge::constraints::RemoveCsts
• RemoveLigandFilter() : protocols::enzdes::RemoveLigandFilter
• RemoveNorCTermMPM() : protocols::match::RemoveNorCTermMPM
• rename_checkpoint_files() : protocols::genetic_algorithm::GeneticAlgorithmBase
• rename_tags_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• render_fold_tree() : protocols::environment::EnvClaimBroker
• RenderGridsToKinemage() : protocols::qsar::RenderGridsToKinemage
• renormalize_quota_pools() : protocols::frag_picker::quota::QuotaCollector
• renumber_after_variant_changes() : protocols::toolbox::AllowInsert
• renumber_pdb() : protocols::simple_filters::SaveResfileToDiskFilter
• renumber_pdb_ : protocols::simple_filters::SaveResfileToDiskFilter
• reorder_foldtree_around_mobile_regions() : protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::MinimizeBackbone
• reorder_foldtree_find_jump() : protocols::analysis::InterfaceAnalyzerMover
• reorder_poses() : protocols::antibody::design::AntibodyDesignMover
• reorder_restypes() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• reorient_and_slide_into_surface() : protocols::surface_docking::FullatomRelaxMover
• 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
• repack() : protocols::mpi_refinement::WorkUnit_Sampler , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::FASTER_IG_Repacker , protocols::pack_daemon::QuickRepacker , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::GreenPacker
• repack_ : protocols::enzdes::EnzRepackMinimize , protocols::relax::FastRelax , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::RotamerBoltzmannWeight
• repack_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• repack_and_minimize_pose() : protocols::optimize_weights::IterativeOptEDriver
• repack_antibody_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_antigen_ab_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_antigen_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• repack_bound() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• repack_bound_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• repack_buffer_ : protocols::abinitio::ResolutionSwitcher
• repack_c_terminus_ : protocols::toolbox::task_operations::RestrictToTerminiOperation
• repack_cdrs() : protocols::antibody::design::AntibodyDesignModeler
• repack_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain1_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain2_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_cst_set_mut_ : protocols::ddg::ddGMover
• repack_cst_set_wt_ : protocols::ddg::ddGMover
• repack_every_Nth_ : protocols::ligand_docking::HighResDocker
• repack_foldpose_ : protocols::seeded_abinitio::SeedSetupMover
• repack_fragments_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• repack_mut_types_ : protocols::ddg::ddGMover
• repack_n_terminus_ : protocols::toolbox::task_operations::RestrictToTerminiOperation
• repack_neighbors() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• repack_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::loops::loop_mover::refine::LoopMover_Refine_CCD
• 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_query_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• repack_rate_ : protocols::dna::DesignProteinBackboneAroundDNA
• repack_sc_ : protocols::relax::CentroidRelax
• repack_scorefxn_ : protocols::topology_broker::TopologyBroker
• repack_shell() : protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• repack_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , 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_to_matrix() : protocols::frag_picker::CSTalosIO
• repack_unbound_ : protocols::simple_moves::ddG
• repack_wt_types_ : protocols::ddg::ddGMover
• repacked_poses_ : protocols::simple_moves::SetReturningPackRotamersMover
• repacker_ : protocols::pack_daemon::PackDaemon
• repacking_radius() : protocols::simple_filters::RotamerBoltzmannWeight , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• repacking_radius_ : protocols::simple_filters::RotamerBoltzmannWeight , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• RepackingRefiner() : protocols::loop_modeling::refiners::RepackingRefiner
• RepackLigandSiteWithoutLigandMover() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• RepackMinimize() : protocols::protein_interface_design::movers::RepackMinimize
• RepackSidechainsMover() : protocols::simple_moves::RepackSidechainsMover
• RepackTrial() : protocols::loops::loop_mover::refine::RepackTrial
• RepackTrialCreator() : protocols::loops::loop_mover::refine::RepackTrialCreator
• RepackWithoutLigandFilter() : protocols::enzdes::RepackWithoutLigandFilter
• repeat_generation_with_additional_residue() : protocols::forge::remodel::RemodelLoopMover
• repeat_job_ : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• repeat_length_ : protocols::forge::remodel::RemodelLoopMover
• repeat_pose_ : protocols::forge::remodel::RemodelLoopMover
• repeat_propagation() : protocols::forge::remodel::RemodelLoopMover
• repeat_sync() : protocols::forge::remodel::RemodelLoopMover
• repeat_tail_length_ : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• repeat_without_replacing_pose_ : protocols::simple_moves::RepeatPropagationMover
• RepeatMover() : protocols::moves::RepeatMover
• RepeatParameterFilter() : protocols::simple_filters::RepeatParameterFilter
• RepeatPropagationMover() : protocols::simple_moves::RepeatPropagationMover
• repeats : protocols::ligand_docking::Transform_info , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ddG
• 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
• RepGrid() : protocols::qsar::scoring_grid::RepGrid
• replace_ : protocols::seeded_abinitio::CAcstGenerator
• replace_noesy_filter_constraints() : protocols::abinitio::IterativeBase
• replace_residue() : protocols::environment::ProtectedConformation
• replace_residue_sandbox() : protocols::environment::ProtectedConformation
• replace_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio
• ReplaceRegionMover() : protocols::grafting::simple_movers::ReplaceRegionMover
• ReplaceString() : protocols::pockets::GenPharmacophore
• ReplicaExchangeMC() : protocols::moves::ReplicaExchangeMC
• ReplicateFilter() : protocols::filters::ReplicateFilter
• replicates_ : protocols::filters::ReplicateFilter
• report() : protocols::analysis::PeptideDeriverFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::dna::RotamerDNAHBondFilter , protocols::docking::DockingLowResFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter
• Report() : protocols::features::Report
• report() : protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::ReportSequenceDifferences , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter
• report_ab_H3_kink_metrics_features() : protocols::antibody::AntibodyFeatures
• report_ab_metrics_features() : protocols::antibody::AntibodyFeatures
• report_all() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::rosetta_scripts::ParsedProtocol
• report_all_ : protocols::protein_interface_design::filters::FilterScanFilter
• report_all_interface_features() : protocols::features::InterfaceFeatures
• report_aln_components() : protocols::evaluation::AlignEvaluator
• report_aln_components_ : protocols::evaluation::AlignEvaluator
• report_as_silent() : protocols::md::MDBase
• report_as_silent_ : protocols::md::MDBase
• report_atom_pairs() : protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures
• report_CA_rmsd() : protocols::idealize::IdealizeMover
• report_CA_rmsd_ : protocols::idealize::IdealizeMover
• report_call_order() : protocols::rosetta_scripts::ParsedProtocol
• report_call_order_ : protocols::rosetta_scripts::ParsedProtocol
• report_cdr_metrics_features() : protocols::antibody::AntibodyFeatures
• report_cdr_residue_features() : protocols::antibody::AntibodyFeatures
• report_cdr_residue_features_row() : protocols::antibody::AntibodyFeatures
• report_data() : protocols::analysis::InterfaceAnalyzerMover
• report_ddG() : protocols::simple_moves::ddG
• report_dev() : protocols::mpi_refinement::StructAvrgMover
• report_diffs() : protocols::simple_filters::DdGScan
• report_diffs_ : protocols::simple_filters::DdGScan
• report_features() : protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ReportToDB , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures
• report_features_implementation() : protocols::features::PoseConformationFeatures
• report_filter_at_end_ : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• report_filter_name() : protocols::simple_filters::ReportFilter
• report_filter_name_ : protocols::simple_filters::ReportFilter
• report_filters_to_job() : protocols::rosetta_scripts::ParsedProtocol
• report_filters_to_pose() : protocols::rosetta_scripts::ParsedProtocol
• report_format_ : protocols::analysis::PeptideDeriverFilter
• report_gdt_components() : protocols::comparative_modeling::Align_RmsdEvaluator , protocols::simple_filters::RmsdEvaluator
• report_gdt_components_ : protocols::comparative_modeling::Align_RmsdEvaluator , protocols::simple_filters::RmsdEvaluator
• report_haro_orbital_interactions() : protocols::features::OrbitalsFeatures
• report_hpol_orbital_interactions() : protocols::features::OrbitalsFeatures
• report_interface_features() : protocols::features::InterfaceFeatures
• report_interface_residue_features() : protocols::features::InterfaceFeatures
• report_interface_side_features() : protocols::features::InterfaceFeatures
• report_interres_angles() : protocols::features::ProteinBondGeometryFeatures
• report_interres_lengths() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_angles() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_lengths() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_torsions() : protocols::features::ProteinBondGeometryFeatures
• report_MD() : protocols::md::CartesianMD
• report_per_residue_sasa_ : protocols::simple_filters::TotalSasaFilter
• report_predicted_features() : protocols::rotamer_recovery::RRReporterSQLite
• report_property() : protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::rosetta_scripts::PosePropertyReporter
• report_residue_pair_energies_ : protocols::simple_filters::ScoreCutoffFilter
• report_residue_pairs() : protocols::features::PairFeatures
• report_rotamer_recovery() : protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_features() : protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_full() : protocols::rotamer_recovery::RRReporterSQLite
• report_scorecomp_ : protocols::md::MDBase
• report_silent() : protocols::md::MDBase
• report_sm() : protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter
• report_string() : protocols::simple_filters::ReportFilter
• report_string_ : protocols::simple_filters::ReportFilter
• report_structure_features() : protocols::features::ReportToDB
• report_structure_to_emperor() : protocols::loophash::MPI_LoopHashRefine_Master
• report_subvalues() : protocols::simple_filters::Operator
• report_subvalues_ : protocols::simple_filters::Operator
• report_symmetry() : protocols::simple_filters::AlaScan
• report_time() : protocols::mpi_refinement::MPI_Refinement
• report_to_db_ : protocols::rotamer_recovery::RRReporterSQLite
• report_type_ : protocols::fldsgn::filters::NcontactsFilter
• ReportEffectivePKA() : protocols::simple_moves::ReportEffectivePKA
• 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
• ReportFilter() : protocols::simple_filters::ReportFilter
• ReportFSC() : protocols::electron_density::ReportFSC
• reporting_ : protocols::docking::DockingProtocol
• ReportPSSMDifferences() : protocols::protein_interface_design::ReportPSSMDifferences
• ReportSequenceDifferences() : protocols::protein_interface_design::ReportSequenceDifferences
• ReportToDB() : protocols::features::ReportToDB
• reposition_above_surface() : protocols::surface_docking::FullatomRelaxMover
• reprepare_ : protocols::abinitio::abscript::ConstraintPreparer
• representative_downstream_algorithm() : protocols::match::Matcher
• representative_downstream_algorithm_ : protocols::match::Matcher
• representative_dspos_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• representative_group_matches() : protocols::match::output::CloudPDBWriter
• representative_group_matches_ : protocols::match::output::CloudPDBWriter
• representative_seqpos() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• 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
• repulsive_ramp() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody_legacy::AntibodyModeler
• repulsive_ramp_ : protocols::antibody::RefineBetaBarrel
• RepulsiveOnlyMover() : protocols::simple_moves::RepulsiveOnlyMover
• repW : protocols::pockets::PocketExemplarMultifunc
• req_residue_str_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• reqfile_name_ : protocols::enzdes::EnzdesScorefileFilter
• request_fold_tree() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopMover
• request_new_jobs() : protocols::wum::MPI_WorkUnitManager_Slave
• requested_level_ : protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest
• require_all_target_residue_atom_coordinates() : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• require_atom_to_reside_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• require_candidate_residue_atoms_to_lie_near_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• require_mm_bend() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• require_mm_bend_ : protocols::backrub::BackrubMover
• require_target_atom_coordinate() : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• required_connections_ : protocols::simple_filters::RegionalConnections
• required_connections_between_regions_ : protocols::simple_filters::PackerNeighborGraphFilter
• required_connections_per_res_ : protocols::simple_filters::PackerNeighborGraphFilter
• required_separation_distance() : protocols::match::BumpGrid
• requires_pose() : protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver
• rerelax_type : protocols::mpi_refinement::MethodParams
• reroot_fold_tree() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• reroot_fold_tree_simple() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• rerun_motifsearch_ : protocols::motifs::MotifSearch
• res : protocols::cartesian::CartesianAtom
• res1() : protocols::fldsgn::topology::DimerPairing
• res1_ : 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_index_ : protocols::motifs::Motif
• res1_atom1_int() : protocols::motifs::Motif
• res1_atom1_int_ : protocols::motifs::Motif
• res1_atom1_name() : protocols::motifs::Motif
• res1_atom1_name_ : protocols::motifs::Motif
• res1_atom2_index() : protocols::motifs::Motif
• res1_atom2_index_ : protocols::motifs::Motif
• res1_atom2_int() : protocols::motifs::Motif
• res1_atom2_int_ : protocols::motifs::Motif
• res1_atom2_name() : protocols::motifs::Motif
• res1_atom2_name_ : protocols::motifs::Motif
• res1_atom3_index() : protocols::motifs::Motif
• res1_atom3_index_ : protocols::motifs::Motif
• res1_atom3_int() : protocols::motifs::Motif
• res1_atom3_int_ : protocols::motifs::Motif
• res1_atom3_name() : protocols::motifs::Motif
• res1_atom3_name_ : protocols::motifs::Motif
• res2() : protocols::fldsgn::topology::DimerPairing
• res2_ : 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_index_ : protocols::motifs::Motif
• res2_atom1_int() : protocols::motifs::Motif
• res2_atom1_int_ : protocols::motifs::Motif
• res2_atom1_name() : protocols::motifs::Motif
• res2_atom1_name_ : protocols::motifs::Motif
• res2_atom2_index() : protocols::motifs::Motif
• res2_atom2_index_ : protocols::motifs::Motif
• res2_atom2_int() : protocols::motifs::Motif
• res2_atom2_int_ : protocols::motifs::Motif
• res2_atom2_name() : protocols::motifs::Motif
• res2_atom2_name_ : protocols::motifs::Motif
• res2_atom3_index() : protocols::motifs::Motif
• res2_atom3_index_ : protocols::motifs::Motif
• res2_atom3_int() : protocols::motifs::Motif
• res2_atom3_int_ : protocols::motifs::Motif
• res2_atom3_name() : protocols::motifs::Motif
• res2_atom3_name_ : protocols::motifs::Motif
• res3_ : protocols::cyclic_peptide::CreateTorsionConstraint
• res4_ : protocols::cyclic_peptide::CreateTorsionConstraint
• res_anchor() : protocols::sic_dock::Rose
• res_center_ : protocols::cyclic_peptide::CreateAngleConstraint
• res_check_task_factory_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• res_energy1_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_energy2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_first : protocols::rbsegment_relax::RBResidueRange
• res_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_high_ : protocols::cryst::SetRefinementOptionsMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• res_ids() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• res_ids_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• res_indices_to_output_ : protocols::dna::PDBOutput
• res_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• res_interactions_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• res_last : protocols::rbsegment_relax::RBResidueRange
• res_links() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• res_links_ : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• res_list_ : protocols::noesy_assign::FloatingResonance
• res_low_ : protocols::cryst::SetRefinementOptionsMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• res_map() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• res_map_ : protocols::farna::ChunkSet , protocols::simple_moves::CopyDofMover , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• res_name() : protocols::simple_moves::MutateResidue
• res_name1() : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences
• res_name1_ : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences
• res_name2() : protocols::protein_interface_design::ReportSequenceDifferences
• res_name2_ : protocols::protein_interface_design::ReportSequenceDifferences
• res_name_ : protocols::simple_moves::MutateResidue
• res_num_cur_ : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• res_num_total_ : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• res_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_recovered_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• res_scores_ : protocols::rotamer_recovery::PerNativeRRReporterHuman
• res_switch() : protocols::abinitio::KinematicTaskControl
• res_switch_ : protocols::abinitio::KinematicTaskControl
• res_to_add_in_full_model_numbering_ : protocols::stepwise::monte_carlo::mover::AddMover
• res_to_build_off_in_full_model_numbering_ : protocols::stepwise::monte_carlo::mover::AddMover
• res_to_superimpose_ : protocols::enzdes::EnzdesBaseProtocol
• res_types() : protocols::simple_filters::ResidueCountFilter
• res_types_ : protocols::simple_filters::ResidueCountFilter
• resA() : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resA_ : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resA_basename_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_modname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resA_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resample_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• ResampleMover() : protocols::stepwise::monte_carlo::mover::ResampleMover
• resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• resB_basename_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_modname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_seqpos_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• resB_varname_ : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• rescale() : protocols::md::Thermostat
• rescore() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeBase , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• rescore_all_decoys() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• rescore_nonlocal_archive() : protocols::abinitio::IterativeBase
• rescore_only_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• ResElemVect : protocols::environment::EnvClaimBroker
• reserve() : protocols::toolbox::DecoySetEvaluation
• reserve_size_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• reset() : protocols::abinitio::hConvergenceCheck , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::checkpoint::Timer , protocols::contact_map::ContactMap , protocols::evaluation::TimeEvaluator , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper , protocols::hybridization::hConvergenceCheck , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::StateAccumulatingMatchFilter , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::TrialCounter , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::StepWiseSampleAndScreen
• reset_ : protocols::cyclic_peptide::PeptideStubMover
• reset_3d_projection() : protocols::match::OccupiedSpaceHash
• reset_accept_counter() : protocols::jd2::archive::ArchiveBase
• reset_accounting() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• reset_accounting_impl() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• reset_all_rotamer_substitution_bookkeeping_data() : protocols::flexpack::interaction_graph::FlexbbNode
• reset_alternate_states_for_uncommited_substitution() : protocols::flexpack::interaction_graph::FlexbbEdge
• reset_baseline() : protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• reset_baselines() : protocols::simple_moves::GenericMonteCarloMover
• reset_baselines_ : protocols::simple_moves::GenericMonteCarloMover
• reset_calibration_constants() : protocols::noesy_assign::PeakCalibrator
• reset_chain_endings() : protocols::environment::ProtectedConformation
• reset_count() : protocols::contact_map::Contact
• reset_count_ : protocols::contact_map::ContactMap
• reset_counters() : protocols::moves::MonteCarlo
• reset_cycle_index() : protocols::docking::DockMCMCycle , protocols::moves::CycleMover
• reset_delta_filter_baselines() : protocols::matdes::MatDesGreedyOptMutationMover
• reset_delta_filters_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• reset_delta_omega1() : protocols::helical_bundle::parameters::BundleParameters
• reset_delta_z1() : protocols::helical_bundle::parameters::BundleParameters
• reset_DMC() : protocols::moves::DualMonteCarlo
• reset_filters() : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::match::output::MatchProcessor
• reset_filters_ : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter
• reset_from_interface() : protocols::dna::DnaInterfaceMinMover
• reset_from_ref() : protocols::scoring::methods::pcs2::PcsTensor
• reset_grid() : protocols::match::Bool3DGrid
• reset_grid_bb_ : protocols::match::downstream::ActiveSiteGrid
• reset_grouper() : protocols::match::output::MatchConsolidator
• reset_mode() : protocols::helical_bundle::BundleGridSampler
• reset_mode_ : protocols::helical_bundle::BundleGridSampler
• reset_move_data() : protocols::environment::ProtectedConformation
• reset_mover_data() : protocols::cyclic_peptide::PeptideStubMover
• reset_node_in_moving_flexseg_count() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• reset_num_connections() : protocols::simple_filters::RegionalConnections
• reset_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• reset_pose() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix
• reset_pose_ : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix
• reset_r1() : protocols::helical_bundle::parameters::BundleParameters
• reset_raw_counter() : protocols::canonical_sampling::SimulatedTempering
• reset_recovery() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• reset_scorefxn() : protocols::moves::MonteCarlo
• reset_slide_ : protocols::simple_moves::symmetry::SymmetrySlider
• reset_statistics() : protocols::backrub::BackrubSidechainMover , protocols::noesy_assign::PeakCalibrator
• reset_status() : protocols::moves::Mover
• reset_temp_counter() : protocols::canonical_sampling::TemperingBase
• reset_tensor() : 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
• reset_timing_stats() : protocols::wum::MPI_WorkUnitManager
• reset_to_original_pose() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• reset_trans_axis() : protocols::rigid::UniformSphereTransMover
• reset_unique_id() : protocols::motifs::IRCollection
• reset_x() : protocols::evaluation::PCA
• ResetBaselineMover() : protocols::simple_moves::ResetBaselineMover
• resfile() : protocols::flxbb::DesignTask , protocols::forge::components::BDR
• 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_at() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• resfile_general_property() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_general_property_ : protocols::outputter::ResFileOutputter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_name() : 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_prefix_ : protocols::simple_filters::SaveResfileToDiskFilter
• resfile_suffix() : protocols::simple_filters::SaveResfileToDiskFilter
• resfile_suffix_ : protocols::simple_filters::SaveResfileToDiskFilter
• ResfileContentsOP : protocols::pack_daemon::DaemonSet
• resfilename_ : protocols::enzdes::DetectProteinLigandInterface
• ResFileOutputter() : protocols::outputter::ResFileOutputter
• resfiles() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• resfiles_ : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• reshash_ : protocols::sic_dock::scores::MotifHashRigidScore
• resi() : protocols::frag_picker::VallResidue , protocols::toolbox::Node
• resi_ : protocols::frag_picker::VallResidue
• ResId() : protocols::moves::ResId
• resid() : protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance
• resID : protocols::sparta::RingData
• resid() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• resid1_ : protocols::enzdes::DiffAtomSasaFilter
• resid2_ : protocols::enzdes::DiffAtomSasaFilter
• resid_ : protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::ResidueTorsionRestraints , protocols::moves::ResId , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• resid_2_entity_id_ : protocols::pack_daemon::EntityCorrespondence
• resid_2_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• resid_2_moltenres_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• resid_to_replace_ : protocols::match::output::PoseInserter
• ResIDList : protocols::pack_daemon::EntityCorrespondence
• residList : protocols::sparta::GDB , protocols::sparta::PDB
• ResidList : protocols::sparta::Sparta::SpartaLib
• residList : protocols::sparta::Sparta::SpartaLib
• ResIDListConstIter : protocols::pack_daemon::EntityCorrespondence
• residListOne : protocols::sparta::PDB
• resids_to_entries_map_ : protocols::frag_picker::CSTalosIO
• ResidualDipolarCouplingEnergyRigidSegments() : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• ResidualDipolarCouplingRigidSegments() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• Residue : protocols::dna::PDBOutput , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbNode
• residue() : protocols::hotspot_hashing::HotspotStub
• Residue : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• residue() : protocols::sic_dock::NoPoseXYX_Func , protocols::simple_filters::ResidueBurialFilter
• Residue : protocols::simple_moves::BBGaussianMover , protocols::simple_moves::MinimalRotamer
• residue1_ : protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter
• residue2_ : protocols::simple_filters::AtomicDistanceFilter
• residue_ : protocols::hotspot_hashing::HotspotStub , 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_set() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• residue_alternative_sets_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler
• residue_alternatives_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• residue_alternatives_rotamer_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• residue_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• residue_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_base2_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• residue_base_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_conformation_features_ : protocols::features::ProteinSilentReport
• residue_conformations_redundant() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• residue_covered_by_template_ : protocols::hybridization::ChunkTrialMover
• residue_dbio_ : protocols::features::ResidueTypesFeatures
• residue_decomposition() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_decomposition_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_decomposition_calculator() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• residue_decomposition_to_set_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_end : protocols::features::SecondaryStructureSegment
• residue_energy() : protocols::fldsgn::potentials::AACompositionEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::SpecialRotamerEnergy
• residue_features_ : protocols::features::ProteinSilentReport
• residue_fraction_buried() : protocols::simple_filters::ResidueBurialFilter
• residue_fraction_buried_ : protocols::simple_filters::ResidueBurialFilter
• residue_has_bad_bfactor() : protocols::optimize_weights::IterativeOptEDriver
• residue_has_unacceptably_bad_dunbrack_energy() : protocols::optimize_weights::IterativeOptEDriver
• residue_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• residue_index_ : protocols::ligand_docking::AddHydrogen
• residue_is_in_h3_loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• residue_level_tasks_for_placed_hotspots_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• residue_list() : protocols::simple_moves::SetTorsion
• residue_list_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::simple_moves::RingConformationMover , protocols::simple_moves::Tumble
• residue_max_registry_shift_ : protocols::hybridization::HybridizeProtocol
• residue_name() : protocols::helical_bundle::MakeBundleHelix
• residue_name_ : protocols::helical_bundle::MakeBundleHelix , protocols::hotspot_hashing::movers::PlaceProbeMover
• residue_neighbors() : protocols::simple_filters::NonSequentialNeighborsFilter
• residue_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• residue_nlscore_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• residue_num() : 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_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_ : 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_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_ : protocols::fldsgn::topology::StrandPairing
• residue_pair_constraint_exists() : protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• residue_pair_energy() : protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::scoring::methods::InterchainPairEnergy
• residue_pair_jump_ : protocols::topology_broker::MetalloClaimer
• residue_partition() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• residue_range_is_protein() : protocols::features::BetaTurnDetection
• 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_scores_ : protocols::analysis::PackStatMover
• residue_selection_ : protocols::comparative_modeling::ExtraThreadingMover
• residue_selection_big_frags_ : protocols::hybridization::hConvergenceCheck
• residue_selection_small_frags_ : protocols::hybridization::hConvergenceCheck
• residue_semiexpl_score_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• residue_set_ : protocols::inputter::FastaInputter
• residue_set_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_set_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_set_numbers_to_decomposition() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_surface_energy_ : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• residue_to_constrain() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• residue_type_ : protocols::simple_moves::MinimalRotamer
• residue_type_set() : protocols::forge::build::BuildInstruction , protocols::simple_moves::ExtendedPoseMover
• residue_type_set_ : protocols::simple_moves::ExtendedPoseMover
• residue_types_ : protocols::fldsgn::topology::BB_Pos , protocols::simple_filters::NeighborTypeFilter
• residue_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• residue_variants_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• ResidueAlternativeSet() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• ResidueAlternativeStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• ResidueAlternativeStepWiseSamplerComb() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• ResidueAuction : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• ResidueAuctionItem : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• ResidueBurialFeatures() : protocols::features::ResidueBurialFeatures
• ResidueBurialFeaturesCreator() : protocols::features::ResidueBurialFeaturesCreator
• ResidueBurialFilter() : protocols::simple_filters::ResidueBurialFilter
• ResidueChunkSelection() : protocols::abinitio::abscript::ResidueChunkSelection
• ResidueConformationFeatures() : protocols::features::ResidueConformationFeatures
• ResidueConformationFeaturesCreator() : protocols::features::ResidueConformationFeaturesCreator
• ResidueConformerFilter() : protocols::enzdes::ResidueConformerFilter
• ResidueContactScreener() : protocols::stepwise::screener::ResidueContactScreener
• ResidueCOP : protocols::flexpack::interaction_graph::OTFFlexbbNode
• ResidueCOPs : protocols::viewer::ConformationViewer
• ResidueCountFilter() : protocols::simple_filters::ResidueCountFilter
• ResidueDecompositionByChainCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• ResidueDecompositionCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• ResidueDistanceFilter() : protocols::simple_filters::ResidueDistanceFilter
• ResidueElement() : protocols::environment::claims::ResidueElement
• ResidueFeatureFactory() : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueFeatures() : protocols::features::ResidueFeatures
• ResidueFeaturesCreator() : protocols::features::ResidueFeaturesCreator
• ResidueFeatureTypes : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueGridScoresFeatures() : protocols::features::ResidueGridScoresFeatures
• ResidueGridScoresFeaturesCreator() : protocols::features::ResidueGridScoresFeaturesCreator
• ResidueGroupIGEdgeUpweighter() : protocols::toolbox::ResidueGroupIGEdgeUpweighter
• ResidueIEFilter() : protocols::simple_filters::ResidueIEFilter
• ResidueIndexDescription() : protocols::loops::ResidueIndexDescription
• ResidueIndexDescriptionFromFile() : protocols::loops::ResidueIndexDescriptionFromFile
• ResidueKinemageWriter() : protocols::match::output::ResidueKinemageWriter
• ResidueList : protocols::noesy_assign::PeakAssignmentResidueMap , protocols::sparta::GDB
• ResidueListStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler
• ResidueMap : protocols::noesy_assign::ResonanceList
• ResidueNetwork() : protocols::toolbox::ResidueNetwork
• ResiduePairJump() : protocols::jumping::ResiduePairJump
• ResiduePairJumps_ : protocols::jumping::ResiduePairJumpSetup
• ResiduePairJumpSetup() : protocols::jumping::ResiduePairJumpSetup
• ResiduePairJumpSingle() : protocols::jumping::ResiduePairJumpSingle
• ResidueProbDesignOperation() : protocols::antibody::design::ResidueProbDesignOperation
• residues() : protocols::constraints_additional::SequenceCouplingConstraint , protocols::forge::remodel::Segment , protocols::kinematic_closure::ClosureProblem , protocols::ligand_docking::Ligand_info , protocols::pockets::PocketExemplarMultifunc , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• residues1() : protocols::simple_filters::ShapeComplementarityFilter
• residues1_ : protocols::simple_filters::ShapeComplementarityFilter
• residues2() : protocols::simple_filters::ShapeComplementarityFilter
• residues2_ : protocols::simple_filters::ShapeComplementarityFilter
• residues_ : 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::simple_moves::SetTorsion , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::viewer::ConformationViewer
• residues_are_different() : protocols::dna::PDBOutput
• residues_compatible() : protocols::enzdes::SecondaryMatchProtocol
• 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_each_type_ : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• residues_for_entity_begin() : protocols::pack_daemon::EntityCorrespondence
• residues_for_entity_end() : protocols::pack_daemon::EntityCorrespondence
• residues_in_interface_threshold_ : protocols::simple_filters::ResiduesInInterfaceFilter
• residues_to_exclude_ : protocols::hybridization::CartesianSampler
• residues_to_mutate() : protocols::ddg::ddGMover
• residues_to_mutate_ : protocols::ddg::ddGMover
• ResidueScoresFeatures() : protocols::features::ResidueScoresFeatures
• ResidueScoresFeaturesCreator() : protocols::features::ResidueScoresFeaturesCreator
• ResidueSecondaryStructureFeatures() : protocols::features::ResidueSecondaryStructureFeatures
• ResidueSecondaryStructureFeaturesCreator() : protocols::features::ResidueSecondaryStructureFeaturesCreator
• ResidueSelector : protocols::environment::claims::JumpClaim
• ResidueSelectorCOP : protocols::environment::claims::EnvClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• ResidueSelectorLoader() : protocols::jd2::parser::ResidueSelectorLoader
• ResidueSelectorOP : protocols::environment::claims::XYZClaim
• ResidueSetChainEnergyFilter() : protocols::simple_filters::ResidueSetChainEnergyFilter
• ResiduesInInterfaceFilter() : protocols::simple_filters::ResiduesInInterfaceFilter
• residueStubCentroid() : protocols::hotspot_hashing::StubGenerator
• residueStubCentroidFrame() : protocols::hotspot_hashing::StubGenerator
• residueStubOrientFrame() : protocols::hotspot_hashing::StubGenerator
• ResidueSubset : protocols::environment::claims::EnvLabelSelector
• ResidueTorsionRestraints() : protocols::ligand_docking::ResidueTorsionRestraints
• ResidueTotalScoresFeatures() : protocols::features::ResidueTotalScoresFeatures
• ResidueTotalScoresFeaturesCreator() : protocols::features::ResidueTotalScoresFeaturesCreator
• residueType() : protocols::jumping::ResiduePairJumpSingle
• ResidueType : protocols::simple_moves::MinimalRotamer
• residueType_ : protocols::jumping::ResiduePairJumpSingle
• ResidueTypeConstraint : protocols::simple_moves::ResidueTypeConstraintMover
• ResidueTypeConstraintMover() : protocols::simple_moves::ResidueTypeConstraintMover
• ResidueTypeSet : protocols::forge::build::BuildInstruction
• ResidueTypeSetCAP : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• ResidueTypeSetCOP : protocols::forge::build::BuildInstruction
• ResidueTypesFeatures() : protocols::features::ResidueTypesFeatures
• ResidueTypesFeaturesCreator() : protocols::features::ResidueTypesFeaturesCreator
• ResidueVicinityInfo() : protocols::forge::remodel::ResidueVicinityInfo
• ResidueVicinityRCG() : protocols::forge::remodel::ResidueVicinityRCG
• resindex() : protocols::loops::ResidueIndexDescription
• resindex_ : protocols::loops::ResidueIndexDescription
• ResInteractions() : protocols::toolbox::match_enzdes_util::ResInteractions
• resize() : protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::SS_Info2 , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frags::TorsionFragmentLibrary , protocols::jumping::JumpSample , protocols::loops::LoopsFileData , protocols::simple_moves::BBGaussianMover
• resize_arrays() : protocols::match::output::UpstreamHitCacher
• resize_bb_ids() : protocols::make_rot_lib::RotData
• resize_bbs() : protocols::make_rot_lib::RotData
• resize_espGrid_to_match_pocketGrid() : protocols::pockets::ElectrostaticpotentialGrid
• resize_semi_vectors() : protocols::make_rot_lib::RotData
• ResizeArray() : protocols::hybridization::TMalign
• reslist_ : protocols::sic_dock::scores::MotifHashRigidScore
• resname() : protocols::contact_map::ContactPartner , protocols::forge::remodel::LineObject , protocols::helical_bundle::BackboneGridSampler
• resName : protocols::sparta::CORdata , protocols::sparta::RingData
• 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 : protocols::antibody::design::PDBNumbering , protocols::antibody::PDBLandmark , protocols::comparative_modeling::features::ResidueFeature , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::jd2::parser::BluePrint , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::sidechain_moves::SetChiMover
• resNum : protocols::sparta::CORdata
• resnum_ : 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::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_exists_in_set() : protocols::antibody::design::ResidueProbDesignOperation
• resnum_map() : protocols::jd2::parser::BluePrint
• resnum_map_ : protocols::jd2::parser::BluePrint
• resnums() : protocols::simple_filters::ResidueIEFilter
• resnums_ : protocols::simple_filters::ResidueIEFilter
• resnums_allow_design() : protocols::toolbox::task_operations::DesignAroundOperation
• resnums_allow_design_ : protocols::toolbox::task_operations::DesignAroundOperation
• resolution : protocols::antibody::CDRPose
• resolution_ : protocols::qsar::scoring_grid::GridManager
• ResolutionSwitcher() : protocols::abinitio::ResolutionSwitcher
• resolve_address_and_assign_tag() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• resolve_as_serialized_loop_from_pose() : protocols::loops::LoopFromFileData
• resolve_as_serialized_loops() : protocols::loops::LoopsFileData
• resolve_index() : protocols::loops::ResidueIndexDescription , protocols::loops::ResidueIndexDescriptionFromFile
• resolve_loop_indices() : protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_mover::LoopMover
• resolve_loop_indices_once() : protocols::loops::GuardedLoopsFromFile
• resolve_loopfile_indices() : protocols::comparative_modeling::LoopRelaxMover
• resolve_loops() : protocols::loops::LoopsFileData
• resolve_sequence_label() : protocols::topology_broker::TopologyBroker
• resolve_symmetry_claims() : protocols::topology_broker::TopologyBroker
• resolve_uncommitted_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• resolved_anchor_residue_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• resolved_level_best_rmsd() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• resolver() : protocols::environment::ProtectedConformation
• resonance() : protocols::noesy_assign::PeakAssignment
• Resonance() : protocols::noesy_assign::Resonance
• resonance1_ : protocols::noesy_assign::PeakAssignment
• resonance2_ : protocols::noesy_assign::PeakAssignment
• resonance_id() : protocols::noesy_assign::PeakAssignment
• ResonanceAPs : protocols::noesy_assign::Resonance
• ResonanceIDs : protocols::noesy_assign::Resonance , protocols::noesy_assign::ResonanceList
• ResonanceList() : protocols::noesy_assign::ResonanceList
• ResonancePair : protocols::noesy_assign::Resonance
• ResonancePairs : protocols::noesy_assign::Resonance
• resonances() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignment
• Resonances : protocols::noesy_assign::ResonanceList
• resonances_ : protocols::noesy_assign::CrossPeak
• resonances_at_residue() : protocols::noesy_assign::ResonanceList
• resource_description() : protocols::loops::LoopsFileFallbackConfigurationCreator , protocols::surface_docking::SurfaceVectorFallbackConfigurationCreator
• ResourceDescription : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• respair_evaluators_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respect_this_movemap() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• respond_to_peripheral_hitlist_change() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respond_to_primary_hitlist_change() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respos_from_external_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• ResSurfaceFullList : protocols::sparta::PDB
• ResSurfacePartList : protocols::sparta::PDB
• restart() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor
• restart_mode() : protocols::forge::components::VarLengthBuild
• restart_mode_ : protocols::forge::components::VarLengthBuild
• restart_simulation() : protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::ThermodynamicObserver
• restore() : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• restore_ : protocols::rbsegment_relax::MakeStarTopologyMover
• restore_archive() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• restore_best_exemplars() : protocols::cluster::APCluster
• restore_csts_ : protocols::hybridization::CartesianSampler
• restore_cter() : protocols::ub_e2c::ubi_e2c_modeler
• restore_from_file() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeCentroid , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• restore_original_cst() : protocols::forge::remodel::RemodelGlobalFrame
• restore_original_foldtree() : protocols::hybridization::FoldTreeHybridize
• restore_phi_psi_omega_over_loop_residues() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• restore_phi_psi_over_loop_residues() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• restore_pose_ : protocols::rosetta_scripts::SavePoseMover
• restore_pose_variants_after_chain_closure() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• restore_status() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeBase , protocols::jd2::archive::ArchiveBase
• restorePSER() : protocols::flexpep_docking::FlexPepDockingAbInitio
• restrain_ligand_chis() : protocols::ligand_docking::LigandDockProtocol
• restrain_ligand_nbr_atom() : protocols::ligand_docking::LigandBaseProtocol
• restrain_protein_Calpha() : protocols::ligand_docking::MinimizeBackbone
• restrain_protein_Calphas() : protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::MinimizeBackbone
• Restraints : protocols::ligand_docking::UnconstrainedTorsionsMover
• restraints_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• restrict_aatypes_for_selection() : protocols::toolbox::SelectResiduesByLayer
• restrict_design_operation_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• restrict_identities() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_identities_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_only_design_ : protocols::toolbox::task_operations::RestrictToLoops
• restrict_only_design_to_loops() : 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_sequence_profile() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• restrict_to_aligned_segments() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_aligned_segments_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_interface_ : protocols::docking::DockTaskFactory
• restrict_to_interfacial_loop_packing() : protocols::ub_e2c::ubi_e2c_modeler
• restrict_to_nbrhood_ : protocols::ddg::ddGMover
• restrict_to_nbrs() : protocols::ddg::ddGMover
• restrict_to_repacking() : protocols::simple_moves::DesignRepackMover
• restrict_to_repacking_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_wt_ : protocols::motifs::MotifSearch
• RestrictByCalculatorsOperation() : protocols::toolbox::task_operations::RestrictByCalculatorsOperation
• RestrictChainToRepackingOperation() : protocols::toolbox::task_operations::RestrictChainToRepackingOperation
• RestrictConservedLowDdgOperation() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• RestrictDesignToProteinDNAInterface() : protocols::dna::RestrictDesignToProteinDNAInterface
• restricted_aatypes_for_selection_ : protocols::toolbox::SelectResiduesByLayer
• RestrictIdentitiesAtAlignedPositionsOperation() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• RestrictIdentitiesOperation() : protocols::toolbox::task_operations::RestrictIdentitiesOperation
• RestrictInterGroupVectorOperation() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• RestrictNativeResiduesOperation() : protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• RestrictNonSurfaceToRepackingOperation() : protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
• RestrictOperationsBase() : protocols::toolbox::task_operations::RestrictOperationsBase
• RestrictResiduesToRepackingOperation() : protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• restrictSize_ : protocols::pockets::PocketGrid
• RestrictToAlignedSegmentsOperation() : protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• RestrictToCDRH3Loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• RestrictToInterface() : protocols::toolbox::task_operations::RestrictToInterface
• RestrictToInterfaceOperation() : protocols::toolbox::task_operations::RestrictToInterfaceOperation
• RestrictToInterfaceVectorOperation() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• RestrictToLoops() : protocols::toolbox::task_operations::RestrictToLoops
• RestrictToLoopsAndNeighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• RestrictToMoveMapChiOperation() : protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• RestrictToNeighborhoodOperation() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• RestrictToTerminiOperation() : protocols::toolbox::task_operations::RestrictToTerminiOperation
• restype() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::TargetRotamerCoords , protocols::match::upstream::BuildSet , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• restype_ : protocols::enzdes::ResidueConformerFilter , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::upstream::BuildSet , protocols::simple_filters::ResidueIEFilter
• restype_atom_id_2_nonchi_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• restype_atomno() : protocols::match::downstream::TargetRotamerCoords
• restype_geom_ : protocols::match::upstream::BuildSet
• restype_geometry() : protocols::match::upstream::BuildSet
• restype_id_2_collision_check_id() : protocols::toolbox::match_enzdes_util::LigandConformer
• restype_id_2_collision_check_id_ : protocols::toolbox::match_enzdes_util::LigandConformer
• restype_name1() : protocols::motifs::Motif
• restype_name1_ : protocols::motifs::Motif
• restype_name2() : protocols::motifs::Motif
• restype_name2_ : protocols::motifs::Motif
• restype_name_ : protocols::match::upstream::UpstreamResTypeGeometry
• restype_possible_at_position() : protocols::enzdes::SecondaryMatchProtocol
• restype_set() : protocols::enzdes::EnzdesBaseProtocol
• 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
• ResTypeFragmentMover() : protocols::simple_moves::ResTypeFragmentMover
• RestypeToTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• result() : protocols::environment::EnvClaimBroker
• 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
• result_query_string_ : protocols::wum::DatabaseEntryWorkUnit
• resume_support_ : protocols::rosetta_scripts::ParsedProtocol
• retag_library() : protocols::mpi_refinement::MPI_Refinement
• retrieve() : protocols::hotspot_hashing::HotspotStubSet
• retrieve_index : protocols::loophash::FilterBucket
• retrieve_relevant_poses_for_entity() : protocols::pack_daemon::DaemonSet
• retrieve_tensor_from_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• RetrieveStoredTaskOperation() : protocols::toolbox::task_operations::RetrieveStoredTaskOperation
• retry_count_ : protocols::jd2::FileSystemJobDistributor
• return_centroid() : protocols::abinitio::Protocol
• return_centroid_ : protocols::abinitio::Protocol
• return_combine_history() : protocols::simple_moves::CombinePoseMover
• return_key() : protocols::loophash::LoopHashMap
• return_lowest_poses_in_clusters() : protocols::cluster::ClusterBase
• return_pseudo_hits() : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_pseudo_hits_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_silent() : protocols::simple_moves::CombinePoseMover
• return_top_poses_in_clusters() : protocols::cluster::ClusterBase
• ReturnSidechainMover() : protocols::simple_moves::ReturnSidechainMover
• reverse_add_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• reverse_add_submotif_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• reverse_delete_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• reverse_mapping_ : protocols::abinitio::Template
• reverse_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• reverse_resample_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• reversed() : protocols::features::helixAssembly::HelicalFragment
• Reversion() : protocols::dna::Reversion
• reversion_scan() : protocols::dna::DnaInterfacePacker
• reversion_scan_ : protocols::dna::DnaInterfacePacker
• reversion_score() : protocols::dna::Reversion
• Revert() : protocols::protein_interface_design::Revert
• revert_facts_params() : protocols::mpi_refinement::WorkUnit_Sampler
• revert_to_template_ : protocols::toolbox::task_operations::DatabaseThread
• revision_id() : protocols::match::OccupiedSpaceHash
• revision_id_ : protocols::match::OccupiedSpaceHash
• REWARD : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• reweight() : protocols::canonical_sampling::SimulatedTempering
• reweight_stride_ : protocols::canonical_sampling::SimulatedTempering
• rg() : protocols::simple_moves::symmetry::SymmetrySlider
• RGF_ : protocols::forge::remodel::RemodelLoopMover
• RGFilter() : protocols::simple_filters::RGFilter
• rgstr_shift() : protocols::fldsgn::topology::StrandPairing
• 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
• rhoC_ : protocols::electron_density::BfactorMultifunc
• rhoMask_ : protocols::electron_density::BfactorMultifunc
• right : protocols::forge::build::Interval , protocols::topology_broker::claims::DofClaim
• right_ : protocols::topology_broker::claims::DofClaim
• right_named_stub_id() : protocols::forge::build::ConnectRight
• right_position() : protocols::forge::build::ConnectRight
• right_position_ : protocols::forge::build::ConnectRight
• right_stub_atoms() : protocols::forge::build::ConnectRight
• 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_DeNovoProtocol , protocols::simple_moves::CoupledMover
• rigid_body_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• rigid_body_rotamer_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• rigid_body_trial() : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• rigid_core_ : protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::RigidChunkClaimer
• RIGID_CORE_RESAMPLING : protocols::abinitio::IterativeBase
• 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
• rigidbody_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• rigidbody_monte_carlo_minimize() : protocols::flexpep_docking::FlexPepDockingProtocol
• RigidBodyDeterministicSpinMover() : protocols::rigid::RigidBodyDeterministicSpinMover
• RigidBodyDofPerturbMover() : protocols::rigid::RigidBodyDofPerturbMover
• RigidBodyDofRandomizeMover() : protocols::rigid::RigidBodyDofRandomizeMover
• RigidBodyDofRandomTransMover() : protocols::rigid::RigidBodyDofRandomTransMover
• RigidBodyDofSeqPerturbMover() : protocols::rigid::RigidBodyDofSeqPerturbMover
• RigidBodyDofSeqRandomizeMover() : protocols::rigid::RigidBodyDofSeqRandomizeMover
• RigidBodyDofSeqTransMover() : protocols::rigid::RigidBodyDofSeqTransMover
• RigidBodyDofTransMover() : protocols::rigid::RigidBodyDofTransMover
• RigidBodyInfo() : protocols::docking::RigidBodyInfo
• RigidBodyMotionMover() : protocols::rigid::RigidBodyMotionMover
• RigidBodyMoveBaseRSO() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• RigidBodyMover() : protocols::rigid::RigidBodyMover
• RigidBodyMoveRSO() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
• RigidBodyPerturbMover() : protocols::rigid::RigidBodyPerturbMover
• RigidBodyPerturbNoCenterMover() : protocols::rigid::RigidBodyPerturbNoCenterMover
• RigidBodyPerturbRandomJumpMover() : protocols::rigid::RigidBodyPerturbRandomJumpMover
• RigidBodyRandomizeMover() : protocols::rigid::RigidBodyRandomizeMover
• RigidBodyRandomTMHMover() : protocols::topology_broker::RigidBodyRandomTMHMover
• RigidBodySpinMover() : protocols::rigid::RigidBodySpinMover
• RigidBodyStepWiseSampler() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• RigidBodyStepWiseSamplerValueRange() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• RigidBodyStepWiseSamplerWithResidueAlternatives() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• RigidBodyStepWiseSamplerWithResidueList() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• RigidBodyTransMover() : protocols::rigid::RigidBodyTransMover
• RigidChunkClaimer() : protocols::topology_broker::RigidChunkClaimer
• RigidChunkCM() : protocols::abinitio::abscript::RigidChunkCM
• RigidLigandBuilder() : protocols::match::downstream::RigidLigandBuilder
• RigidSearchMover() : protocols::ligand_docking::RigidSearchMover
• RingConformationMover() : protocols::simple_moves::RingConformationMover
• ringFact : protocols::sparta::RingData
• RingNo : protocols::sparta::PDB
• Rings : protocols::sparta::PDB
• rise() : protocols::dna::DNABasestep
• rise_ : protocols::dna::DNABasestep
• rm_virt_phosphate() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• rm_virt_phosphate_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• rmax_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• rmdl_attempts_ : protocols::fldsgn::BluePrintBDR
• rms() : protocols::optimize_weights::SingleStructureData
• 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_pose_list() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• rms_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• 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::PlaidFingerprint , protocols::pockets::SmallMol , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• RMSD : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• rmsd() : protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::rna::output_data_struct , protocols::toolbox::DecoySetEvaluation
• rmsd_ : protocols::anchored_design::AnchoredDesignMover , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWisePoseAligner
• rmsd_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• rmsd_ca_list_ : protocols::toolbox::KClusterData
• rmsd_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• rmsd_cutoff() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• 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_1_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_cutoff_2() : 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_max_cutoff_ : protocols::farna::RNA_Relaxer
• rmsd_min_cutoff_ : protocols::farna::RNA_Relaxer
• RMSD_only_this_ : protocols::anchored_design::AnchoredDesignMover
• RMSD_only_this_pose_ : protocols::anchored_design::AnchoredDesignMover
• rmsd_over_alignment_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• 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_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
• RmsdEvaluator() : protocols::simple_filters::RmsdEvaluator
• RmsdEvaluatorCreator() : protocols::simple_filters::RmsdEvaluatorCreator
• RmsdFilter() : protocols::protein_interface_design::filters::RmsdFilter
• RMSDReporter() : protocols::pose_reporters::RMSDReporter
• RmsdSimpleFilter() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• RmsdTargetEvaluatorCreator() : protocols::simple_filters::RmsdTargetEvaluatorCreator
• rmsf() : protocols::toolbox::DecoySetEvaluation
• RMSVallData() : protocols::frags::RMSVallData
• 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_AddDeleteMonteCarlo() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• RNA_AnalyticLoopCloser() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• rna_atr_rep_checker_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• RNA_AtrRepChecker() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• RNA_AtrRepScreener() : protocols::stepwise::legacy::screener::RNA_AtrRepScreener
• RNA_BaseCentroidChecker() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• rna_ccd_close() : protocols::farna::RNA_LoopCloser
• rna_centroid_info_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• 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_ChainClosableGeometryChecker() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• RNA_ChainClosableGeometryResidueBasedScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener
• RNA_ChainClosableGeometryScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryScreener
• RNA_ChainClosableGeometryStubBasedScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• RNA_ChainClosureChecker() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• RNA_ChainClosureScreener() : protocols::stepwise::screener::RNA_ChainClosureScreener
• RNA_ChiStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• rna_chunk_library_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• RNA_ChunkLibrary() : protocols::farna::RNA_ChunkLibrary
• rna_cutpoints_closed_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_data_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• rna_data_reader_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• rna_delete_mover_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• RNA_DeNovoProtocol() : protocols::farna::RNA_DeNovoProtocol
• rna_fitted_torsion_info_ : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• rna_five_prime_chain_breaks_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_fragment_mover_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Relaxer
• RNA_FragmentMover() : protocols::farna::RNA_FragmentMover
• RNA_Fragments() : protocols::farna::RNA_Fragments
• rna_fragments_ : protocols::farna::RNA_FragmentMover
• rna_from_scratch_mover_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• RNA_HelixAssembler() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• rna_jump_library_ : protocols::farna::RNA_StructureParameters
• RNA_JumpLibrary() : protocols::farna::RNA_JumpLibrary
• RNA_KIC_Sampler() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• RNA_KinematicCloser() : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• rna_loop_closer_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::MultipleDomainMover , protocols::farna::RNA_DeNovoProtocol
• RNA_LoopCloser() : protocols::farna::RNA_LoopCloser
• RNA_MC_MultiSuite() : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite
• RNA_MC_Sugar() : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• RNA_MC_Suite() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• RNA_Minimizer() : protocols::farna::RNA_Minimizer
• rna_minimizer_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Relaxer
• RNA_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• RNA_NucleosideStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler
• rna_o2prime_mover_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• RNA_O2PrimeMover() : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• RNA_Pairing() : protocols::farna::RNA_Pairing
• rna_pairing_list_ : protocols::farna::RNA_StructureParameters
• rna_pairing_template_map_ : protocols::farna::RNA_JumpLibrary
• RNA_PairingTemplate() : protocols::farna::RNA_PairingTemplate
• rna_params_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• RNA_Relaxer() : protocols::farna::RNA_Relaxer
• rna_relaxer_ : protocols::farna::RNA_DeNovoProtocol
• rna_secstruct_ : protocols::farna::RNA_SecStructInfo , protocols::farna::RNA_StructureParameters
• RNA_SecStructInfo() : protocols::farna::RNA_SecStructInfo
• rna_structure_parameters_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• RNA_StructureParameters() : protocols::farna::RNA_StructureParameters
• RNA_SugarStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• RNA_SuiteStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• rna_three_prime_chain_breaks_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rna_torsion_mover_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• RNA_TorsionScreener() : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• RNA_VDW_BinChecker() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• rna_virt_sugar_atr_rep_checker_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• rnl_pose_ : protocols::enzdes::EnzdesScorefileFilter
• role_available_mem_ : protocols::wum2::EndPoint
• roll() : protocols::dna::DNABasestep
• roll_ : protocols::dna::DNABasestep
• RollMover() : protocols::rigid::RollMover
• root() : protocols::jumping::ResiduePairJumpSetup
• root_ : protocols::jumping::ResiduePairJumpSetup , protocols::topology_broker::CoordConstraintClaimer
• root_at_first_rigid_body_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_StructureParameters
• root_expression() : protocols::pack_daemon::SurrogateVariableExpression
• 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
• Rose() : protocols::sic_dock::Rose
• rosetta2methyl() : protocols::noesy_assign::MethylNames
• rosetta2methyl_ : protocols::noesy_assign::MethylNames
• rosetta2nmr() : protocols::noesy_assign::MethylNames
• rosetta2nmr_ : protocols::noesy_assign::MethylNames
• 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
• RosettaScriptsParser() : protocols::rosetta_scripts::RosettaScriptsParser
• rot_center() : protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodySpinMover
• rot_center_ : protocols::membrane::RotationMover , protocols::rigid::RigidBodyMover
• rot_db : protocols::constraints_additional::BindingSiteConstraint
• rot_level() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rot_level_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rot_mag_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , 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::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover
• 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_number_ : protocols::optimize_weights::PNatAAOptERotamerData
• rot_prob_accumulation_limit_ : protocols::match::upstream::BuildSet
• rot_sets() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• rot_sets_ : protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• rotamer() : protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_boltzmann_weight_ : protocols::features::RotamerBoltzmannWeightFeatures
• rotamer_combo_indexer_ : protocols::match::output::SameRotamerComboGrouper
• rotamer_data_begin() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• rotamer_data_end() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• rotamer_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_for_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_id : protocols::loophash::BBExtraData
• rotamer_index() : protocols::optimize_weights::PNatRotOptERotamerData
• rotamer_index_ : protocols::optimize_weights::PNatRotOptERotamerData
• rotamer_index_2_well_id() : protocols::optimize_weights::PNatRotOptEPositionData
• rotamer_is_glycine() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• rotamer_is_glycine_ : protocols::flexpack::interaction_graph::OTFFlexbbNode
• rotamer_is_proline() : 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_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• rotamer_list_ : protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• rotamer_probabilities_ : protocols::simple_filters::RotamerBoltzmannWeight
• rotamer_recovery_ : protocols::rotamer_recovery::RotamerRecoveryMover
• rotamer_recovery_context_poses_ : protocols::optimize_weights::IterativeOptEDriver
• rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• rotamer_set_contains_rotamer() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• rotamer_sets() : protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• rotamer_sets_ : protocols::motifs::IRCollection , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• rotamer_well_counts_ : protocols::optimize_weights::PNatRotOptEPositionData
• RotamerAssignment : protocols::pack_daemon::PackDaemon
• RotamerAssignmentAndEnergy : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• RotamerBoltzCalculator() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• RotamerBoltzmannWeight() : protocols::simple_filters::RotamerBoltzmannWeight
• RotamerBoltzmannWeightFeatures() : protocols::features::RotamerBoltzmannWeightFeatures
• RotamerBoltzmannWeightFeaturesCreator() : protocols::features::RotamerBoltzmannWeightFeaturesCreator
• RotamerComboCountMap : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameRotamerComboGrouper
• RotamerDNAHBondFilter() : protocols::dna::RotamerDNAHBondFilter
• RotamerDumpMover() : protocols::RotamerDump::RotamerDumpMover
• RotamerFeatures() : protocols::features::RotamerFeatures
• RotamerFeaturesCreator() : protocols::features::RotamerFeaturesCreator
• RotamerizeMover() : protocols::simple_moves::RotamerizeMover
• RotamerList : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• RotamerRecovery() : protocols::rotamer_recovery::RotamerRecovery , protocols::toolbox::pose_metric_calculators::RotamerRecovery
• RotamerRecoveryFactory() : protocols::rotamer_recovery::RotamerRecoveryFactory
• RotamerRecoveryFeatures() : protocols::features::RotamerRecoveryFeatures
• RotamerRecoveryFeaturesCreator() : protocols::features::RotamerRecoveryFeaturesCreator
• RotamerRecoveryMover() : protocols::rotamer_recovery::RotamerRecoveryMover
• RotamerRecoveryRegistrator() : protocols::rotamer_recovery::RotamerRecoveryRegistrator< T >
• Rotamers : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• rotamers_ : protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::make_rot_lib::MakeRotLibMover
• rotamers_on_same_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamers_recovered_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• RotamerSet : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSetOP : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• RotamerSetOperationOP : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• rotamersets() : protocols::multistate_design::PackingState
• RotamerSets : protocols::pack_daemon::PackDaemon , protocols::simple_moves::GreenPacker
• rotamersets_p_ : protocols::multistate_design::PackingState
• RotamerSetsCOP : protocols::pack_daemon::PackDaemon , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• RotamerSetsOP : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::GreenPacker , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• RotamerSubsetRepacker() : protocols::pack_daemon::RotamerSubsetRepacker
• RotamerSubsetsOP : protocols::pack_daemon::RotamerSubsetRepacker
• RotamerTrialsMinMover() : protocols::simple_moves::RotamerTrialsMinMover
• RotamerTrialsMover() : protocols::simple_moves::RotamerTrialsMover
• Rotate() : protocols::ligand_docking::Rotate
• rotate_anchor_to_x_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover
• rotate_around_atom() : protocols::ligand_docking::RigidSearchMover
• rotate_around_downstream_centroid() : protocols::ligand_docking::RigidSearchMover
• rotate_atom_ : protocols::ligand_docking::RigidSearchMover
• rotate_deg_ : protocols::ligand_docking::RigidSearchMover
• rotate_info_ : protocols::ligand_docking::Rotate
• rotate_ligand() : protocols::ligand_docking::Rotate
• rotate_rsd_ : protocols::ligand_docking::RigidSearchMover
• rotate_segment() : protocols::backrub::BackrubMover
• rotate_vec() : protocols::evaluation::PCA
• RotateJumpAxisMover() : protocols::rigid::RotateJumpAxisMover
• rotatePoint() : protocols::pockets::PocketGrid
• Rotates() : protocols::ligand_docking::Rotates
• rotates_ : protocols::ligand_docking::Rotates
• rotation() : protocols::ligand_docking::RigidSearchMover
• rotation_axes_ : protocols::matdes::SymDofMover
• rotation_mag_ : protocols::rigid::MembraneNormalPerturbationMover , protocols::rigid::UniformRigidBodyMover , protocols::topology_broker::TMHTopologySamplerClaimer
• rotation_magnitude_ : protocols::simple_moves::CoupledMover
• rotation_matrix_ : protocols::rigid::RigidBodyRandomizeMover
• rotation_std_dev_ : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• RotationMover() : protocols::membrane::RotationMover
• RotationSearchPattern() : protocols::hotspot_hashing::RotationSearchPattern
• RotData() : protocols::make_rot_lib::RotData
• rotid_on_moltenresidue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• RotM : protocols::motif_grafting::movers::motif2scaffold_data
• rots2add_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rots_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• rotset_ : protocols::protein_interface_design::movers::TryRotamers , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• rotset_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotset_for_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotsets_ : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::jumping::ResiduePairJump
• rottrials_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• rotx : protocols::loophash::LegacyLeapIndex
• roty : protocols::loophash::LegacyLeapIndex
• rotz : protocols::loophash::LegacyLeapIndex
• round() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::features::strand_assembly::StrandBundleFeatures , protocols::frag_picker::quota::QuotaSelector
• round_expired() : protocols::mpi_refinement::Scheduler
• round_to_Real() : protocols::simple_filters::ResidueCountFilter
• rounds_ : protocols::antibody::design::AntibodySeqDesignMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer , protocols::relax::CentroidRelax
• roundtype : protocols::mpi_refinement::MethodParams , protocols::mpi_refinement::Scheduler
• row_format_ : protocols::contact_map::ContactMap
• row_map_ : protocols::wum::DatabaseEntryWorkUnit
• row_names_ : protocols::contact_map::ContactMap
• rp_ : protocols::forge::build::RelativeConnectRight
• RRComparerAutomorphicRMSD() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• RRComparerAutomorphicRMSDCreator() : protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator
• RRComparerChiDiff() : protocols::rotamer_recovery::RRComparerChiDiff
• RRComparerChiDiffCreator() : protocols::rotamer_recovery::RRComparerChiDiffCreator
• RRComparerCreator() : protocols::rotamer_recovery::RRComparerCreator
• RRComparerCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRComparerElecDensDiff() : protocols::rotamer_recovery::RRComparerElecDensDiff
• RRComparerElecDensDiffCreator() : protocols::rotamer_recovery::RRComparerElecDensDiffCreator
• RRComparerRotBins() : protocols::rotamer_recovery::RRComparerRotBins
• RRComparerRotBinsCreator() : protocols::rotamer_recovery::RRComparerRotBinsCreator
• RRProtocolCreator() : protocols::rotamer_recovery::RRProtocolCreator
• RRProtocolCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRProtocolMinPack() : protocols::rotamer_recovery::RRProtocolMinPack
• RRProtocolMinPackCreator() : protocols::rotamer_recovery::RRProtocolMinPackCreator
• RRProtocolMover() : protocols::rotamer_recovery::RRProtocolMover
• RRProtocolMoverCreator() : protocols::rotamer_recovery::RRProtocolMoverCreator
• RRProtocolPackRotamers() : protocols::rotamer_recovery::RRProtocolPackRotamers
• RRProtocolPackRotamersCreator() : protocols::rotamer_recovery::RRProtocolPackRotamersCreator
• RRProtocolReferenceStructure() : protocols::rotamer_recovery::RRProtocolReferenceStructure
• RRProtocolReferenceStructureCreator() : protocols::rotamer_recovery::RRProtocolReferenceStructureCreator
• RRProtocolRelax() : protocols::rotamer_recovery::RRProtocolRelax
• RRProtocolRelaxCreator() : protocols::rotamer_recovery::RRProtocolRelaxCreator
• RRProtocolRotamerTrials() : protocols::rotamer_recovery::RRProtocolRotamerTrials
• RRProtocolRotamerTrialsCreator() : protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator
• RRProtocolRTMin() : protocols::rotamer_recovery::RRProtocolRTMin
• RRProtocolRTMinCreator() : protocols::rotamer_recovery::RRProtocolRTMinCreator
• RRReporterCreator() : protocols::rotamer_recovery::RRReporterCreator
• RRReporterCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRReporterHuman() : protocols::rotamer_recovery::RRReporterHuman
• RRReporterHumanCreator() : protocols::rotamer_recovery::RRReporterHumanCreator
• RRReporterSimple() : protocols::rotamer_recovery::RRReporterSimple
• RRReporterSimpleCreator() : protocols::rotamer_recovery::RRReporterSimpleCreator
• RRReporterSQLite() : protocols::rotamer_recovery::RRReporterSQLite
• RRReporterSQLiteCreator() : protocols::rotamer_recovery::RRReporterSQLiteCreator
• rsd() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• rsd_ : protocols::kinmatch::FunGroupTK , protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• rsd_id_ : 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_ : protocols::toolbox::SelectResiduesByLayer
• rsd_sasa() : protocols::toolbox::SelectResiduesByLayer
• rsd_sasa_ : protocols::toolbox::SelectResiduesByLayer
• 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_set_ : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::topology_broker::SequenceClaimer
• rsigma_dot_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rsigma_dot_initializer() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rsigma_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• rsrfilename_ : protocols::md::MDBase
• rt() : protocols::forge::build::ConnectRight
• RT : protocols::forge::build::ConnectRight
• rt() : protocols::forge::build::ConnectRight
• rt_ : protocols::forge::build::ConnectRight , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• rt_min() : protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy
• 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
• rt_templates() : protocols::jumping::MembraneJump
• rtmin() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::RelativePoseFilter
• rtmin_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , 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() : protocols::abinitio::AbrelaxApplication , protocols::dna::DnaInterfaceMultiStateDesign , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::hybridization::DomainAssembly , protocols::jd2::MpiFileBuffer , protocols::loophash::WorkUnit_LoopHash , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Relax , protocols::mpi_refinement::WorkUnit_Sampler , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::relax::WorkUnit_BatchRelax , protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRProtocol , protocols::rotamer_recovery::RRProtocolMinPack , protocols::rotamer_recovery::RRProtocolMover , protocols::rotamer_recovery::RRProtocolPackRotamers , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRotamerTrials , protocols::rotamer_recovery::RRProtocolRTMin , protocols::rpc::JSON_RPC , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::stepwise::StepWiseSampleAndScreen , protocols::wum2::WorkUnit , protocols::wum2::WorkUnit_ElScripts , protocols::wum2::WorkUnit_Wait , protocols::wum::WorkUnit_MoverWrapper , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnit_Wait , protocols::wum::WorkUnitBase
• run_ : protocols::abinitio::FoldConstraints
• run_A_ANN_Prediction() : protocols::sparta::Sparta
• run_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• run_basic_mc_algorithm() : protocols::antibody::design::AntibodyGraftDesignMover
• run_calculator() : protocols::forge::remodel::RemodelDesignMover , protocols::toolbox::task_operations::RestrictOperationsBase
• run_cluster() : protocols::forge::remodel::RemodelAccumulator
• run_design_on_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• run_deterministic_graft_algorithm() : protocols::antibody::design::AntibodyGraftDesignMover
• run_graft() : protocols::antibody::design::AntibodyGraftDesignMover
• run_graft_designer_ : protocols::antibody::design::AntibodyDesignMover
• run_kic_ : protocols::cyclic_peptide::DeclareBond
• run_mc() : protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• run_motifs() : protocols::motifs::MotifDnaPacker
• run_motifs_ : protocols::motifs::MotifDnaPacker
• run_one_job() : protocols::jd2::JobDistributor
• run_packer() : protocols::multistate_design::PackingState
• run_post_design_modeling_ : protocols::antibody::design::AntibodyDesignMover
• run_post_graft_min() : protocols::antibody::design::AntibodyGraftDesignMover
• run_post_graft_modeling_ : protocols::antibody::design::AntibodyDesignMover
• run_rattle1() : protocols::md::Rattle
• run_rattle2() : protocols::md::Rattle
• run_sa() : protocols::simple_moves::GreenPacker
• run_sequence_designer_ : protocols::antibody::design::AntibodyDesignMover
• RunAll : protocols::hotspot_hashing::movers::PlaceProbeMover
• running_average_pair() : protocols::make_rot_lib::running_average_pair
• runSpartaANN() : protocols::sparta::ANN
• runtime() : protocols::rpc::JSON_RPC
• RuntimeFeatures() : protocols::features::RuntimeFeatures
• rv_infos_ : protocols::forge::remodel::ResidueVicinityRCG
• rvec : protocols::evaluation::PCA
• rvjump_pose : protocols::forge::remodel::RemodelWorkingSet