- r -

• R() : core::scoring::ResidualDipolarCoupling
• r() : core::scoring::packing::Ball
• R_PARAM() : core::scoring::APBSConfig::R_PARAM
• radial_count() : protocols::loophash::LoopHashMap
• radial_lookup() : protocols::loophash::LoopHashMap
• radial_lookup_withkey() : protocols::loophash::LoopHashMap
• radius() : core::scoring::packing::Ball , core::scoring::packstat::CavityBall , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• radius_for_attype() : core::pack::interaction_graph::RotamerDots
• RadiusOfGyrationFeatures() : protocols::features::RadiusOfGyrationFeatures
• RadiusOfGyrationFeaturesCreator() : protocols::features::RadiusOfGyrationFeaturesCreator
• Ramachandran() : core::scoring::Ramachandran
• Ramachandran2B() : core::scoring::Ramachandran2B
• RamachandranEnergy() : core::scoring::methods::RamachandranEnergy
• RamachandranEnergy2B() : core::scoring::methods::RamachandranEnergy2B
• RamaE() : core::scoring::Ramachandran2B
• RamaE_Lower() : core::scoring::Ramachandran2B
• RamaE_Upper() : core::scoring::Ramachandran2B
• RamaScore() : protocols::frag_picker::scores::RamaScore
• ramp_chainbreak() : protocols::loops::loop_closure::ccd::LoopClosure
• ramp_down_constraints() : protocols::relax::RelaxProtocolBase
• ramping_scorefxn() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• RampingMover() : protocols::moves::RampingMover
• random_angle() : protocols::backrub::BackrubMover
• random_basepair() : protocols::dna::DNAParameters
• random_basestep() : protocols::dna::DNAParameters
• random_chunk() : protocols::nonlocal::SingleFragmentMover
• random_chunk_insertion() : protocols::rna::RNA_ChunkLibrary
• random_chunk_trial() : protocols::rna::RNA_DeNovoProtocol
• random_conformer() : protocols::ligand_docking::LigandDockProtocol
• random_domain_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• random_entity() : protocols::genetic_algorithm::EntityRandomizer
• random_fragment_insertion() : protocols::rna::RNA_FragmentMover
• random_fragment_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• random_jump_change() : protocols::rna::RNA_StructureParameters
• random_jump_trial() : protocols::rna::RNA_DeNovoProtocol
• random_limit_groupsize() : protocols::cluster::ClusterBase
• random_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• random_order_protocol() : protocols::rosetta_scripts::ParsedProtocol
• random_peptide_phi_psi_perturbation() : protocols::flexpep_docking::FlexPepDockingProtocol
• random_perturbation() : protocols::rna::RNA_HelixAssembler
• random_phipsi_from_rama() : core::scoring::Ramachandran
• random_phipsi_from_rama_by_torsion_bin() : core::scoring::Ramachandran
• random_phipsi_from_rama_by_torsion_bin_left() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_by_torsion_bin_right() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_left() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_right() : core::scoring::Ramachandran2B
• random_position() : protocols::nonlocal::BiasedFragmentMover
• random_rb_pert() : protocols::flexpep_docking::FlexPepDockingProtocol
• random_single_protocol() : protocols::rosetta_scripts::ParsedProtocol
• random_stub() : protocols::hotspot_hashing::HotspotStubSet
• random_tempname() : core::pack::dunbrack::RotamerLibrary
• random_torsion_move() : protocols::swa::monte_carlo::RNA_TorsionMover
• random_trans() : core::kinematics::Jump
• random_tree_from_jump_points() : core::kinematics::FoldTree
• randomAngle() : protocols::pockets::PocketGrid
• RandomConformerMover() : protocols::ligand_docking::RandomConformerMover
• RandomConformers() : protocols::ligand_docking::RandomConformers
• randomize() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::optimization::GA_Minimizer
• randomize_cut() : protocols::protein_interface_design::movers::Splice
• randomize_input_sequence() : protocols::anchored_design::AnchoredDesignMover
• randomize_loop() : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• randomize_loop_coords() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• randomize_loops() : protocols::forge::remodel::RemodelLoopMover
• randomize_missing_coords() : core::io::pdb::FileData , core::io::pdb::FileDataOptions
• randomize_orientations() : protocols::rna::MultipleDomainMover
• randomize_pose_rigid_bodies() : protocols::rna::MultipleDomainMover
• randomize_rigid_body_orientations() : protocols::rna::RNA_DeNovoProtocol
• randomize_stage() : protocols::forge::remodel::RemodelLoopMover
• randomlySlidePeptideJump() : protocols::flexpep_docking::FlexPepDockingProtocol
• RandomMover() : protocols::moves::RandomMover
• RandomMutation() : protocols::protein_interface_design::movers::RandomMutation
• RandomSheetBuilder() : protocols::jumping::RandomSheetBuilder
• RandomSymmetrySlider() : protocols::simple_moves::symmetry::RandomSymmetrySlider
• range() : core::scoring::PairEPotential , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::simple_filters::DeltaFilter
• range1_lower() : core::conformation::symmetry::SymDof
• range1_upper() : core::conformation::symmetry::SymDof
• range2_lower() : core::conformation::symmetry::SymDof
• range2_upper() : core::conformation::symmetry::SymDof
• range_check() : core::scoring::dssp::StrandPairing
• RangeFilter() : protocols::simple_filters::RangeFilter
• rank() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::jd2::MPIFileBufJobDistributor
• ranked_model() : protocols::abinitio::PairingStatistics
• ranking_cenfilter() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ranking_fafilter() : protocols::loophash::LoopHashMoverWrapper
• rate_threshold() : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• ratio() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• ratio_cutoff() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• RationalMonteCarlo() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• raw_array() : core::scoring::APBSConfig::I_PARAM , core::scoring::APBSConfig::R_PARAM
• raw_data_dump() : protocols::wum::WorkUnitBase
• raw_data_load() : protocols::wum::WorkUnitBase
• raw_data_size() : protocols::wum::WorkUnitBase
• raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• RawFileData() : core::io::raw_data::RawFileData
• rb_index() : core::kinematics::Jump
• rb_jump() : core::pack::task::operation::RestrictToInterface , protocols::rigid::RigidBodyMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ddG , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::task_operations::RestrictToInterface
• rb_minimizable() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• rb_minimize_all_confs() : protocols::enzdes::MinimizeStoredRBConfs
• RBResidueRange() : protocols::rbsegment_relax::RBResidueRange
• RBSegment() : protocols::rbsegment_relax::RBSegment
• RBSegmentMover() : protocols::rbsegment_relax::RBSegmentMover
• RBSegmentRelax() : protocols::rbsegment_relax::RBSegmentRelax
• RBSegmentRelaxImpl() : protocols::RBSegmentRelaxImpl
• RDC() : core::scoring::RDC
• rdc_atoms() : protocols::frag_picker::scores::RDCScore
• RDC_Evaluator() : protocols::simple_filters::RDC_Evaluator
• rdc_from_pose() : core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• RDC_Rohl() : core::scoring::RDC_Rohl
• rdc_segments_from_pose() : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• RdcEvaluatorCreator() : protocols::simple_filters::RdcEvaluatorCreator
• RDCScore() : protocols::frag_picker::scores::RDCScore
• RdcSelectEvaluatorCreator() : protocols::simple_filters::RdcSelectEvaluatorCreator
• RdcTargetEvaluatorCreator() : protocols::simple_filters::RdcTargetEvaluatorCreator
• re_init() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager , protocols::scoring::methods::pcs2::PcsInputCenterManager
• read() : core::conformation::symmetry::SymDof , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::Frame , core::fragment::NonContinuousFrame , core::fragment::DownJumpSRFD , core::grid::CartGrid< T > , core::io::serialization::BUFFER , 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_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• read_adjust_table() : protocols::frag_picker::CS2ndShift
• read_all_files_() : core::import_pose::pose_stream::SilentFilePoseInputStream
• read_all_variables_from_input_file() : protocols::pack_daemon::DynamicAggregateFunction
• read_alternate_parameter_set() : core::scoring::etable::Etable
• read_anchorfile() : protocols::anchored_design::Anchor
• read_and_set_project_prefs() : protocols::boinc::Boinc
• read_and_set_properties() : core::chemical::carbohydrates::CarbohydrateInfo
• read_and_store_fragments() : protocols::antibody::AntibodyModeler , protocols::antibody2::H3PerturbCCD
• read_assignments() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• read_atom_type_extra_parameters_table() : core::chemical::AtomTypeSet
• read_atom_type_properties_table() : core::chemical::AtomTypeSet
• read_average_res_hASA_database_file() : core::pack::interaction_graph::SurfacePotential
• read_batch() : protocols::jd2::BatchJobInputter
• read_bbdep_continuous_minimization_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• read_bbdep_table() : core::scoring::methods::IdealParametersDatabase
• read_bbind_continuous_minimization_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• read_blueprint() : protocols::jd2::parser::BluePrint
• read_BooleanOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_BooleanVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_burial_info() : protocols::rna::RNA_DataReader
• read_chain_connection() : protocols::rna::RNA_StructureParameters
• read_checkpoint() : protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::GeneticAlgorithm , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::SingleStateEntityData
• read_checkpoint_file() : protocols::frag_picker::nonlocal::NonlocalFrags
• 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_config_file() : protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• read_constraint() : core::scoring::constraints::Constraint
• read_constraints() : core::scoring::constraints::ConstraintIO , 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_constraints_new() : core::scoring::constraints::ConstraintIO
• read_CSA_file() : core::scoring::ChemicalShiftAnisotropy
• read_cst_angles() : core::scoring::constraints::ConstraintIO
• read_cst_atom_pairs() : core::scoring::constraints::ConstraintIO
• read_cst_bindingsites() : core::scoring::constraints::ConstraintIO
• read_cst_coordinates() : core::scoring::constraints::ConstraintIO
• read_cst_pose() : protocols::topology_broker::CoordConstraintClaimer
• read_data() : core::fragment::BBTorsionSRFD , core::fragment::FragmentIO , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::BoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::constraints::CircularHarmonicFunc , core::scoring::constraints::CircularSigmoidalFunc , core::scoring::constraints::ConstantFunc , core::scoring::constraints::Constraint , core::scoring::constraints::CountViolFunc , core::scoring::constraints::EtableFunc , core::scoring::constraints::FadeFunc , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::Func , core::scoring::constraints::GaussianFunc , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::KarplusFunc , core::scoring::constraints::LinearPenaltyFunction , core::scoring::constraints::MinMultiHarmonicFunc , core::scoring::constraints::MixtureFunc , core::scoring::constraints::PeriodicFunc , core::scoring::constraints::ScalarWeightedFunc , core::scoring::constraints::SigmoidFunc , core::scoring::constraints::SkipViolFunc , core::scoring::constraints::SoedingFunc , core::scoring::constraints::SOGFunc , core::scoring::constraints::SOGFunc_Impl , core::scoring::constraints::SplineFunc , core::scoring::constraints::SquareWell2Func , core::scoring::constraints::SquareWellFunc , core::scoring::constraints::SumFunc , core::scoring::constraints::TopOutFunc , core::scoring::constraints::USOGFunc , core::sequence::MatrixScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::hotspot_hashing::HotspotStubSet , protocols::toolbox::match_enzdes_util::ResInteractions , protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• read_data_file() : core::scoring::packing::HolesParams , core::scoring::packing::HolesParamsRes
• read_Data_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_data_from_file() : protocols::rna::RNA_DataReader
• read_data_info() : protocols::rna::RNA_DataReader
• read_database() : protocols::branch_angle::BranchAngleOptimizer
• read_database_file() : core::scoring::UnfoldedStatePotential
• read_datafile() : core::scoring::geometric_solvation::DatabaseOccSolEne
• read_db() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_DC_file() : core::scoring::DipolarCoupling
• read_def() : core::pack::dunbrack::DunbrackConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• read_default_parameters() : protocols::relax::CentroidRelax
• read_depth() : protocols::frag_picker::FragmentPicker
• read_disulfide_database() : core::scoring::disulfides::DisulfideMatchingDatabase
• read_done_jobs() : protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• read_eigvec_file() : protocols::evaluation::PCA
• read_energy_weight_table() : core::scoring::methods::SequenceDependentRefEnergy
• read_entities_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithm
• read_enzyme_cstfile() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• read_existing_batches() : protocols::jd2::archive::ArchiveManager
• read_exp_data() : protocols::ddG::ddGData
• read_file() : core::chemical::AtomTypeSet , core::chemical::CSDAtomTypeSet , core::chemical::ElementSet , core::chemical::IdealBondLengthSet , core::chemical::MMAtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , core::chemical::Patch , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::io::silent::SilentFileData , protocols::frags::RMSVallData , protocols::frags::TorsionFragmentLibrary , protocols::frags::VallData , protocols::jumping::JumpSetup , protocols::jumping::JumpSelector , protocols::jumping::ResiduePairJumpSetup
• read_FileOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_files() : core::chemical::ResidueTypeSet , core::coarse::CoarseEtable
• read_FileVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_fold_tree() : core::import_pose::ImportPoseOptions
• read_frag_data() : core::fragment::FragmentIO
• read_fragment_file() : core::fragment::ConstantLengthFragSet
• read_fragment_stream() : core::fragment::ConstantLengthFragSet
• read_from_binary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• read_from_binary_file() : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::OptEData
• read_from_checkpoint() : core::sequence::SequenceProfile
• read_from_cmd_line() : protocols::wum::SilentStructStore
• read_from_database() : core::sequence::MatrixScoringScheme
• read_from_file() : core::fragment::SecondaryStructure , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::sequence::ChemicalShiftSequence , core::sequence::CompositeScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , core::sequence::SimpleScoringScheme , protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary , protocols::noesy_assign::FragsToAtomDist , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::OptEData , protocols::wum::SilentStructStore
• read_from_file_no_filters() : protocols::jumping::PairingLibrary
• read_from_files() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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::GeneticAlgorithm
• read_H3_cter_fragment() : protocols::antibody2::H3CterInsert
• read_hASA_score_database_file() : core::pack::interaction_graph::SurfacePotential
• read_header() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• read_homologs() : protocols::loophash::BackboneDB
• read_hpatch_score_database_file() : core::pack::interaction_graph::SurfacePotential
• read_in_and_set_disulfides() : core::io::raw_data::DisulfideFile
• read_in_structures() : protocols::pmut_scan::PointMutScanDriver
• read_individual_constraint_new() : core::scoring::constraints::ConstraintIO
• read_info_file() : protocols::jd2::archive::Batch
• read_input_files() : protocols::noesy_assign::NoesyModule
• read_input_pose_and_copy_dofs() : protocols::swa::rna::StepWiseRNA_PoseSetup
• read_IntegerOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_IntegerVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_intensities() : core::scoring::saxs::SAXSEnergy
• read_jumps_from_file() : protocols::rna::RNA_JumpLibrary
• read_legacydb() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_ligand_superposition_file() : protocols::enzdes::EnzdesBaseProtocol
• read_list_of_residues() : core::chemical::ResidueTypeSet
• read_loop_file() : protocols::loops::Loops , protocols::loops::LoopsFileIO , protocols::loops::JSONFormattedLoopsFileReader
• 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_next_frames() : core::fragment::FragmentIO
• read_nmer_pssm() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_pssm_list() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_pssms_from_options() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_table() : core::scoring::methods::NMerRefEnergy
• read_nmer_table_list() : core::scoring::methods::NMerRefEnergy
• read_nmer_tables_from_options() : core::scoring::methods::NMerRefEnergy
• read_omega_tables() : core::scoring::OmegaTether
• read_Option_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_options() : core::pack::dunbrack::SingleResidueDunbrackLibrary , 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_P_AA() : core::scoring::P_AA
• read_P_AA_n() : core::scoring::P_AA
• read_P_AA_pp() : core::scoring::P_AA
• read_pairings() : protocols::abinitio::Templates
• read_parameters_from_file() : protocols::rna::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::pcs::PCS_file_data , protocols::scoring::methods::pcs2::PcsInputFile
• read_pdb_profile() : protocols::protein_interface_design::movers::SpliceSegment
• read_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• read_peak() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• read_pose() : core::import_pose::atom_tree_diffs::AtomTreeDiff , protocols::hybridization::TMalign
• read_pose_numbered_loops_file() : protocols::loops::PoseNumberedLoopFileReader
• read_poses() : protocols::protein_interface_design::PatchdockReader
• read_potential() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::methods::dfire::DFIRE_Potential
• read_profile() : protocols::protein_interface_design::movers::SpliceSegment
• read_psipred_ss2() : core::fragment::SecondaryStructure , protocols::frag_picker::FragmentPicker
• read_queue() : protocols::wum::WorkUnitManager
• read_queues_from_file() : protocols::wum::WorkUnitManager
• read_rama() : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• read_RDC_file() : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , protocols::frag_picker::scores::RDCScore
• 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_residue_type() : core::chemical::ResidueDatabaseIO
• read_residue_type_atom() : core::chemical::ResidueDatabaseIO
• read_residue_type_bond() : core::chemical::ResidueDatabaseIO
• read_residue_type_chi() : core::chemical::ResidueDatabaseIO
• read_residue_type_chi_rotamer() : core::chemical::ResidueDatabaseIO
• read_residue_type_cut_bond() : core::chemical::ResidueDatabaseIO
• read_residue_type_icoor() : core::chemical::ResidueDatabaseIO
• read_residue_type_properties() : core::chemical::ResidueDatabaseIO
• read_residue_type_proton_chi() : core::chemical::ResidueDatabaseIO
• read_residue_type_variant() : core::chemical::ResidueDatabaseIO
• read_ResidueType_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_residuetype_from_database() : core::chemical::ResidueDatabaseIO
• read_resonances() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• 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_rotamer_definitions() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• read_rotameric_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• read_score_headers() : core::io::silent::SilentStruct
• read_script_file() : protocols::relax::FastRelax
• read_secstruct_from_file() : protocols::rna::RNA_StructureParameters
• read_sequence() : core::io::silent::SilentStruct
• read_silent_struct() : core::conformation::symmetry::SymmetryInfo
• read_silent_struct_type_from_remark() : core::io::silent::SilentFileData
• read_spectrum() : core::scoring::saxs::SAXSEnergy
• read_spine_x() : protocols::frag_picker::FragmentPicker
• read_splice_segments() : protocols::protein_interface_design::movers::Splice
• 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_stream() : core::io::silent::SilentFileData
• read_strength() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• 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_symmetry_data_from_file() : core::conformation::symmetry::SymmData
• read_symmetry_data_from_stream() : core::conformation::symmetry::SymmData
• read_symmetry_info_from_pdb() : core::conformation::symmetry::SymmData
• read_table_from_stream() : core::scoring::OmegaTether
• read_tag() : protocols::topology_broker::AsymFoldandDockClaimer , 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::JumpClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TopologyClaimer
• read_tagfile_to_taskfactory() : protocols::optimize_weights::IterativeOptEDriver
• read_tags_fast() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• read_talos_phi_psi() : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::PhiPsiRmsd
• read_talos_ss() : core::fragment::SecondaryStructure , protocols::frag_picker::FragmentPicker
• read_template_structures() : protocols::hybridization::HybridizeProtocol
• read_topol_file() : protocols::topology_broker::TemplateJumpClaimer
• read_torsion_database() : protocols::protein_interface_design::movers::Splice
• read_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• read_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• read_vall() : protocols::frag_picker::FragmentPicker
• read_vall_torsions() : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• read_work_unit() : protocols::wum::WorkUnitManager
• read_wt_data() : protocols::ddG::ddGData
• readMRCandResize() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• ReadResfile() : core::pack::task::operation::ReadResfile
• ReadResfileAndObeyLengthEvents() : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• ReadResfileFromDB() : protocols::toolbox::task_operations::ReadResfileFromDB
• ReadScRadii() : core::scoring::sc::MolecularSurfaceCalculator
• ready() : protocols::forge::build::BuildInstruction
• ready_for_batch() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom
• ready_to_align() : protocols::swa::StepWisePoseSetup
• reassign_atoms_for_intra_residue_stubs() : core::kinematics::FoldTree
• reassign_noesy_data() : protocols::abinitio::IterativeBase
• rebuild_filter() : protocols::comparative_modeling::LoopRelaxMover
• rebuild_pdb2pose() : core::pose::PDBInfo
• rebuild_polymer_bond_dependent_atoms() : core::conformation::Conformation
• rebuild_residue_connection_dependent_atoms() : core::conformation::Conformation
• recalculate_rmsd_and_output_silent_file() : protocols::swa::rna::StepWiseRNA_Clusterer
• recalculate_transforms() : core::conformation::symmetry::SymmetricConformation
• receive_and_output_structures() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• receive_batch() : protocols::jd2::archive::MPIArchiveJobDistributor
• 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_observers_from() : core::conformation::Conformation
• 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_me() : protocols::topology_broker::ClaimerMessage
• recent_score() : protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter
• recenter() : protocols::pockets::PocketGrid
• receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• receptor_last_res() : 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::swa::StepWiseClusterer
• recompute() : core::pose::metrics::PoseMetricCalculator , core::pose::metrics::StructureDependentCalculator , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator , 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::ExplicitWaterUnsatisfiedPolarsCalculator , 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::SurfaceCalculator
• 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::OutputWriter , protocols::match::output::PDBWriter , protocols::match::output::CloudPDBWriter , protocols::match::output::WriteKinemageOutputter
• record_statistics() : protocols::backrub::BackrubSidechainMover
• 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::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• recover_original_on_failure() : protocols::forge::components::VarLengthBuild
• recover_poses_from_states() : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::MPIMultistateFitnessFunction
• recover_relevant_poses_for_entity() : protocols::pack_daemon::MultistateFitnessFunction
• recover_sidechains() : protocols::symmetric_docking::SymDockProtocol
• RecoverSideChainsMover() : protocols::comparative_modeling::RecoverSideChainsMover
• recovery_rate() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• recreate_pose_for_entity() : protocols::pack_daemon::PackDaemon
• redefine_begin_end() : protocols::fldsgn::topology::StrandPairing
• redefine_chi() : core::chemical::ResidueType
• RedefineChi() : core::chemical::RedefineChi
• rederive_chain_endings() : core::conformation::Conformation
• rederive_chain_ids() : core::conformation::Conformation
• 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_Jdipolar() : core::scoring::RDC , core::scoring::RDC_Rohl
• reduced_scorefxn() : protocols::enzdes::EnzdesBaseProtocol
• ref_baseline() : protocols::simple_filters::DeltaFilter
• ref_pose() : protocols::toolbox::DecoySetEvaluation
• ref_pose_for() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• reference_pose() : protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::features::ProteinRMSDFeatures , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• reference_structure() : protocols::rotamer_recovery::RRProtocolReferenceStructure
• reference_xyz_consistency_check() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• ReferenceEnergy() : core::scoring::methods::ReferenceEnergy
• ReferenceEnergyNoncanonical() : core::scoring::methods::ReferenceEnergyNoncanonical
• refill_torsion_string_vector() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• refine() : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• refine_grid_and_subsample_for_hit_subsets() : protocols::match::Matcher
• RefineBetaBarrel() : protocols::antibody2::RefineBetaBarrel
• RefineOneCDRLoop() : protocols::antibody2::RefineOneCDRLoop
• RefineOneCDRLoopCentroid() : protocols::antibody2::RefineOneCDRLoopCentroid
• reformat() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• refresh() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::RepGrid , 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_ex1_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex2_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex3_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex4_sample_levels() : core::pack::task::ResidueLevelTask_
• region() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet
• Region() : protocols::nonlocal::Region
• region1() : protocols::simple_filters::RegionalConnections
• region2() : protocols::simple_filters::RegionalConnections
• region_all() : core::fragment::FragSet
• region_simple() : core::fragment::FragSet
• RegionalConnections() : protocols::simple_filters::RegionalConnections
• register_batch() : protocols::jd2::archive::ArchiveManager
• register_bg_node_affected_by_rotsub() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_calculator() : core::pose::metrics::CalculatorFactory
• register_calculators() : protocols::analysis::InterfaceAnalyzerMover
• register_factory_prototypes() : protocols::jd2::DockDesignParser
• register_fc_node_affected_by_rotsub() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_fc_node_in_state0() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_ff() : core::scoring::saxs::FormFactorManager
• register_frag_id() : core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T >
• register_intergroup_calculator() : protocols::analysis::InterfaceAnalyzerMover
• register_mover() : protocols::wum::MoverList
• 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::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::PairingStatistics , protocols::abinitio::Protocol , protocols::abinitio::Template , protocols::abinitio::Templates , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::SnugDock , protocols::antibody2::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::TemperedDocking , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::AddLigandMotifRotamers , 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::FASelectSlidingWindowLoopClosure , 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::moves::CanonicalSamplingMover , 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::carbohydrates::RingConformationMover , protocols::simple_moves::ScoreMover , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::sparta::Sparta , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::DecoySetEvaluation , protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• register_score_maker() : protocols::frag_picker::scores::FragmentScoreManager
• 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::MPI_Relax , protocols::wum::WorkUnitManager
• rehash_form_factors() : core::scoring::saxs::SAXSEnergy
• reindex_residues() : core::fragment::picking_old::vall::VallSection
• reindex_sections() : core::fragment::picking_old::vall::VallLibrary
• reinitialize() : protocols::cluster::APCluster
• reinitialize_active_energy_methods() : core::scoring::MinimizationEdge
• reinitialize_for_each_job() : 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::anchored_design::AnchoredDesignMover , protocols::antibody2::SnugDock , protocols::antibody2::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
• reinitialize_minnode_for_residue() : core::scoring::ScoreFunction
• reinstate_pose() : protocols::enzdes::PredesignPerturbMover
• reinstate_side_chain_angles() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• reject_change() : core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SimpleInteractionGraph
• reject_mutant() : protocols::pmut_scan::AlterSpecDisruptionDriver , protocols::pmut_scan::PointMutScanDriver
• reject_on_chains() : protocols::pmut_scan::AlterSpecDisruptionDriver
• reject_on_interface() : protocols::pmut_scan::AlterSpecDisruptionDriver
• reject_perturbation() : core::pack::interaction_graph::FASTERInteractionGraph
• rel_deriv_dev() : core::optimization::SimpleDerivCheckResult
• relative_pose_names() : protocols::simple_filters::Operator
• relative_tmh_ori() : core::scoring::MembraneTopology
• RelativeConnectRight() : protocols::forge::build::RelativeConnectRight
• RelativePoseFilter() : protocols::simple_filters::RelativePoseFilter
• RelativeSegmentFilter() : protocols::protein_interface_design::filters::RelativeSegmentFilter
• relax() : core::pack::interaction_graph::FASTERNode , protocols::abinitio::AbrelaxApplication , protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• relax_after_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• relax_bound() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• relax_cdrs() : protocols::antibody::AntibodyModeler
• relax_favorable_poses() : protocols::vip::VIP_Mover
• relax_in_current_context() : core::pack::interaction_graph::FASTERInteractionGraph
• relax_mover() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::loophash::LoopHashMoverWrapper , 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_neighbors() : core::pack::interaction_graph::FASTERNode
• relax_optimized_CDR_grafts() : protocols::antibody::GraftMover
• relax_protocol() : protocols::abinitio::AbrelaxMover
• relax_unbound() : protocols::simple_filters::DeltaFilter
• relax_wildtype_structure() : protocols::ddg::ddGMover
• RelaxProtocolBase() : protocols::relax::RelaxProtocolBase
• RelaxScriptCommand() : protocols::relax::RelaxScriptCommand
• relay_message() : protocols::topology_broker::TopologyBroker
• release() : protocols::ligand_docking::TetherLigand
• release_buffers() : core::scoring::ResidualDipolarCoupling
• release_file() : protocols::jd2::MpiFileBuffer
• relevant_downstream_atoms() : protocols::match::MatcherTask
• remap() : protocols::comparative_modeling::features::ResidueFeature , protocols::rbsegment_relax::RBSegment
• remap_atomid_vector() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms
• remap_resid() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesFlexibleRegion , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• remap_residue_level_tasks() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• remap_residue_positions() : core::scoring::constraints::ConstraintSet
• remap_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• remap_value() : core::fragment::BaseCacheUnit , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T >
• remapped_clone() : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet
• remark() : protocols::motifs::Motif
• RemarkInfo() : core::pose::RemarkInfo
• remarks() : core::pose::PDBInfo
• rematchResToPatterson() : core::scoring::electron_density::ElectronDensity
• remember_unrecognized_res() : core::io::pdb::FileDataOptions
• remember_unrecognized_water() : core::io::pdb::FileDataOptions
• remodel() : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• remodel_max_length() : protocols::enzdes::EnzdesFlexibleRegion
• remodel_min_length() : protocols::enzdes::EnzdesFlexibleRegion
• remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• RemodelAccumulator() : protocols::forge::remodel::RemodelAccumulator
• RemodelConstraintGenerator() : protocols::forge::remodel::RemodelConstraintGenerator
• RemodelData() : protocols::forge::remodel::RemodelData
• RemodelDesignMover() : protocols::forge::remodel::RemodelDesignMover
• RemodelEnzdesCstModule() : protocols::forge::remodel::RemodelEnzdesCstModule
• RemodelLoopMover() : protocols::forge::remodel::RemodelLoopMover
• RemodelMover() : protocols::forge::remodel::RemodelMover
• remote_close_file() : protocols::jd2::MpiFileBuffer
• remove() : protocols::noesy_assign::PeakAssignmentResidueMap , protocols::topology_broker::JumpClaim , protocols::topology_broker::CutClaim , protocols::topology_broker::RootClaim
• 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_calculator() : core::pose::metrics::CalculatorFactory
• remove_chainbreaks() : protocols::jumping::JumpSample
• remove_constraint() : core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet
• remove_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet
• 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_cut() : protocols::hybridization::HybridizeFoldtreeDynamic
• remove_decoys() : protocols::abinitio::HedgeArchive
• remove_downstream_object_from_upstream_pose() : protocols::match::MatcherTask
• remove_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• remove_evaluation() : protocols::jd2::archive::EvaluatedArchive
• remove_favor_native_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• remove_gapped_positions() : core::sequence::SequenceAlignment
• 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_filter() : protocols::filters::FilterCollection
• remove_ligand_tethers() : protocols::ligand_docking::HighResDocker
• remove_member() : protocols::cluster::Cluster
• remove_method() : core::scoring::ScoreFunction
• 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_residue_pair_constraint() : core::scoring::constraints::ConstraintSet
• remove_residue_type() : core::chemical::ResidueTypeSet
• remove_residue_type_from_maps() : core::chemical::ResidueTypeSet
• remove_seqpos() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• remove_seqpos_from_template_res() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• remove_singletons() : protocols::cluster::ClusterBase
• remove_stub() : protocols::hotspot_hashing::HotspotStubSet
• remove_stubs_from_set() : protocols::hotspot_hashing::HotspotStubSet
• remove_surface_waters() : core::scoring::packstat::SimplePDB
• remove_system_signal_handler() : protocols::jd2::JobDistributor
• remove_terminal_loops() : protocols::loops::Loops
• remove_trigger() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• remove_variants_at_extra_cutpoints() : protocols::rna::RNA_LoopCloser
• remove_vector_exclude_residues() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• RemoveCsts() : protocols::forge::constraints::RemoveCsts
• RemoveNorCTermMPM() : protocols::match::RemoveNorCTermMPM
• rename_checkpoint_files() : protocols::genetic_algorithm::GeneticAlgorithm
• rename_energies() : core::io::silent::SilentStruct
• RenderGridsToKinemage() : protocols::qsar::RenderGridsToKinemage
• renormalize_quota_pools() : protocols::frag_picker::quota::QuotaCollector
• renormalize_weights() : core::scoring::constraints::SOGFunc_Impl
• renumber_after_variant_changes() : protocols::toolbox::AllowInsert
• renumber_all_decoys() : core::io::silent::SilentFileData
• renumber_decoys() : core::import_pose::pose_stream::SilentFilePoseInputStream
• renumber_jumps() : core::kinematics::FoldTree
• reorder() : core::kinematics::FoldTree
• reorder_foldtree_around_mobile_regions() : protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::MinimizeBackbone
• reorder_foldtree_find_jump() : protocols::analysis::InterfaceAnalyzerMover
• reorder_primary_data() : core::chemical::ResidueType
• reorder_restypes() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• rep_scoretype() : core::scoring::etable::BaseEtableEnergy< Derived >
• rep_weight() : core::scoring::etable::EtableEvaluator
• repack() : protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::FASTER_IG_Repacker , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::GreenPacker
• repack_and_minimize_pose() : protocols::optimize_weights::IterativeOptEDriver
• repack_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• repack_bound() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• repack_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_connection_and_residues_in_movemap() : protocols::grafting::AnchoredGraftMover
• repack_connection_and_residues_in_movemap_and_piece() : protocols::grafting::AnchoredGraftMover
• repack_period() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• repack_query() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• repack_shell() : protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• repack_to_matrix() : protocols::frag_picker::CSTalosIO
• repacking_radius() : protocols::simple_filters::RotamerBoltzmannWeight , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• repacking_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• 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() : protocols::forge::remodel::RemodelLoopMover
• repeat_generation_with_additional_residue() : protocols::forge::remodel::RemodelLoopMover
• repeat_propagation() : protocols::forge::remodel::RemodelLoopMover
• repeat_sync() : protocols::forge::remodel::RemodelLoopMover
• RepeatMover() : protocols::moves::RepeatMover
• repeats() : protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• RepGrid() : protocols::qsar::scoring_grid::RepGrid
• replace_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• replace_creator() : core::io::silent::SilentStructFactory , core::scoring::constraints::ConstraintFactory , core::sequence::SequenceFactory
• replace_noesy_filter_constraints() : protocols::abinitio::IterativeBase
• replace_res() : core::pose::PDBInfo
• replace_residue() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose
• replace_residue_subtree() : core::kinematics::AtomTree
• replace_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio
• replace_stub1() : core::chemical::orbitals::ICoorOrbitalData
• replace_stub2() : core::chemical::orbitals::ICoorOrbitalData
• replace_stub3() : core::chemical::orbitals::ICoorOrbitalData
• replace_tree() : core::kinematics::AtomTree
• replaces() : core::chemical::Patch
• ReplicaExchangeMC() : protocols::moves::ReplicaExchangeMC
• ReplicateFilter() : protocols::filters::ReplicateFilter
• ReplicateTask() : core::pack::task::operation::ReplicateTask
• report() : protocols::dna::RotamerDNAHBondFilter , protocols::docking::DockingLowResFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::filters::StochasticFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::MoveBeforeFilter , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , 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::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TerminusDistanceFilter
• Report() : protocols::features::Report
• report_adducts() : core::chemical::ResidueType
• report_all() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::rosetta_scripts::ParsedProtocol
• report_all_sm() : protocols::rosetta_scripts::ParsedProtocol
• report_aln_components() : protocols::evaluation::AlignEvaluator
• report_atom_pairs() : protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures
• report_CA_rmsd() : protocols::idealize::IdealizeMover
• report_call_order() : protocols::rosetta_scripts::ParsedProtocol
• report_data() : protocols::analysis::InterfaceAnalyzerMover
• report_ddG() : protocols::simple_moves::ddG
• report_features() : protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::HelixBundleFeatures , 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::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::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::UnrecognizedAtomFeatures
• report_features_implementation() : protocols::features::PoseConformationFeatures
• report_filter_name() : protocols::simple_filters::ReportFilter
• report_filters_to_job() : protocols::rosetta_scripts::ParsedProtocol
• 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_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_parameter_features() : core::scoring::hbonds::HBondDatabase
• report_parameter_features_schema_to_db() : core::scoring::hbonds::HBondDatabase
• report_residue_pairs() : protocols::features::PairFeatures
• report_residue_type() : core::chemical::ResidueDatabaseIO
• report_residue_type_atom() : core::chemical::ResidueDatabaseIO
• report_residue_type_bond() : core::chemical::ResidueDatabaseIO
• report_residue_type_chi() : core::chemical::ResidueDatabaseIO
• report_residue_type_chi_rotamer() : core::chemical::ResidueDatabaseIO
• report_residue_type_cut_bond() : core::chemical::ResidueDatabaseIO
• report_residue_type_icoor() : core::chemical::ResidueDatabaseIO
• report_residue_type_properties() : core::chemical::ResidueDatabaseIO
• report_residue_type_proton_chi() : core::chemical::ResidueDatabaseIO
• report_residue_type_variant() : core::chemical::ResidueDatabaseIO
• report_rotamer_recovery() : protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_features() : protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_full() : protocols::rotamer_recovery::RRReporterSQLite
• report_sm() : protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::MoveBeforeFilter , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , 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::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::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , 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::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TerminusDistanceFilter
• report_string() : protocols::simple_filters::ReportFilter
• report_structure_features() : protocols::features::ReportToDB
• report_structure_to_emperor() : protocols::loophash::MPI_LoopHashRefine_Master
• report_symmetry() : protocols::simple_filters::AlaScan
• ReportFilter() : protocols::simple_filters::ReportFilter
• ReportPSSMDifferences() : protocols::protein_interface_design::ReportPSSMDifferences
• ReportSequenceDifferences() : protocols::protein_interface_design::ReportSequenceDifferences
• ReportToDB() : protocols::features::ReportToDB
• representative_atom_name() : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• representative_downstream_algorithm() : protocols::match::Matcher
• representative_group_matches() : protocols::match::output::CloudPDBWriter
• repulsive_ramp() : protocols::antibody::AntibodyModeler , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy
• RepulsiveOnlyMover() : protocols::simple_moves::RepulsiveOnlyMover
• request_new_jobs() : protocols::wum::MPI_WorkUnitManager_Slave
• request_symmetrize_by_intersection() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• request_symmetrize_by_union() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• 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_context_graph() : core::scoring::Energies
• require_context_graph_() : core::scoring::Energies , core::scoring::symmetry::SymmetricEnergies
• require_final() : core::chemical::ResidueType
• require_mm_bend() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• require_scoring() : core::scoring::Energies
• require_target_atom_coordinate() : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• required_context_graphs() : core::scoring::Energies
• required_separation_distance() : protocols::match::BumpGrid
• requires_a_setup_for_derivatives_for_residue_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy
• requires_a_setup_for_derivatives_for_residue_pair_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::TwoBodyEnergy
• requires_a_setup_for_scoring_for_residue_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy
• requires_a_setup_for_scoring_for_residue_pair_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• requires_actcoord() : core::chemical::ResidueType , core::conformation::Residue
• requires_context_graph() : core::scoring::ScoreFunctionInfo
• requires_pose() : protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver
• reroot_fold_tree() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• reroot_fold_tree_simple() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• res() : core::scoring::constraints::BigBinConstraint , core::scoring::RDC_Rohl
• res1() : core::scoring::CSA , core::scoring::DC , core::scoring::RDC , protocols::fldsgn::topology::DimerPairing
• res1_atom1_index() : protocols::motifs::Motif
• res1_atom1_int() : protocols::motifs::Motif
• res1_atom1_name() : protocols::motifs::Motif
• res1_atom2_index() : protocols::motifs::Motif
• res1_atom2_int() : protocols::motifs::Motif
• res1_atom2_name() : protocols::motifs::Motif
• res1_atom3_index() : protocols::motifs::Motif
• res1_atom3_int() : protocols::motifs::Motif
• res1_atom3_name() : protocols::motifs::Motif
• res1_data() : core::scoring::hbonds::HBondResPairMinData
• res2() : core::scoring::CSA , core::scoring::DC , core::scoring::RDC , protocols::fldsgn::topology::DimerPairing
• res2_atom1_index() : protocols::motifs::Motif
• res2_atom1_int() : protocols::motifs::Motif
• res2_atom1_name() : protocols::motifs::Motif
• res2_atom2_index() : protocols::motifs::Motif
• res2_atom2_int() : protocols::motifs::Motif
• res2_atom2_name() : protocols::motifs::Motif
• res2_atom3_index() : protocols::motifs::Motif
• res2_atom3_int() : protocols::motifs::Motif
• res2_atom3_name() : protocols::motifs::Motif
• res2_data() : core::scoring::hbonds::HBondResPairMinData
• res3() : core::scoring::CSA
• res_anchor() : protocols::sic_dock::Rose
• res_for_rotamer() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_ids() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• res_index() : core::scoring::methods::dfire::DFIRE_Potential
• res_inds() : core::scoring::disulfides::DisulfMinData
• res_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• res_labels() : core::scoring::packstat::SimplePDB
• res_min_data() : core::scoring::MinimizationNode
• res_move() : protocols::protein_interface_design::movers::Splice
• res_moved() : core::scoring::Energies
• res_name() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• res_name1() : protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::ReportPSSMDifferences
• res_name2() : protocols::protein_interface_design::ReportSequenceDifferences
• res_num() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_pair_min_data() : core::scoring::MinimizationEdge
• res_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_res_burial() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• res_res_burial_for_scoring() : core::scoring::FACTSPotential
• res_res_carbon_hbond_derivs_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• res_res_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• res_res_geometric_sol_one_way() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• res_res_occ_sol_one_way() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• res_res_weight() : core::pack::task::IGEdgeReweightContainer
• res_switch() : protocols::abinitio::KinematicTaskControl
• res_type_linking_constraint_energy() : core::scoring::constraints::ConstraintEdge
• res_types() : protocols::simple_filters::ResidueCountFilter
• resA() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::CstResInteractions
• resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• rescale() : core::sequence::SequenceProfile
• ResConnID() : core::chemical::ResConnID
• 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
• reserve() : core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , protocols::toolbox::DecoySetEvaluation
• reserve_buffers() : core::scoring::ResidualDipolarCoupling
• reserve_edge_space() : core::graph::UEVertex< V, E >
• Reset() : core::scoring::sc::MolecularSurfaceCalculator
• reset() : core::import_pose::pose_stream::ExtendedPoseInputStream , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::MetaPoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::kinematics::Jump , core::kinematics::RT , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::pack::rotamer_set::BumpSelector , core::scoring::packstat::AreaAccumulator , core::scoring::ScoreFunction , protocols::abinitio::hConvergenceCheck , 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::hybridization::hConvergenceCheck , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::StateAccumulatingMatchFilter , protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::moves::MonteCarlo , protocols::moves::TrialCounter , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::swa::InputStreamWithResidueInfo , protocols::swa::protein::StepWiseProteinFragmentSampleGenerator , protocols::swa::protein::StepWiseProteinJumpSampleGenerator , protocols::swa::protein::StepWiseProteinMainChainSampleGenerator , protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::StepWiseCombineSampleGenerator , protocols::swa::StepWiseDoNothingSampleGenerator , protocols::swa::StepWiseIdentitySampleGenerator , protocols::swa::StepWisePoseCombineSampleGenerator , protocols::swa::StepWisePoseSampleGenerator
• 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_allowed_scoring() : core::scoring::MembraneTopology
• reset_alt_state_dots() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• reset_alt_state_total_hASA() : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• reset_alternate_states_for_uncommited_substitution() : protocols::flexpack::interaction_graph::FlexbbEdge
• reset_baseline() : protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• reset_baselines() : protocols::simple_moves::GenericMonteCarloMover
• reset_boundaries() : core::grid::CartGrid< T >
• reset_calibration_constants() : protocols::noesy_assign::PeakCalibrator
• reset_chain_endings() : core::conformation::Conformation
• reset_count() : protocols::contact_map::Contact
• reset_counters() : protocols::moves::MonteCarlo
• reset_cycle_index() : protocols::docking::DockMCMCycle , protocols::moves::CycleMover
• reset_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• reset_edge_list_iterator_for_node() : core::pack::interaction_graph::InteractionGraphBase
• reset_energy_methods() : core::scoring::ScoreFunction
• reset_eval_count() : core::optimization::func_1d
• reset_filters() : protocols::match::output::MatchProcessor
• reset_from_interface() : protocols::dna::DnaInterfaceMinMover
• reset_from_previous_deltaHpatch_comp() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• reset_from_ref() : protocols::scoring::methods::pcs2::PcsTensor
• reset_grid() : protocols::match::Bool3DGrid
• reset_grouper() : protocols::match::output::MatchConsolidator
• reset_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• reset_jump_rb_deltas() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• reset_last_accepted() : protocols::moves::MonteCarlo
• reset_move_data() : core::conformation::Conformation
• reset_nblist() : core::scoring::Energies
• 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_raw_counter() : protocols::canonical_sampling::SimulatedTempering
• reset_recent_network_state_history() : core::pack::annealer::FASTERAnnealer
• reset_recovery() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• reset_relaxed() : core::pack::interaction_graph::FASTERNode
• reset_relaxed_for_neighbors() : core::pack::interaction_graph::FASTERNode
• reset_res_moved() : core::scoring::Energies
• reset_rpe_calculations_count() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• reset_scorefxn() : protocols::moves::MonteCarlo
• reset_state_energies() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge
• reset_statistics() : protocols::backrub::BackrubSidechainMover , protocols::noesy_assign::PeakCalibrator
• reset_status() : protocols::moves::Mover
• reset_structure_moved() : core::conformation::Conformation
• reset_surf() : core::scoring::packing::PoseBalls
• reset_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• reset_surface_residue_information() : core::scoring::solid_surface::SurfaceEnergies
• reset_tensor() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcs2::PcsTensor
• reset_timing_stats() : protocols::wum::MPI_WorkUnitManager
• reset_tmh_insert() : core::scoring::MembraneTopology
• reset_trans_axis() : protocols::rigid::UniformSphereTransMover
• reset_unique_id() : protocols::motifs::IRCollection
• reset_x() : protocols::evaluation::PCA
• resetInstance() : core::scoring::constraints::USOGFunc
• resfile() : protocols::flxbb::DesignTask , protocols::forge::components::BDR
• resfile_commands() : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• resfile_general_property() : protocols::protein_interface_design::filters::FilterScanFilter
• resfile_name() : protocols::protein_interface_design::filters::FilterScanFilter
• ResfileContents() : core::pack::task::ResfileContents
• ResFileOutputter() : protocols::outputter::ResFileOutputter
• ResfileReaderException() : core::pack::task::ResfileReaderException
• ResFilterComposition() : core::pack::task::operation::ResFilterComposition
• ResFilterFactory() : core::pack::task::operation::ResFilterFactory
• ResFilterRegistrator() : core::pack::task::operation::ResFilterRegistrator< T >
• resi() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• ResId() : protocols::moves::ResId
• resid() : core::chemical::ResConnID , core::conformation::RotamerSetBase , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::task::operation::RotamerExplosion , core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance , protocols::protein_interface_design::movers::BBDofs
• resid_2_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• resid_2_moltenres_vector() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• resid_2_moltenresid() : core::pack::rotamer_set::ContinuousRotamerSets
• resid_for_entry() : core::scoring::trie::CPDataCorrespondence
• ResidualDipolarCoupling() : core::scoring::ResidualDipolarCoupling
• ResidualDipolarCoupling_Rohl() : core::scoring::ResidualDipolarCoupling_Rohl
• ResidualDipolarCouplingEnergy() : core::scoring::methods::ResidualDipolarCouplingEnergy
• ResidualDipolarCouplingEnergy_Rohl() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• ResidualDipolarCouplingEnergyRigidSegments() : core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• ResidualDipolarCouplingRigidSegments() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• residue() : core::conformation::Conformation , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::pose::Pose , core::scoring::constraints::FourPointsFunc , core::scoring::constraints::XYZ_Func , core::scoring::constraints::ResidueXYZ , core::scoring::constraints::ResiduePairXYZ , core::scoring::constraints::ConformationXYZ , protocols::hotspot_hashing::HotspotStub
• Residue() : core::conformation::Residue
• residue_() : core::conformation::Conformation
• residue_action() : core::pack::task::ResfileCommand , core::pack::task::NATRO , core::pack::task::NATAA , core::pack::task::ALLAA , core::pack::task::ALLAAxc , core::pack::task::ALLAAwc , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::NOTAA , core::pack::task::EMPTY , core::pack::task::POLAR , core::pack::task::APOLAR , core::pack::task::APOLA , core::pack::task::EX , core::pack::task::NC , core::pack::task::EX_CUTOFF , core::pack::task::USE_INPUT_SC , core::pack::task::AUTO , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::NO_ADDUCTS , core::pack::task::FIX_HIS_TAUTOMER
• residue_atom_pair_energy() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_backbone_backbone() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_sidechain_backbone() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_sidechain_sidechain() : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric
• residue_atom_pair_energy_sidechain_whole() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator
• residue_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_atomtree_collection() : core::pack::scmin::AtomTreeCollection
• residue_atomtree_collection_op() : core::pack::scmin::AtomTreeCollection
• residue_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_conformations_redundant() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• residue_connect_atom_index() : core::chemical::ResidueType , core::conformation::Residue
• residue_connection() : core::chemical::ResidueType , core::conformation::Residue
• residue_connection_conn_id() : core::conformation::Residue
• residue_connection_id_for_atom() : core::chemical::ResidueType
• residue_connection_is_polymeric() : core::chemical::ResidueType
• residue_connection_partner() : core::conformation::Residue
• residue_connections_for_atom() : core::chemical::ResidueType
• 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_energy() : core::pack::dunbrack::DunbrackEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::methods::BurialEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::pHEnergy , core::scoring::methods::PyContextIndependentOneBodyEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::nv::NVscore , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SugarCloseEnergy , protocols::fldsgn::potentials::AACompositionEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::SpecialRotamerEnergy
• residue_energy_ext() : core::scoring::methods::OneBodyEnergy
• residue_fast_pair_energy_attached_H() : core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
• residue_forms_disulfide() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• 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_id() : core::conformation::AtomGraphVertexData
• residue_in_chains() : core::scoring::methods::PoissonBoltzmannEnergy
• residue_indices() : core::pack::task::operation::OperateOnCertainResidues
• residue_info() : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• residue_is_in_h3_loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• residue_is_surface() : core::scoring::solid_surface::SurfaceEnergies
• residue_iterated_on() : core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator
• residue_neighbors() : protocols::simple_filters::NonSequentialNeighborsFilter
• residue_neighbors_updated() : core::scoring::Energies
• residue_num() : protocols::scoring::methods::pcs::PCS_line_data
• residue_packed() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• residue_pair() : protocols::fldsgn::topology::StrandPairing
• residue_pair_constraint_exists() : core::scoring::constraints::ConstraintSet , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_begin() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_end() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_exists() : core::scoring::constraints::ConstraintSet
• residue_pair_energy() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::VDW_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_FA_Stack , core::scoring::methods::LK_hack , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::CSD_TorsionEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface::DDPscore , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::PyContextIndependentTwoBodyEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::sym_e::symEnergy , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::scoring::methods::InterchainPairEnergy
• residue_pair_energy_aro_aro() : core::scoring::hackaro::HackAroEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro
• residue_pair_energy_ext() : core::scoring::hbonds::HBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::methods::TwoBodyEnergy
• residue_pair_energy_one_way() : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_Mg_Energy
• residue_pair_energy_RNA() : core::scoring::hackelec::RNAHackElecEnergy
• residue_pair_energy_sorted() : core::scoring::methods::CartesianBondedEnergy
• residue_range_is_protein() : protocols::features::BetaTurnDetectionFeatures
• residue_range_is_relevant() : protocols::features::BetaTurnDetectionFeatures
• residue_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• residue_set_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_set_numbers_to_decomposition() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_task() : core::pack::task::PackerTask_ , core::pack::task::PackerTask
• residue_total_energies() : core::scoring::Energies
• residue_total_energy() : core::scoring::Energies
• residue_type() : core::pose::Pose , core::conformation::Conformation
• residue_type_param_set() : core::scoring::methods::MMBondAngleEnergy
• residue_type_set() : core::import_pose::ImportPoseOptions , core::chemical::ChemicalManager , core::chemical::ResidueType , core::conformation::Residue , protocols::forge::build::BuildInstruction , protocols::simple_moves::ExtendedPoseMover
• residue_type_set_tag() : core::chemical::ResidueLoaderOptions
• residue_types() : core::chemical::ResidueTypeSet
• residue_xyz_change_list_begin() : core::kinematics::AtomTree
• residue_xyz_change_list_end() : core::kinematics::AtomTree
• ResidueAtomTreeCollection() : core::pack::scmin::ResidueAtomTreeCollection
• ResidueAtomTreeCollectionMomento() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• ResidueBBDofs() : protocols::protein_interface_design::movers::ResidueBBDofs
• ResidueBurialFeatures() : protocols::features::ResidueBurialFeatures
• ResidueBurialFeaturesCreator() : protocols::features::ResidueBurialFeaturesCreator
• ResidueBurialFilter() : protocols::simple_filters::ResidueBurialFilter
• ResidueCartBondedParameters() : core::scoring::methods::ResidueCartBondedParameters
• ResidueConformationFeatures() : protocols::features::ResidueConformationFeatures
• ResidueConformationFeaturesCreator() : protocols::features::ResidueConformationFeaturesCreator
• ResidueConnection() : core::chemical::ResidueConnection
• ResidueCoordinateChangeList() : core::kinematics::ResidueCoordinateChangeList
• ResidueCountFilter() : protocols::simple_filters::ResidueCountFilter
• ResidueDatabaseIO() : core::chemical::ResidueDatabaseIO
• ResidueDecompositionByChainCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• ResidueDecompositionCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• ResidueDistanceFilter() : protocols::simple_filters::ResidueDistanceFilter
• ResidueFeatureFactory() : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueFeatures() : protocols::features::ResidueFeatures
• ResidueFeaturesCreator() : protocols::features::ResidueFeaturesCreator
• ResidueGridScoresFeatures() : protocols::features::ResidueGridScoresFeatures
• ResidueGridScoresFeaturesCreator() : protocols::features::ResidueGridScoresFeaturesCreator
• ResidueGroupIGEdgeUpweighter() : protocols::toolbox::ResidueGroupIGEdgeUpweighter
• ResidueHasProperty() : core::pack::task::operation::ResidueHasProperty
• ResidueIEFilter() : protocols::simple_filters::ResidueIEFilter
• ResidueIndexDescription() : protocols::loops::ResidueIndexDescription
• ResidueIndexDescriptionFromFile() : protocols::loops::ResidueIndexDescriptionFromFile
• ResidueIndexIs() : core::pack::task::operation::ResidueIndexIs
• ResidueIndexIsnt() : core::pack::task::operation::ResidueIndexIsnt
• ResidueInformation() : core::io::pdb::ResidueInformation
• ResidueKey() : core::pose::PDBPoseMap::ResidueKey
• ResidueKinemageWriter() : protocols::match::output::ResidueKinemageWriter
• ResidueKinWriter() : core::conformation::ResidueKinWriter
• ResidueLacksProperty() : core::pack::task::operation::ResidueLacksProperty
• ResidueLevelTask_() : core::pack::task::ResidueLevelTask_
• ResidueLoader() : core::chemical::ResidueLoader
• ResidueLoaderOptions() : core::chemical::ResidueLoaderOptions
• ResidueName3Is() : core::pack::task::operation::ResidueName3Is
• ResidueName3Isnt() : core::pack::task::operation::ResidueName3Isnt
• ResidueNblistData() : core::scoring::ResidueNblistData
• ResiduePairJump() : protocols::jumping::ResiduePairJump
• ResiduePairJumpSetup() : protocols::jumping::ResiduePairJumpSetup
• ResiduePairJumpSingle() : protocols::jumping::ResiduePairJumpSingle
• ResiduePairNeighborList() : core::scoring::ResiduePairNeighborList
• ResiduePairXYZ() : core::scoring::constraints::ResiduePairXYZ
• ResiduePDBIndexIs() : core::pack::task::operation::ResiduePDBIndexIs
• ResiduePDBIndexIsnt() : core::pack::task::operation::ResiduePDBIndexIsnt
• ResidueRecord() : core::pose::PDBInfo::ResidueRecord
• residues() : core::fragment::picking_old::vall::VallSection , core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , core::scoring::packing::HolesParamsRes , core::fragment::picking_old::vall::VallSection , core::scoring::constraints::NonResidueTypeConstraint
• residues_adjacent_for_subunit_pair() : core::pack::interaction_graph::SymmOnTheFlyEdge
• residues_append() : core::conformation::Conformation
• residues_are_different() : protocols::dna::PDBOutput
• residues_compatible() : protocols::enzdes::SecondaryMatchProtocol
• residues_delete() : core::conformation::Conformation
• residues_for_entity_begin() : protocols::pack_daemon::EntityCorrespondence
• residues_for_entity_end() : protocols::pack_daemon::EntityCorrespondence
• residues_insert() : core::conformation::Conformation
• residues_moved_begin() : core::kinematics::ResidueCoordinateChangeList
• residues_moved_end() : core::kinematics::ResidueCoordinateChangeList
• residues_replace() : core::conformation::Conformation
• residues_to_mutate() : protocols::ddg::ddGMover
• ResidueScoresFeatures() : protocols::features::ResidueScoresFeatures
• ResidueScoresFeaturesCreator() : protocols::features::ResidueScoresFeaturesCreator
• ResidueSecondaryStructureFeatures() : protocols::features::ResidueSecondaryStructureFeatures
• ResidueSecondaryStructureFeaturesCreator() : protocols::features::ResidueSecondaryStructureFeaturesCreator
• ResidueSelectorSingle() : core::chemical::ResidueSelectorSingle
• 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
• ResidueTorsionRestraints() : protocols::ligand_docking::ResidueTorsionRestraints
• ResidueTotalScoresFeatures() : protocols::features::ResidueTotalScoresFeatures
• ResidueTotalScoresFeaturesCreator() : protocols::features::ResidueTotalScoresFeaturesCreator
• ResidueType() : core::chemical::ResidueType
• residueType() : protocols::jumping::ResiduePairJumpSingle
• ResidueTypeConstraint() : core::scoring::constraints::ResidueTypeConstraint
• ResidueTypeFilter() : core::pack::task::operation::ResidueTypeFilter
• ResidueTypeLinkingConstraint() : core::scoring::constraints::ResidueTypeLinkingConstraint
• ResidueTypeSet() : core::chemical::ResidueTypeSet
• ResidueTypesFeatures() : protocols::features::ResidueTypesFeatures
• ResidueTypesFeaturesCreator() : protocols::features::ResidueTypesFeaturesCreator
• ResidueVicinityInfo() : protocols::forge::remodel::ResidueVicinityInfo
• ResidueVicinityRCG() : protocols::forge::remodel::ResidueVicinityRCG
• ResidueXYZ() : core::scoring::constraints::ResidueXYZ
• resindex() : protocols::loops::ResidueIndexDescription
• ResInteractions() : protocols::toolbox::match_enzdes_util::ResInteractions
• resize() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::SequenceMapping , core::io::raw_data::DecoyStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::rotamer_set::RotamerCouplings , core::pack::rotamer_set::RotamerLinks , core::scoring::dna::BasePartner , core::scoring::electron_density_atomwise::ElectronDensityAtomwise , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::Strands , core::scoring::Helices , core::scoring::SS_Info , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::SS_Info2 , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frags::TorsionFragmentLibrary , protocols::jumping::JumpSample , protocols::loops::LoopsFileData , protocols::frag_picker::quota::SecondaryStructurePool , core::scoring::BB_Pos , core::pack::interaction_graph::RotamerDotsCache , core::scoring::electron_density::ElectronDensity , core::id::DOF_ID_Map< T > , core::id::AtomID_Map< T >
• resize_arrays() : protocols::match::output::UpstreamHitCacher
• resize_asu() : core::conformation::symmetry::SymmetryInfo
• resize_atom_records() : core::pose::PDBInfo
• resize_bb_donor_acceptor_arrays() : core::scoring::hbonds::HBondSet
• resize_chi() : core::io::silent::ProteinSilentStruct_Template< T >
• resize_residue_records() : core::pose::PDBInfo
• ResizeArray() : protocols::hybridization::TMalign
• ResLvlTaskOperationFactory() : core::pack::task::operation::ResLvlTaskOperationFactory
• ResLvlTaskOperationRegistrator() : core::pack::task::operation::ResLvlTaskOperationRegistrator< T >
• resn() : protocols::protein_interface_design::movers::BBDofs
• resname() : protocols::contact_map::ContactPartner
• resnum() : core::sequence::Sequence , protocols::comparative_modeling::features::ResidueFeature , 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::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::protein_interface_design::movers::AddChainBreak , protocols::comparative_modeling::features::ResidueFeature
• resnum_map() : protocols::jd2::parser::BluePrint
• resnum_to_rosetta_num() : core::io::raw_data::DisulfideFile
• resnums() : protocols::simple_filters::ResidueIEFilter
• 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::loop_mover::LoopMover , protocols::loops::GuardedLoopsFromFile
• resolve_loop_indices_once() : protocols::loops::GuardedLoopsFromFile
• resolve_loopfile_indices() : protocols::comparative_modeling::LoopRelaxMover
• resolve_loops() : protocols::loops::LoopsFileData
• resolve_residue() : protocols::topology_broker::TopologyBroker
• resolve_sequence_label() : protocols::topology_broker::TopologyBroker
• resolve_trie_vs_path() : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3
• resolve_trie_vs_trie() : core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrieBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::TrieCountPairBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::TrieCountPairBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::trie::RotamerTrieBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrieBase , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::hbonds::hbtrie::HBCountPairFunction
• resolve_uncommitted_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• resolved_level_best_rmsd() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• Resonance() : protocols::noesy_assign::Resonance
• resonance_id() : protocols::noesy_assign::PeakAssignment
• ResonanceList() : protocols::noesy_assign::ResonanceList
• resonances() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignment
• resonances_at_residue() : protocols::noesy_assign::ResonanceList
• resource_description() : protocols::loops::LoopsFileFallbackConfigurationCreator
• RespairInteractions() : core::scoring::custom_pair_distance::RespairInteractions
• ResPairMinimizationData() : core::scoring::ResPairMinimizationData
• respect_this_movemap() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• respond_to_peripheral_hitlist_change() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm
• respond_to_primary_hitlist_change() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::ClassicMatchAlgorithm
• ResRangePredicate() : core::scoring::ResRangePredicate
• ResResEnergyInvoker() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• ResSingleMinimizationData() : core::scoring::ResSingleMinimizationData
• restart() : protocols::jd2::FileSystemJobDistributor , protocols::frag_picker::quota::TorsionBinPool , protocols::jd2::JobDistributor
• restart_mode() : protocols::forge::components::VarLengthBuild
• restart_simulation() : protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::ThermodynamicObserver
• restore_archive() : protocols::jd2::archive::ArchiveManager
• restore_best_exemplars() : protocols::cluster::APCluster
• restore_cter() : protocols::ub_e2c::ubi_e2c_modeler
• restore_from_file() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::abinitio::IterativeAbrelax , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::AbstractArchiveBase
• restore_original_foldtree() : protocols::hybridization::FoldTreeHybridize
• restore_phi_psi_omega_over_loop_residues() : protocols::swa::protein::StepWiseProteinCCD_Closer
• restore_phi_psi_over_loop_residues() : protocols::swa::protein::StepWiseProteinCCD_Closer
• restore_status() : protocols::jd2::archive::DebugArchive , protocols::abinitio::HedgeArchive , protocols::jd2::archive::ArchiveBase , protocols::abinitio::IterativeBase
• 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
• restrict_aatypes_for_selection() : protocols::toolbox::SelectResiduesByLayer
• restrict_absent_canonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_absent_nas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_identities() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_nonnative_canonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_sequence_profile() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• restrict_to_interfacial_loop_packing() : protocols::ub_e2c::ubi_e2c_modeler
• restrict_to_nbrs() : protocols::ddg::ddGMover
• restrict_to_repacking() : core::pack::task::ResidueLevelTask_ , protocols::simple_moves::DesignRepackMover , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::PackerTask
• restrict_to_residue() : core::pack::task::operation::DisallowIfNonnative
• restrict_to_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• RestrictAbsentCanonicalAAS() : core::pack::task::operation::RestrictAbsentCanonicalAAS
• RestrictAbsentCanonicalAASRLT() : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• RestrictByCalculatorsOperation() : protocols::toolbox::task_operations::RestrictByCalculatorsOperation
• RestrictChainToRepackingOperation() : protocols::toolbox::task_operations::RestrictChainToRepackingOperation
• RestrictConservedLowDdgOperation() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• RestrictDesignToProteinDNAInterface() : protocols::dna::RestrictDesignToProteinDNAInterface
• RestrictIdentitiesAtAlignedPositionsOperation() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• 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
• RestrictToAlignedSegmentsOperation() : protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• RestrictToCDRH3Loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• RestrictToInterface() : protocols::toolbox::task_operations::RestrictToInterface , core::pack::task::operation::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterface , core::pack::task::operation::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterface , core::pack::task::operation::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterface
• RestrictToInterfaceOperation() : protocols::toolbox::task_operations::RestrictToInterfaceOperation
• RestrictToInterfaceVectorOperation() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• RestrictToLoopsAndNeighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• RestrictToNeighborhoodOperation() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• RestrictToTerminiOperation() : protocols::toolbox::task_operations::RestrictToTerminiOperation
• RestrictYSDesign() : core::pack::task::operation::RestrictYSDesign
• restype() : protocols::match::upstream::BuildSet , protocols::match::upstream::UpstreamBuilder , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::downstream::TargetRotamerCoords
• restype_atomno() : protocols::match::downstream::TargetRotamerCoords
• restype_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• restype_geometry() : protocols::match::upstream::BuildSet
• restype_id_2_collision_check_id() : protocols::toolbox::match_enzdes_util::LigandConformer
• restype_index() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• restype_name1() : protocols::motifs::Motif
• restype_name2() : protocols::motifs::Motif
• restype_possible_at_position() : protocols::enzdes::SecondaryMatchProtocol
• restype_set() : protocols::enzdes::EnzdesBaseProtocol
• result_query_string() : protocols::wum::DatabaseEntryWorkUnit
• retrieve() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::VectorCacheUnit< T > , core::fragment::MapCacheUnit< T > , core::fragment::CacheWrapper< T, XCacheUnit > , protocols::hotspot_hashing::HotspotStubSet , core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::VectorCacheUnit< T >
• retrieve_calculator() : core::pose::metrics::CalculatorFactory
• retrieve_energy() : core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::ResidueNeighborIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::constraints::CstResNeighbIterator
• retrieve_relevant_poses_for_entity() : protocols::pack_daemon::DaemonSet
• retrieve_tensor_from_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• retrieve_values() : protocols::protein_interface_design::movers::Splice
• return_centroid() : protocols::abinitio::Protocol
• return_key() : protocols::loophash::LoopHashMap
• return_lowest_poses_in_clusters() : protocols::cluster::ClusterBase
• return_pseudo_hits() : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_top_poses_in_clusters() : protocols::cluster::ClusterBase
• ReturnSidechainMover() : protocols::simple_moves::ReturnSidechainMover
• revamp_weight_by_burial() : core::scoring::methods::PoissonBoltzmannEnergy
• reverse() : core::id::SequenceMapping , core::kinematics::Jump , core::kinematics::RT , core::id::BondID , core::scoring::dssp::Pairing
• reverse_score_filter() : core::io::silent::SilentFileData
• reversed() : core::id::BondID , protocols::features::helixAssembly::HelicalFragment , core::kinematics::Jump
• Reversion() : protocols::dna::Reversion
• reversion_scan() : protocols::dna::DnaInterfacePacker
• reversion_score() : protocols::dna::Reversion
• Revert() : protocols::protein_interface_design::Revert
• revert_conformer() : protocols::ligand_docking::Transform
• revert_jumps() : protocols::ligand_docking::Transform
• revert_loops_to_original() : protocols::hybridization::FoldTreeHybridize
• revert_move() : protocols::ligand_docking::Transform
• revision_id() : core::scoring::constraints::ConstraintSet , protocols::match::OccupiedSpaceHash
• reweight() : protocols::canonical_sampling::SimulatedTempering
• reweighters_begin() : core::pack::task::IGEdgeReweightContainer
• reweighters_end() : core::pack::task::IGEdgeReweightContainer
• rg() : protocols::simple_moves::symmetry::SymmetrySlider
• RG_Energy() : core::scoring::methods::RG_Energy
• RG_Energy_Fast() : core::scoring::methods::RG_Energy_Fast
• RG_Energy_RNA() : core::scoring::rna::RG_Energy_RNA
• RG_MinData() : core::scoring::methods::RG_MinData
• RGFilter() : protocols::simple_filters::RGFilter
• rgstr_shift() : protocols::fldsgn::topology::StrandPairing
• rho() : core::scoring::packstat::PackingScore , core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore , core::scoring::packing::HolesParamsRes
• right() : protocols::topology_broker::DofClaim
• right_named_stub_id() : protocols::forge::build::ConnectRight
• right_position() : protocols::forge::build::ConnectRight
• right_stub_atoms() : protocols::forge::build::ConnectRight
• rigid_body_trial() : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• rigid_perturb_vector() : core::scoring::MembranePotential
• 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
• RigidBodyRandomizeMover() : protocols::rigid::RigidBodyRandomizeMover
• RigidBodySampler() : protocols::swa::RigidBodySampler
• RigidBodySpinMover() : protocols::rigid::RigidBodySpinMover
• RigidBodyTransMover() : protocols::rigid::RigidBodyTransMover
• RigidChunkClaimer() : protocols::topology_broker::RigidChunkClaimer
• RigidLigandBuilder() : protocols::match::downstream::RigidLigandBuilder
• RigidSearchMover() : protocols::ligand_docking::RigidSearchMover
• ring_current_coeff() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_height() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_intensity() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_radius() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_size() : core::chemical::carbohydrates::CarbohydrateInfo
• RingConformationMover() : protocols::simple_moves::carbohydrates::RingConformationMover
• rise() : protocols::dna::DNABasestep
• rms() : protocols::optimize_weights::SingleStructureData
• rms_cutoff() : protocols::protein_interface_design::movers::Splice
• RMS_Energy() : core::scoring::methods::RMS_Energy
• rmsd() : protocols::toolbox::DecoySetEvaluation , core::fragment::FragmentRmsd , protocols::pockets::PlaidFingerprint
• rmsd_cutoff() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• rmsd_cutoff_1() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_cutoff_2() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rmsd_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• RmsdEvaluator() : protocols::simple_filters::RmsdEvaluator
• RmsdEvaluatorCreator() : protocols::simple_filters::RmsdEvaluatorCreator
• RmsdFilter() : protocols::protein_interface_design::filters::RmsdFilter
• RmsdTargetEvaluatorCreator() : protocols::simple_filters::RmsdTargetEvaluatorCreator
• rmsf() : protocols::toolbox::DecoySetEvaluation
• RMSVallData() : protocols::frags::RMSVallData
• rna() : core::import_pose::ImportPoseOptions
• RNA_AddMover() : protocols::swa::monte_carlo::RNA_AddMover
• RNA_AddOrDeleteMover() : protocols::swa::monte_carlo::RNA_AddOrDeleteMover
• RNA_AnalyticLoopCloser() : protocols::swa::rna::RNA_AnalyticLoopCloser
• RNA_AtomVDW() : core::scoring::rna::RNA_AtomVDW
• rna_backbone_backbone_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_base_atoms() : core::chemical::rna::RNA_ResidueType
• rna_base_axis_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_backbone_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_backbone_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_pair_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stack_axis_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stack_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stagger_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• RNA_BaseBaseEnergy() : core::scoring::rna::RNA_BaseBaseEnergy
• rna_bond_geometry_energy() : core::scoring::constraints::ConstraintEdge
• RNA_BulgeEnergy() : core::scoring::rna::RNA_BulgeEnergy
• rna_ccd_close() : protocols::rna::RNA_LoopCloser
• rna_centroid_info() : core::scoring::rna::RNA_ScoringInfo
• RNA_CentroidInfo() : core::scoring::rna::RNA_CentroidInfo
• RNA_ChemicalShiftEnergy() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy
• RNA_ChemicalShiftPotential() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• RNA_ChunkLibrary() : protocols::rna::RNA_ChunkLibrary
• RNA_CS_parameters() : core::scoring::rna::chemical_shift::RNA_CS_parameters
• RNA_CS_residue_parameters() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• rna_data() : core::scoring::rna::RNA_DataInfo
• rna_data_info() : core::scoring::rna::RNA_ScoringInfo
• RNA_DataBackboneEnergy() : core::scoring::rna::RNA_DataBackboneEnergy
• RNA_DataInfo() : core::scoring::rna::RNA_DataInfo
• RNA_DataReader() : protocols::rna::RNA_DataReader
• RNA_Datum() : core::scoring::rna::RNA_Datum
• RNA_DeNovoProtocol() : protocols::rna::RNA_DeNovoProtocol
• RNA_FA_Stack() : core::scoring::rna::RNA_FA_Stack
• rna_filtered_base_base_info() : core::scoring::rna::RNA_ScoringInfo
• RNA_FilteredBaseBaseInfo() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• RNA_FittedTorsionInfo() : core::scoring::rna::RNA_FittedTorsionInfo
• RNA_FragmentMover() : protocols::rna::RNA_FragmentMover
• RNA_Fragments() : protocols::rna::RNA_Fragments
• RNA_FullAtomStackingEnergy() : core::scoring::rna::RNA_FullAtomStackingEnergy
• RNA_FullAtomVDW_BasePhosphate() : core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
• RNA_HelixAssembler() : protocols::rna::RNA_HelixAssembler
• RNA_IdealCoord() : protocols::rna::RNA_IdealCoord
• RNA_JumpLibrary() : protocols::rna::RNA_JumpLibrary
• RNA_LJ_BaseEnergy() : core::scoring::rna::RNA_LJ_BaseEnergy
• RNA_LoopCloser() : protocols::rna::RNA_LoopCloser
• RNA_LoopCloseSampler() : protocols::swa::rna::RNA_LoopCloseSampler
• RNA_LowResolutionPotential() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_Mg_Energy() : core::scoring::rna::RNA_Mg_Energy
• RNA_Mg_KnowledgeBasedPotential() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• RNA_Minimizer() : protocols::rna::RNA_Minimizer
• RNA_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• rna_note_chi_controls_atom() : core::chemical::rna::RNA_ResidueType
• RNA_O2StarMover() : protocols::swa::monte_carlo::RNA_O2StarMover
• RNA_PairingTemplate() : protocols::rna::RNA_PairingTemplate
• RNA_PairwiseLowResolutionEnergy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_raw_base_base_info() : core::scoring::rna::RNA_ScoringInfo
• RNA_RawBaseBaseInfo() : core::scoring::rna::RNA_RawBaseBaseInfo
• RNA_Relaxer() : protocols::rna::RNA_Relaxer
• rna_repulsive_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_ResidueType() : core::chemical::rna::RNA_ResidueType
• RNA_ScoringInfo() : core::scoring::rna::RNA_ScoringInfo
• RNA_SecStructInfo() : protocols::rna::RNA_SecStructInfo
• RNA_SilentStruct() : core::io::silent::RNA_SilentStruct
• RNA_SilentStructCreator() : core::io::silent::RNA_SilentStructCreator
• RNA_StructureParameters() : protocols::rna::RNA_StructureParameters
• RNA_SugarCloseEnergy() : core::scoring::rna::RNA_SugarCloseEnergy
• RNA_suite_list() : protocols::rna::RNA_suite_list
• RNA_SWA_MonteCarloMover() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• RNA_TorsionEnergy() : core::scoring::rna::RNA_TorsionEnergy
• RNA_TorsionPotential() : core::scoring::rna::RNA_TorsionPotential
• RNA_type() : core::chemical::ResidueType , core::conformation::Residue
• rna_update_last_controlling_chi() : core::chemical::rna::RNA_ResidueType
• RNA_VDW_Energy() : core::scoring::rna::RNA_VDW_Energy
• RNAHackElecEnergy() : core::scoring::hackelec::RNAHackElecEnergy
• rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• roll() : protocols::dna::DNABasestep
• RollMover() : protocols::rigid::RollMover
• root() : core::kinematics::FoldTree , core::kinematics::AtomTree , core::kinematics::Node , protocols::jumping::ResiduePairJumpSetup
• root_expression() : protocols::pack_daemon::SurrogateVariableExpression
• root_from_code() : core::chemical::carbohydrates::CarbohydrateInfo
• RootClaim() : protocols::topology_broker::RootClaim
• Rose() : protocols::sic_dock::Rose
• rosetta2methyl() : protocols::noesy_assign::MethylNames
• rosetta2nmr() : protocols::noesy_assign::MethylNames
• rot_center() : protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodySpinMover
• rot_freq() : core::pack::annealer::SimAnnealerBase
• rot_level() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• rot_magnitude() : protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyDofPerturbMover
• rot_number() : protocols::optimize_weights::PNatAAOptERotamerData
• rot_perturb_vector() : core::scoring::MembranePotential
• rot_sets() : protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::PackDaemon
• rot_to_pack() : core::pack::annealer::RotamerAssigningAnnealer
• rot_well() : core::pack::dunbrack::DunbrackRotamerSampleData
• rotAlign2DPose() : core::scoring::electron_density::ElectronDensity
• rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::dunbrack::RotamericData< T > , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSetsBase , protocols::flexpack::interaction_graph::OTFFlexbbNode , core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSubset , core::pack::interaction_graph::RotamerDots , core::pack::rotamer_set::RotamerSets , core::pack::interaction_graph::InvRotamerDots
• rotamer_aa() : core::chemical::ResidueType
• rotamer_couplings() : core::pack::task::PackerTask_ , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::PackerTask
• rotamer_couplings_exist() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_data_begin() : protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData
• rotamer_data_end() : protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData
• rotamer_energy() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• rotamer_energy_deriv() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary
• rotamer_energy_deriv_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• rotamer_energy_deriv_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• rotamer_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSetsBase
• rotamer_for_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_generator_list_size() : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• rotamer_id() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• 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_proline() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• rotamer_library() : protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::sidechain_moves::SidechainMover
• rotamer_links() : core::pack::task::PackerTask_ , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::PackerTask
• rotamer_links_exist() : core::pack::task::PackerTask_ , core::pack::task::PackerTask
• rotamer_operations() : core::pack::task::ResidueLevelTask_ , core::pack::task::ResidueLevelTask
• rotamer_probability() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• rotamer_set_for_moltenres() : core::pack::rotamer_set::ContinuousRotamerSets
• rotamer_set_for_moltenresidue() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• rotamer_set_for_res() : core::pack::rotamer_set::ContinuousRotamerSets
• rotamer_set_for_residue() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets
• rotamer_set_operation_begin() : core::pack::task::ResidueLevelTask_ , core::pack::task::ResidueLevelTask
• rotamer_set_operation_end() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• rotamer_sets() : protocols::simple_moves::PackRotamersMover , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::annealer::RotamerAssigningAnnealer , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• RotamerAssigningAnnealer() : core::pack::annealer::RotamerAssigningAnnealer
• RotamerBoltzCalculator() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• RotamerBoltzmannWeight() : protocols::simple_filters::RotamerBoltzmannWeight
• RotamerBoltzmannWeightFeatures() : protocols::features::RotamerBoltzmannWeightFeatures
• RotamerBoltzmannWeightFeaturesCreator() : protocols::features::RotamerBoltzmannWeightFeaturesCreator
• RotamerConstraint() : core::pack::dunbrack::RotamerConstraint
• RotamerDescriptor() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• RotamerDescriptorAtom() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT >
• RotamerDNAHBondFilter() : protocols::dna::RotamerDNAHBondFilter
• RotamerDots() : core::pack::interaction_graph::RotamerDots
• RotamerDotsCache() : core::pack::interaction_graph::RotamerDotsCache
• RotamerDotsRadiusData() : core::pack::interaction_graph::RotamerDotsRadiusData
• RotamerDumpMover() : protocols::RotamerDump::RotamerDumpMover
• RotamerExplosion() : core::pack::task::operation::RotamerExplosion
• RotamerFeatures() : protocols::features::RotamerFeatures
• RotamerFeaturesCreator() : protocols::features::RotamerFeaturesCreator
• RotamericData() : core::pack::dunbrack::RotamericData< T >
• RotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• RotamerLibrary() : core::pack::dunbrack::RotamerLibrary
• RotamerLibraryScratchSpace() : core::pack::dunbrack::RotamerLibraryScratchSpace
• RotamerOperation() : core::pack::rotamer_set::RotamerOperation
• 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() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• rotamers_on_same_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• RotamerSet() : core::pack::rotamer_set::RotamerSet
• RotamerSet_() : core::pack::rotamer_set::RotamerSet_
• RotamerSetBase() : core::conformation::RotamerSetBase
• RotamerSetOperation() : core::pack::rotamer_set::RotamerSetOperation
• RotamerSets() : core::pack::rotamer_set::RotamerSets
• rotamersets() : protocols::multistate_design::PackingState
• RotamerSetsBase() : core::pack::rotamer_set::RotamerSetsBase
• RotamerSubset() : core::pack::rotamer_set::RotamerSubset
• RotamerSubsetRepacker() : protocols::pack_daemon::RotamerSubsetRepacker
• RotamerSubsets() : core::pack::rotamer_set::RotamerSubsets
• RotamerTrialsMinMover() : protocols::simple_moves::RotamerTrialsMinMover
• RotamerTrialsMover() : protocols::simple_moves::RotamerTrialsMover
• RotamerTrie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• Rotate() : protocols::ligand_docking::Rotate
• rotate_around_atom() : protocols::ligand_docking::RigidSearchMover
• rotate_around_downstream_centroid() : protocols::ligand_docking::RigidSearchMover
• rotate_ligand() : protocols::ligand_docking::Rotate
• rotate_segment() : protocols::backrub::BackrubMover
• rotate_vec() : protocols::evaluation::PCA
• RotateJumpAxisMover() : protocols::rigid::RotateJumpAxisMover
• rotatePoint() : protocols::pockets::PocketGrid
• Rotates() : protocols::ligand_docking::Rotates
• rotation() : protocols::ligand_docking::RigidSearchMover
• rotation_by_axis() : core::kinematics::Jump
• rotation_by_matrix() : core::kinematics::Jump
• RotationSearchPattern() : protocols::hotspot_hashing::RotationSearchPattern
• RotData() : protocols::MakeRotLib::RotData
• rotE() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophipsi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecopsi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotid_on_moltenresidue() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotno_2_packed_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• rots_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• rotset_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotset_for_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotwell() : core::pack::dunbrack::RotamerLibraryScratchSpace , core::pack::dunbrack::DunbrackRotamer< S, P > , core::pack::dunbrack::RotamerLibraryScratchSpace , core::pack::dunbrack::DunbrackRotamer< S, P >
• rotwell_2_packed_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• rotwell_2_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• round() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::quota::TorsionBinPool
• rows() : core::sequence::DP_Matrix
• RPF_ScoreEvaluator() : protocols::simple_filters::RPF_ScoreEvaluator
• 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
• RRComparerRotBins() : protocols::rotamer_recovery::RRComparerRotBins
• RRComparerRotBinsCreator() : protocols::rotamer_recovery::RRComparerRotBinsCreator
• RRProtocolCreator() : protocols::rotamer_recovery::RRProtocolCreator
• 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
• 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
• 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() : core::id::TorsionID , core::optimization::DOF_Node , core::id::NamedAtomID , core::id::AtomID , core::scoring::AtomNeighbor , core::id::AtomID , core::id::DOF_ID , core::optimization::AtomNode , core::id::NamedAtomID , core::id::TorsionID
• rsd1() : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• rsd2() : core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::id::JumpID
• rsd_library_already_loaded() : core::pack::dunbrack::RotamerLibrary
• rsd_rsd_energy() : core::scoring::dna::DirectReadoutPotential
• rsd_sasa() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• rsigma_dot_initializer() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rswitch() : core::scoring::constraints::BoundFunc
• RT() : core::kinematics::RT
• rt() : protocols::forge::build::ConnectRight , core::kinematics::Jump
• RT() : core::kinematics::RT
• rt() : protocols::forge::build::ConnectRight
• RT() : core::kinematics::RT
• RT_from_epos() : core::scoring::disulfides::RT_helper
• rt_min() : protocols::docking::DockingHighRes
• rtmin() : core::pack::RTMin
• RTMin() : core::pack::RTMin
• rtmin() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::RelativePoseFilter , protocols::design_opt::GreedyOptMutationMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::design_opt::PointMutationCalculator , protocols::design_opt::ParetoOptMutationMover , protocols::simple_filters::RelativePoseFilter , protocols::design_opt::GreedyOptMutationMover
• Rule() : core::coarse::Rule
• RuleSet() : core::coarse::RuleSet
• run() : protocols::abinitio::AbrelaxApplication , core::pack::annealer::SimAnnealerBase , core::optimization::GA_Minimizer , core::pack::annealer::FixbbSimAnnealer , protocols::loophash::WorkUnit_LoopHash , protocols::rotamer_recovery::RRProtocol , core::optimization::JJH_Minimizer , protocols::rotamer_recovery::RRProtocolRTMin , core::pack::annealer::FASTERAnnealer , protocols::dna::DnaInterfaceMultiStateDesign , core::optimization::symmetry::SymAtomTreeMinimizer , protocols::rotamer_recovery::RRProtocolMinPack , protocols::wum::WorkUnit_SilentStructStore , core::optimization::Minimizer , protocols::wum::WorkUnit_MoverWrapper , protocols::rotamer_recovery::RotamerRecovery , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::optimization::CartesianMinimizer , core::pack::annealer::DebuggingAnnealer , protocols::motifs::LigandMotifSearch , protocols::rotamer_recovery::RRProtocolMover , protocols::wum::WorkUnit_Wait , protocols::wum2::WorkUnit_Wait , protocols::motifs::LigandMotifSearch , protocols::simple_moves::PackRotamersMover , protocols::wum2::WorkUnit , protocols::hybridization::DomainAssembly , core::optimization::ParticleSwarmMinimizer , protocols::rotamer_recovery::RRProtocolRotamerTrials , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolPackRotamers , protocols::motifs::MotifSearch , core::optimization::ParticleSwarmMinimizer , protocols::relax::WorkUnit_BatchRelax , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::wum2::WorkUnit_ElScripts , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::motifs::LigandMotifSearch , protocols::wum::WorkUnitBase , core::optimization::AtomTreeMinimizer , protocols::jd2::MpiFileBuffer , core::pack::annealer::MultiCoolAnnealer , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::optimization::ParticleSwarmMinimizer
• run_A_ANN_Prediction() : protocols::sparta::Sparta
• run_calculator() : protocols::toolbox::task_operations::RestrictOperationsBase
• run_cluster() : protocols::forge::remodel::RemodelAccumulator
• run_constant_temp_rotamer_substitutions() : core::pack::annealer::MultiCoolAnnealer
• run_design_on_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• run_mc() : protocols::simple_moves::symmetry::SymShakeStructureMover , protocols::simple_moves::ShakeStructureMover
• run_motifs() : protocols::motifs::MotifDnaPacker
• run_packer() : protocols::multistate_design::PackingState
• run_quench() : core::pack::annealer::MultiCoolAnnealer
• run_quench_cycles() : core::pack::annealer::FASTERAnnealer
• run_sa() : protocols::simple_moves::GreenPacker
• runSpartaANN() : protocols::sparta::ANN