- r -

• r0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• r1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• r1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• radial_count() : protocols::loophash::LoopHashMap
• radial_disp() : protocols::matdes::GetRBDOFValues
• radial_lookup() : protocols::loophash::LoopHashMap
• radial_lookup_withkey() : protocols::loophash::LoopHashMap
• radius() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• RadiusOfGyrationFeatures() : protocols::features::RadiusOfGyrationFeatures
• RadiusOfGyrationFeaturesCreator() : protocols::features::RadiusOfGyrationFeaturesCreator
• rama() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• rama_delta() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• RamaCheck1B() : protocols::loops::loop_closure::ccd::RamaCheck1B
• RamaCheck2B() : protocols::loops::loop_closure::ccd::RamaCheck2B
• RamaCheckBase() : protocols::loops::loop_closure::ccd::RamaCheckBase
• RamaScore() : protocols::frag_picker::scores::RamaScore
• ramp_chainbreak() : protocols::loops::loop_closure::ccd::LoopClosure
• ramp_down_constraints() : protocols::relax::RelaxProtocolBase
• ramp_minpack_loop2() : protocols::mpi_refinement::WorkUnit_Sampler
• ramp_score_function() : protocols::loop_modeling::LoopProtocol
• ramp_temperature() : protocols::loop_modeling::LoopProtocol
• ramping_scorefxn() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• RampingMover() : protocols::moves::RampingMover
• random() : protocols::stepwise::sampler::StepWiseSamplerBase
• random_access() : protocols::simple_moves::AddChainMover
• random_angle() : protocols::backrub::BackrubMover
• random_basepair() : protocols::dna::DNAParameters
• random_basestep() : protocols::dna::DNAParameters
• random_chunk() : protocols::nonlocal::SingleFragmentMover
• random_chunk_insertion() : protocols::farna::RNA_ChunkLibrary
• random_chunk_trial() : protocols::farna::RNA_DeNovoProtocol
• random_conformer() : protocols::ligand_docking::LigandDockProtocol
• random_domain_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• random_drop_rate() : protocols::abinitio::abscript::ConstraintPreparer
• random_entity() : protocols::genetic_algorithm::EntityRandomizer
• random_entry() : protocols::protein_interface_design::PatchdockReader
• random_fragment_insertion() : protocols::farna::RNA_FragmentMover
• random_fragment_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• random_jump_change() : protocols::farna::RNA_StructureParameters
• random_jump_trial() : protocols::farna::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::stepwise::modeler::rna::helix::RNA_HelixAssembler
• 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_torsion_move() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• randomAngle() : protocols::pockets::PocketGrid
• RandomConformerMover() : protocols::ligand_docking::RandomConformerMover
• RandomConformers() : protocols::ligand_docking::RandomConformers
• randomize_bs() : protocols::cryst::FitBfactorsMover
• 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_orientations() : protocols::farna::MultipleDomainMover
• randomize_pose_rigid_bodies() : protocols::farna::MultipleDomainMover
• randomize_rigid_body_orientations() : protocols::farna::RNA_DeNovoProtocol
• randomize_stage() : protocols::forge::remodel::RemodelLoopMover
• randomlySlidePeptideJump() : protocols::flexpep_docking::FlexPepDockingProtocol
• RandomMover() : protocols::moves::RandomMover
• RandomMutation() : protocols::protein_interface_design::movers::RandomMutation
• RandomOmegaFlipMover() : protocols::simple_moves::RandomOmegaFlipMover
• RandomPositionRotationMover() : protocols::membrane::RandomPositionRotationMover
• RandomPositionTranslationMover() : protocols::membrane::RandomPositionTranslationMover
• RandomSheetBuilder() : protocols::jumping::RandomSheetBuilder
• RandomSymmetrySlider() : protocols::simple_moves::symmetry::RandomSymmetrySlider
• RandomTorsionMover() : protocols::simple_moves::RandomTorsionMover
• range() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::simple_filters::DeltaFilter
• RangeFilter() : protocols::simple_filters::RangeFilter
• rank() : protocols::canonical_sampling::AsyncMPITemperingBase , 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 , protocols::simple_filters::MutationsFilter
• ratio_cutoff() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• RationalMonteCarlo() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• Rattle() : protocols::md::Rattle
• raw_data_dump() : protocols::wum::WorkUnitBase
• raw_data_load() : protocols::wum::WorkUnitBase
• raw_data_size() : protocols::wum::WorkUnitBase
• rb_jump() : protocols::rigid::RigidBodyMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ddG , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::task_operations::RestrictToInterface
• rb_min_jumps() : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzRepackMinimize
• 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_atoms() : protocols::frag_picker::scores::RDCScore
• RDC_Evaluator() : protocols::simple_filters::RDC_Evaluator
• 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
• RDFBase() : protocols::ligand_docking::rdf::RDFBase
• RDFBinaryHbondFunction() : protocols::ligand_docking::rdf::RDFBinaryHbondFunction
• RDFBinaryOrbitalFunction() : protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction
• RDFChargeFunction() : protocols::ligand_docking::rdf::RDFChargeFunction
• RDFElecFunction() : protocols::ligand_docking::rdf::RDFElecFunction
• RDFEtableFunction() : protocols::ligand_docking::rdf::RDFEtableFunction
• RDFFunctionCreator() : protocols::ligand_docking::rdf::RDFFunctionCreator
• RDFFunctionFactory() : protocols::ligand_docking::rdf::RDFFunctionFactory
• RDFFunctionRegistrator() : protocols::ligand_docking::rdf::RDFFunctionRegistrator< T >
• RDFHbondFunction() : protocols::ligand_docking::rdf::RDFHbondFunction
• RDFOrbitalFunction() : protocols::ligand_docking::rdf::RDFOrbitalFunction
• re_init() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager , protocols::scoring::methods::pcs2::PcsInputCenterManager
• read() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::JCouplingIO , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::TorsionBinIO , protocols::toolbox::ClusterBase , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::TopologyClaimer
• read_adjust_table() : protocols::frag_picker::CS2ndShift
• read_all_variables_from_input_file() : protocols::pack_daemon::DynamicAggregateFunction
• read_anchorfile() : protocols::anchored_design::Anchor
• read_and_set_project_prefs() : protocols::boinc::Boinc
• read_and_store_fragments() : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::AntibodyModeler
• read_assignments() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_batch() : protocols::jd2::BatchJobInputter
• read_blueprint() : protocols::jd2::parser::BluePrint
• read_BooleanOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_BooleanVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_cdr_definition_file() : protocols::antibody::AntibodyNumberingParser
• read_cdr_definition_numbering_line() : protocols::antibody::AntibodyNumberingParser
• read_cdr_definition_transform_line() : protocols::antibody::AntibodyNumberingParser
• read_chain_connection() : protocols::farna::RNA_StructureParameters
• read_checkpoint() : protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::SingleStateEntityData
• read_checkpoint_file() : protocols::frag_picker::nonlocal::NonlocalFrags
• read_cmd() : protocols::mpi_refinement::Scheduler
• read_cmd_line_options() : protocols::antibody::design::AntibodyDesignMover
• read_coef1() : protocols::branch_angle::BranchAngleOptimizer
• read_coef1_default() : protocols::branch_angle::BranchAngleOptimizer
• read_coef1_user() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2_default() : protocols::branch_angle::BranchAngleOptimizer
• read_coef2_user() : protocols::branch_angle::BranchAngleOptimizer
• read_command_line_options() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator
• read_config_file() : protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• read_constraints() : protocols::abinitio::Template , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore
• read_constraints_from_file() : protocols::topology_broker::CoordConstraintClaimer
• read_cst_pose() : protocols::topology_broker::CoordConstraintClaimer
• read_data() : protocols::hotspot_hashing::HotspotStubSet , protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList , protocols::toolbox::match_enzdes_util::ResInteractions
• read_Data_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_database() : protocols::branch_angle::BranchAngleOptimizer
• read_db() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_def() : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• read_default_parameters() : protocols::relax::CentroidRelax
• read_depth() : protocols::frag_picker::FragmentPicker
• read_done_jobs() : protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• read_eigvec_file() : protocols::evaluation::PCA
• read_entities_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• read_enzyme_cstfile() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• read_existing_batches() : protocols::jd2::archive::ArchiveManager
• read_exp_data() : protocols::ddG::ddGData
• read_fasta_file() : protocols::topology_broker::SequenceClaimer
• read_file() : protocols::frags::RMSVallData , protocols::frags::TorsionFragmentLibrary , protocols::frags::VallData , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup
• read_FileOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_FileVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_from_binary_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• read_from_cmd_line() : protocols::wum::SilentStructStore
• read_from_file() : protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary , protocols::noesy_assign::FragsToAtomDist , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::wum::SilentStructStore
• read_from_file_no_filters() : protocols::jumping::PairingLibrary
• read_from_pose() : protocols::loophash::BackboneSegment
• read_from_stream() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::ResonanceList , protocols::wum::SilentStructStore
• read_from_string() : protocols::wum::SilentStructStore
• read_generations_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• read_H3_cter_fragment() : protocols::antibody::H3CterInsert
• read_header() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_homologs() : protocols::loophash::BackboneDB
• read_in_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• read_in_structures() : protocols::pmut_scan::PointMutScanDriver
• read_info_file() : protocols::jd2::archive::Batch
• read_input_files() : protocols::noesy_assign::NoesyModule
• read_input_pose_and_copy_dofs() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• read_IntegerOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_IntegerVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_jumps_from_file() : protocols::farna::RNA_JumpLibrary
• read_legacydb() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• read_ligand_superposition_file() : protocols::enzdes::EnzdesBaseProtocol
• read_loop_file() : protocols::loops::JSONFormattedLoopsFileReader , protocols::loops::Loops , protocols::loops::LoopsFileIO
• read_loop_file_stream() : protocols::loops::LoopsFileIO
• read_loops_file() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• read_loops_file_block() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• read_loops_options() : protocols::loops::Loops
• read_mover_weight() : protocols::topology_broker::TopologyClaimer
• read_mut_data() : protocols::ddG::ddGData
• read_mutants_list_file() : protocols::pmut_scan::PointMutScanDriver
• read_native() : protocols::docking::membrane::MPDockingMover
• read_numbering_scheme_file() : protocols::antibody::AntibodyNumberingParser
• read_Option_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_options() : protocols::anchored_design::Anchor , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::anchored_design::AnchorMoversData , protocols::flxbb::FlxbbDesign , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::ConstraintSetMover
• read_pairings() : protocols::abinitio::Templates
• read_parameters_from_file() : protocols::farna::RNA_StructureParameters
• read_params() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• read_patchdock() : protocols::protein_interface_design::PatchdockReader
• read_patchdock_entry() : protocols::protein_interface_design::PatchdockReader
• read_PathOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_PathVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_PCS_file() : protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• read_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• read_peak() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_pose() : protocols::hybridization::TMalign
• read_pose_numbered_loops_file() : protocols::loops::PoseNumberedLoopFileReader
• read_poses() : protocols::docking::membrane::MPDockingSetupMover , protocols::protein_interface_design::PatchdockReader
• read_psipred_ss2() : protocols::frag_picker::FragmentPicker
• read_queue() : protocols::wum::WorkUnitManager
• read_queues_from_file() : protocols::wum::WorkUnitManager
• read_RDC_file() : 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_ResidueType_for_subtag() : protocols::jd2::JD2ResourceManagerJobInputter
• read_resonances() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_resource_locator_items() : protocols::jd2::JD2ResourceManager
• read_resource_locators_tags() : protocols::jd2::JD2ResourceManager
• read_resource_option_item() : protocols::jd2::JD2ResourceManager
• read_resource_options_table_tag() : protocols::jd2::JD2ResourceManager
• read_resource_options_tag_item() : protocols::jd2::JD2ResourceManager
• read_resource_options_tags() : protocols::jd2::JD2ResourceManager
• read_resource_table_tag() : protocols::jd2::JD2ResourceManager
• read_resource_tag_item() : protocols::jd2::JD2ResourceManager
• read_resources_tags() : protocols::jd2::JD2ResourceManager
• read_returning_decoys() : protocols::jd2::archive::BaseArchiveManager
• read_scheme_defines_line() : protocols::antibody::AntibodyNumberingParser
• read_scheme_numbering_line() : protocols::antibody::AntibodyNumberingParser
• read_script_file() : protocols::relax::FastRelax
• read_secstruct_from_file() : protocols::farna::RNA_StructureParameters
• read_spanfiles() : protocols::docking::membrane::MPDockingSetupMover
• read_spine_x() : protocols::frag_picker::FragmentPicker
• read_ss_file() : protocols::frag_picker::FragmentPicker
• read_ss_files() : protocols::frag_picker::FragmentPicker
• read_sslimit_table() : protocols::frag_picker::CS2ndShift
• read_state_vector_file() : protocols::pack_daemon::DynamicAggregateFunction
• read_strength() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• read_StringOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_StringVectorOption_subtag_for_job() : protocols::jd2::JD2ResourceManagerJobInputter
• read_structure() : protocols::evaluation::PCA
• read_structures() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive
• read_tag() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• read_tagfile_to_taskfactory() : protocols::optimize_weights::IterativeOptEDriver
• read_talos_phi_psi() : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::PhiPsiRmsd
• read_talos_ss() : protocols::frag_picker::FragmentPicker
• read_template_structures() : protocols::hybridization::HybridizeProtocol
• read_topol_file() : protocols::topology_broker::TemplateJumpClaimer
• read_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• read_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• read_vall() : protocols::frag_picker::FragmentPicker
• read_vall_torsions() : protocols::farna::FullAtomRNA_Fragments , protocols::farna::RNA_Fragments
• read_work_unit() : protocols::wum::WorkUnitManager
• read_wt_data() : protocols::ddG::ddGData
• ReadResfileFromDB() : protocols::toolbox::task_operations::ReadResfileFromDB
• ready() : protocols::forge::build::BuildInstruction
• ready_for_batch() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom
• ready_to_align() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• realign_templates() : protocols::hybridization::HybridizeSetup
• reassign_noesy_data() : protocols::abinitio::IterativeBase
• rebuild_atoms() : protocols::cyclic_peptide::PeptideStubMover
• rebuild_bulge_mode() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• rebuild_conformation() : protocols::helical_bundle::PerturbBundle
• rebuild_filter() : protocols::comparative_modeling::LoopRelaxMover
• rebuild_polymer_bond_dependent_atoms() : protocols::environment::ProtectedConformation
• rebuild_unaligned() : protocols::rbsegment_relax::OptimizeThreadingMover
• recalculate_rmsd_and_output_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• recalculate_z_coordinate() : protocols::docking::EllipsoidalRandomizationMover
• receive_and_output_structures() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• receive_batch() : protocols::jd2::archive::MPIArchiveJobDistributor
• receive_exchange_requests() : protocols::canonical_sampling::AsyncMPITemperingBase
• receive_is_accepted() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• receive_message() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• receive_MPI_workunit() : protocols::wum::MPI_WorkUnitManager
• receive_newest_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• receive_silent_struct_any_source() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• receive_str() : protocols::jd2::MpiFileBuffer
• receive_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• received() : protocols::topology_broker::ClaimerMessage
• received_by_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::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• recompute() : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::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
• RecomputeDensityMapMover() : protocols::cryst::RecomputeDensityMapMover
• reconstruct_dependencies() : protocols::forge::build::BuildManager
• record() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• record_chi() : protocols::simple_moves::MinimalRotamer
• record_helix_sasas() : protocols::features::helixAssembly::HelixBundleFeatures
• record_histograms() : protocols::backrub::BackrubSidechainMover
• record_internal_geometry() : protocols::simple_moves::MinimalRotamer
• record_inv6() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• record_job() : protocols::jd2::JD2ResourceManagerJobInputter
• record_match() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• record_statistics() : protocols::backrub::BackrubSidechainMover
• recover_checkpoint() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer , protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::nonlocal::NonlocalFrags
• recover_conformer_sidechains() : protocols::docking::DockingEnsemble
• recover_hit() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• recover_hits() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• recover_loops_from_file() : protocols::enzdes::EnzdesFlexBBProtocol
• recover_low() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::ligand_docking::RigidSearchMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• recover_original_on_failure() : protocols::forge::components::VarLengthBuild
• recover_poses_from_states() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• recover_relevant_poses_for_entity() : protocols::pack_daemon::MultistateFitnessFunction
• recover_sidechains() : protocols::symmetric_docking::SymDockProtocol
• RecoverSideChainsMover() : protocols::comparative_modeling::RecoverSideChainsMover
• recovery_rate() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• recreate_pose_for_entity() : protocols::pack_daemon::PackDaemon
• redefine_begin_end() : protocols::fldsgn::topology::StrandPairing
• 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_scorefxn() : protocols::enzdes::EnzdesBaseProtocol
• ref_baseline() : protocols::simple_filters::DeltaFilter
• ref_pKa() : protocols::simple_moves::IonizableResidue
• ref_pose() : protocols::toolbox::DecoySetEvaluation
• ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• reference_pose() : protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• reference_pose_from_options() : protocols::features::ProteinRMSDNoSuperpositionFeatures
• reference_res() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• reference_structure() : protocols::rotamer_recovery::RRProtocolReferenceStructure
• reference_stub() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• reference_xyz_consistency_check() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• refill_torsion_string_vector() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• refine() : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• refine_grid_and_subsample_for_hit_subsets() : protocols::match::Matcher
• RefineBetaBarrel() : protocols::antibody::RefineBetaBarrel
• refinement_cycle() : protocols::surface_docking::FullatomRelaxMover
• RefineOneCDRLoop() : protocols::antibody::RefineOneCDRLoop
• RefineOneCDRLoopCentroid() : protocols::antibody::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::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid
• refresh_bbstub_constraints() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• refresh_coordinate_constraints() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• refresh_normalmode() : protocols::normalmode::NormalModeRelaxMover
• refx() : protocols::simple_filters::AngleToVector
• refy() : protocols::simple_filters::AngleToVector
• refz() : protocols::simple_filters::AngleToVector
• regenerate_round1_hits() : protocols::match::Matcher
• region() : protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover
• Region() : protocols::nonlocal::Region
• region() : protocols::simple_filters::BuriedRegionsFilter
• region1() : protocols::simple_filters::RegionalConnections
• region2() : protocols::simple_filters::RegionalConnections
• region_string() : protocols::simple_filters::BuriedRegionsFilter
• RegionalConnections() : protocols::simple_filters::RegionalConnections
• register_batch() : protocols::jd2::archive::ArchiveManager
• register_calculators() : protocols::analysis::InterfaceAnalyzerMover
• register_factory_prototypes() : protocols::rosetta_scripts::RosettaScriptsParser
• register_intergroup_calculator() : protocols::analysis::InterfaceAnalyzerMover
• register_label_offset() : protocols::topology_broker::SequenceNumberResolver
• register_mover() : protocols::environment::Environment , protocols::wum::MoverList
• register_movers() : protocols::environment::Environment
• register_options() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::PairingStatistics , protocols::abinitio::Protocol , protocols::abinitio::Template , protocols::abinitio::Templates , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory , protocols::docking::TemperedDocking , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::features::ReportToDB , protocols::flxbb::FlxbbDesign , protocols::forge::remodel::RemodelLoopMover , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::RotationMover , protocols::membrane::symmetry::SetupForMembraneSymmetry , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , 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::ConstraintSetMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::ScoreMover , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::sparta::Sparta , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::DecoySetEvaluation , protocols::topology_broker::ConstraintEvaluatorWrapperCreator , protocols::topology_broker::TMHTopologySamplerClaimer
• register_preparer() : protocols::abinitio::abscript::AbscriptMover
• register_score_maker() : protocols::frag_picker::scores::FragmentScoreManager
• register_submover() : protocols::abinitio::abscript::AbscriptMover
• register_user_options() : protocols::forge::remodel::RemodelMover
• register_variable_expression() : protocols::optimize_weights::WrapperOptEMultifunc
• register_work_unit() : protocols::wum::WorkUnitList
• register_work_units() : protocols::wum::MPI_Relax , protocols::wum::WorkUnitManager
• regularize_angle() : protocols::stepwise::sampler::MC_OneTorsion
• reindex_AtomIDs() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• reinitialize() : protocols::cluster::APCluster , protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler , protocols::stepwise::modeler::StepWiseModeler
• reinitialize_CCD_torsions() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• reinitialize_for_each_job() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::floppy_tail::FloppyTailMover , protocols::ligand_docking::LigandDockMain , protocols::moves::Mover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• reinitialize_for_new_input() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::docking::DockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::ligand_docking::LigandDockMain , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::moves::Mover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• reinstantiate_backbone_and_add_constraint_at_moving_res() : protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler
• reinstantiate_backbone_at_moving_res() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• reinstantiate_distal_partition() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• reinstate_original_constraints() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• reinstate_pose() : protocols::enzdes::PredesignPerturbMover
• reinstate_side_chain_angles() : protocols::stepwise::modeler::packer::StepWisePacker
• reject_mutant() : protocols::pmut_scan::AlterSpecDisruptionDriver , protocols::pmut_scan::PointMutScanDriver
• reject_on_chains() : protocols::pmut_scan::AlterSpecDisruptionDriver
• reject_on_interface() : protocols::pmut_scan::AlterSpecDisruptionDriver
• relative() : protocols::environment::claims::XYZClaim
• relative_pose_filter() : protocols::simple_filters::MultipleSigmoids
• relative_pose_names() : protocols::simple_filters::Operator
• RelativeConnectRight() : protocols::forge::build::RelativeConnectRight
• RelativePoseFilter() : protocols::simple_filters::RelativePoseFilter
• RelativeSegmentFilter() : protocols::protein_interface_design::filters::RelativeSegmentFilter
• relax() : protocols::abinitio::AbrelaxApplication , protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• relax_bound() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• relax_cdrs() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody_legacy::AntibodyModeler
• relax_favorable_poses() : protocols::vip::VIP_Mover
• relax_interface() : protocols::antibody::design::AntibodyDesignModeler
• relax_mover() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::loophash::LoopHashMoverWrapper , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_moves::ddG
• relax_optimized_CDR_grafts() : protocols::antibody_legacy::GraftMover
• relax_protocol() : protocols::abinitio::AbrelaxMover
• relax_unbound() : protocols::simple_filters::DeltaFilter
• relax_wildtype_structure() : protocols::ddg::ddGMover
• relaxmode() : protocols::normalmode::NormalModeRelaxMover
• RelaxProtocolBase() : protocols::relax::RelaxProtocolBase
• RelaxScriptCommand() : protocols::relax::RelaxScriptCommand
• relay_message() : protocols::topology_broker::TopologyBroker
• release() : protocols::ligand_docking::TetherLigand
• release_file() : protocols::jd2::MpiFileBuffer
• relevant_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() : protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesFlexibleRegion , protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• remap_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• remapped_clone() : protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet
• remark() : protocols::motifs::Motif
• 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
• remodelData() : protocols::forge::remodel::RemodelLoopMover
• RemodelDesignMover() : protocols::forge::remodel::RemodelDesignMover
• RemodelEnzdesCstModule() : protocols::forge::remodel::RemodelEnzdesCstModule
• RemodelGlobalFrame() : protocols::forge::remodel::RemodelGlobalFrame
• RemodelLoopMover() : protocols::forge::remodel::RemodelLoopMover
• RemodelMover() : protocols::forge::remodel::RemodelMover
• RemodelRotamerLinks() : protocols::forge::remodel::RemodelRotamerLinks
• RemodelWorkingSet() : protocols::forge::remodel::RemodelWorkingSet
• remote_close_file() : protocols::jd2::MpiFileBuffer
• remove() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::protein_interface_design::movers::AddChainBreak , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim
• remove_all_hotspot_constraints() : protocols::hotspot_hashing::HotspotStubSet
• remove_bad_inputs_from_job_list() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• remove_chainbreak_variants() : protocols::environment::Environment
• remove_chainbreaks() : protocols::jumping::JumpSample
• remove_child() : protocols::loop_modeling::LoopMover
• remove_conservative_design_residues_from_prob_set() : protocols::antibody::design::AntibodySeqDesignTFCreator
• remove_constraints_from_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_constraints_from_pose_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_covalent_connection_from_pose() : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• remove_covalent_connections_from_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• remove_cut() : protocols::hybridization::HybridizeFoldtreeDynamic
• remove_cycles_from_request_list() : protocols::canonical_sampling::AsyncMPITemperingBase
• remove_downstream_object_from_upstream_pose() : protocols::match::MatcherTask
• remove_duplicate_phi_psi() : protocols::pockets::NonPlaidFingerprint
• remove_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• remove_evaluation() : protocols::jd2::archive::EvaluatedArchive
• remove_favor_native_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• remove_first_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• remove_from_consideration_first_multi_residue_move_element() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• remove_highest_energy_member_of_each_group() : protocols::cluster::ClusterBase
• remove_info() : protocols::dna::PDBOutput
• remove_invrots_clashing_with_parent_res() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• remove_last_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• remove_last_filter() : protocols::filters::FilterCollection
• remove_ligand_tethers() : protocols::ligand_docking::HighResDocker
• remove_member() : protocols::cluster::Cluster
• remove_nonpermenant_features() : protocols::environment::Environment
• remove_output_observer() : protocols::jd2::Job
• remove_pending_decoys() : protocols::abinitio::HedgeArchive
• remove_position_from_template_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_position_from_template_res_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• remove_random_stubs_from_set() : protocols::hotspot_hashing::HotspotStubSet
• remove_remodel_constraints() : protocols::forge::components::VarLengthBuild
• remove_remodel_constraints_from_pose() : protocols::forge::remodel::RemodelConstraintGenerator
• remove_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• remove_seqpos() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• remove_seqpos_from_template_res() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• remove_singletons() : protocols::cluster::ClusterBase
• remove_singletons_and_update_pose_focus() : protocols::stepwise::monte_carlo::mover::DeleteMover
• remove_stub() : protocols::hotspot_hashing::HotspotStubSet
• remove_stubs_from_set() : protocols::hotspot_hashing::HotspotStubSet
• remove_system_signal_handler() : protocols::jd2::JobDistributor
• remove_terminal_loops() : protocols::loops::Loops
• remove_trigger() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• remove_variants_at_extra_cutpoints() : protocols::farna::RNA_LoopCloser
• remove_vector_exclude_residues() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• RemoveCsts() : protocols::forge::constraints::RemoveCsts
• RemoveLigandFilter() : protocols::enzdes::RemoveLigandFilter
• RemoveNorCTermMPM() : protocols::match::RemoveNorCTermMPM
• rename_checkpoint_files() : protocols::genetic_algorithm::GeneticAlgorithmBase
• render_fold_tree() : protocols::environment::EnvClaimBroker
• RenderGridsToKinemage() : protocols::qsar::RenderGridsToKinemage
• renormalize_quota_pools() : protocols::frag_picker::quota::QuotaCollector
• renumber_after_variant_changes() : protocols::toolbox::AllowInsert
• renumber_pdb() : protocols::simple_filters::SaveResfileToDiskFilter
• reorder_foldtree_around_mobile_regions() : protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::MinimizeBackbone
• reorder_foldtree_find_jump() : protocols::analysis::InterfaceAnalyzerMover
• reorder_poses() : protocols::antibody::design::AntibodyDesignMover
• reorder_restypes() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• reorient_and_slide_into_surface() : protocols::surface_docking::FullatomRelaxMover
• repack() : protocols::mpi_refinement::WorkUnit_Sampler , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::FASTER_IG_Repacker , protocols::pack_daemon::QuickRepacker , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareAlaScan , protocols::simple_moves::GreenPacker
• repack_and_minimize_pose() : protocols::optimize_weights::IterativeOptEDriver
• repack_antibody_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_antigen_ab_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_antigen_interface() : protocols::antibody::design::AntibodyDesignModeler
• repack_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• repack_bound() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• repack_cdrs() : protocols::antibody::design::AntibodyDesignModeler
• repack_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• repack_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• 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
• RepackingRefiner() : protocols::loop_modeling::refiners::RepackingRefiner
• RepackLigandSiteWithoutLigandMover() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• RepackMinimize() : protocols::protein_interface_design::movers::RepackMinimize
• RepackSidechainsMover() : protocols::simple_moves::RepackSidechainsMover
• RepackTrial() : protocols::loops::loop_mover::refine::RepackTrial
• RepackTrialCreator() : protocols::loops::loop_mover::refine::RepackTrialCreator
• RepackWithoutLigandFilter() : protocols::enzdes::RepackWithoutLigandFilter
• repeat_generation_with_additional_residue() : protocols::forge::remodel::RemodelLoopMover
• repeat_propagation() : protocols::forge::remodel::RemodelLoopMover
• repeat_sync() : protocols::forge::remodel::RemodelLoopMover
• RepeatMover() : protocols::moves::RepeatMover
• RepeatParameterFilter() : protocols::simple_filters::RepeatParameterFilter
• RepeatPropagationMover() : protocols::simple_moves::RepeatPropagationMover
• repeats() : protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::TaskAwareAlaScan , protocols::simple_moves::ddG
• RepGrid() : protocols::qsar::scoring_grid::RepGrid
• replace_noesy_filter_constraints() : protocols::abinitio::IterativeBase
• replace_residue() : protocols::environment::ProtectedConformation
• replace_residue_sandbox() : protocols::environment::ProtectedConformation
• replace_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio
• ReplaceRegionMover() : protocols::grafting::simple_movers::ReplaceRegionMover
• ReplaceString() : protocols::pockets::GenPharmacophore
• ReplicaExchangeMC() : protocols::moves::ReplicaExchangeMC
• ReplicateFilter() : protocols::filters::ReplicateFilter
• report() : protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::dna::RotamerDNAHBondFilter , protocols::docking::DockingLowResFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter
• Report() : protocols::features::Report
• report() : protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::ReportSequenceDifferences , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareAlaScan , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter
• report_ab_H3_kink_metrics_features() : protocols::antibody::AntibodyFeatures
• report_ab_metrics_features() : protocols::antibody::AntibodyFeatures
• report_all() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::rosetta_scripts::ParsedProtocol
• report_all_interface_features() : protocols::features::InterfaceFeatures
• report_aln_components() : protocols::evaluation::AlignEvaluator
• report_as_silent() : protocols::md::MDBase
• report_atom_pairs() : protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures
• report_CA_rmsd() : protocols::idealize::IdealizeMover
• report_call_order() : protocols::rosetta_scripts::ParsedProtocol
• report_cdr_metrics_features() : protocols::antibody::AntibodyFeatures
• report_cdr_residue_features() : protocols::antibody::AntibodyFeatures
• report_cdr_residue_features_row() : protocols::antibody::AntibodyFeatures
• report_data() : protocols::analysis::InterfaceAnalyzerMover
• report_ddG() : protocols::simple_moves::ddG
• report_dev() : protocols::mpi_refinement::StructAvrgMover
• report_diffs() : protocols::simple_filters::TaskAwareAlaScan
• report_features() : protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ReportToDB , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures
• report_features_implementation() : protocols::features::PoseConformationFeatures
• report_filter_name() : protocols::simple_filters::ReportFilter
• report_filters_to_job() : protocols::rosetta_scripts::ParsedProtocol
• report_filters_to_pose() : 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_interface_features() : protocols::features::InterfaceFeatures
• report_interface_residue_features() : protocols::features::InterfaceFeatures
• report_interface_side_features() : protocols::features::InterfaceFeatures
• report_interres_angles() : protocols::features::ProteinBondGeometryFeatures
• report_interres_lengths() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_angles() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_lengths() : protocols::features::ProteinBondGeometryFeatures
• report_intrares_torsions() : protocols::features::ProteinBondGeometryFeatures
• report_MD() : protocols::md::CartesianMD
• report_predicted_features() : protocols::rotamer_recovery::RRReporterSQLite
• report_property() : protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::rosetta_scripts::PosePropertyReporter
• report_residue_pairs() : protocols::features::PairFeatures
• report_rotamer_recovery() : protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_features() : protocols::rotamer_recovery::RRReporterSQLite
• report_rotamer_recovery_full() : protocols::rotamer_recovery::RRReporterSQLite
• report_silent() : protocols::md::MDBase
• report_sm() : protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter
• report_string() : protocols::simple_filters::ReportFilter
• report_structure_features() : protocols::features::ReportToDB
• report_structure_to_emperor() : protocols::loophash::MPI_LoopHashRefine_Master
• report_subvalues() : protocols::simple_filters::Operator
• report_symmetry() : protocols::simple_filters::AlaScan
• report_time() : protocols::mpi_refinement::MPI_Refinement
• ReportEffectivePKA() : protocols::simple_moves::ReportEffectivePKA
• ReportFilter() : protocols::simple_filters::ReportFilter
• ReportFSC() : protocols::electron_density::ReportFSC
• ReportPSSMDifferences() : protocols::protein_interface_design::ReportPSSMDifferences
• ReportSequenceDifferences() : protocols::protein_interface_design::ReportSequenceDifferences
• ReportToDB() : protocols::features::ReportToDB
• reposition_above_surface() : protocols::surface_docking::FullatomRelaxMover
• representative_downstream_algorithm() : protocols::match::Matcher
• representative_group_matches() : protocols::match::output::CloudPDBWriter
• representative_seqpos() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• repulsive_ramp() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody_legacy::AntibodyModeler
• RepulsiveOnlyMover() : protocols::simple_moves::RepulsiveOnlyMover
• request_fold_tree() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopMover
• request_new_jobs() : protocols::wum::MPI_WorkUnitManager_Slave
• require_all_target_residue_atom_coordinates() : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• require_atom_to_reside_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• require_candidate_residue_atoms_to_lie_near_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• require_mm_bend() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• require_target_atom_coordinate() : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• required_separation_distance() : protocols::match::BumpGrid
• requires_pose() : protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver
• reroot_fold_tree() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• reroot_fold_tree_simple() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• res1() : 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
• res2() : 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
• res_anchor() : protocols::sic_dock::Rose
• res_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_ids() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• res_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• res_links() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• res_map() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• res_name1() : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences
• res_name2() : protocols::protein_interface_design::ReportSequenceDifferences
• res_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• res_switch() : protocols::abinitio::KinematicTaskControl
• res_types() : protocols::simple_filters::ResidueCountFilter
• resA() : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• ResampleMover() : protocols::stepwise::monte_carlo::mover::ResampleMover
• resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• rescale() : protocols::md::Thermostat
• rescore() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeBase , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• rescore_all_decoys() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• rescore_nonlocal_archive() : protocols::abinitio::IterativeBase
• reserve() : protocols::toolbox::DecoySetEvaluation
• reset() : protocols::abinitio::hConvergenceCheck , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::checkpoint::Timer , protocols::contact_map::ContactMap , protocols::evaluation::TimeEvaluator , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::helical_bundle::BundleGridSamplerHelper , protocols::hybridization::hConvergenceCheck , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::StateAccumulatingMatchFilter , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::TrialCounter , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::StepWiseSampleAndScreen
• reset_3d_projection() : protocols::match::OccupiedSpaceHash
• reset_accept_counter() : protocols::jd2::archive::ArchiveBase
• reset_accounting() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• reset_accounting_impl() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• reset_all_rotamer_substitution_bookkeeping_data() : protocols::flexpack::interaction_graph::FlexbbNode
• reset_alternate_states_for_uncommited_substitution() : protocols::flexpack::interaction_graph::FlexbbEdge
• reset_baseline() : protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::Operator , protocols::simple_filters::Sigmoid
• reset_baselines() : protocols::simple_moves::GenericMonteCarloMover
• reset_calibration_constants() : protocols::noesy_assign::PeakCalibrator
• reset_chain_endings() : protocols::environment::ProtectedConformation
• reset_count() : protocols::contact_map::Contact
• reset_counters() : protocols::moves::MonteCarlo
• reset_cycle_index() : protocols::docking::DockMCMCycle , protocols::moves::CycleMover
• reset_delta_filter_baselines() : protocols::matdes::MatDesGreedyOptMutationMover
• reset_delta_omega1() : protocols::helical_bundle::parameters::BundleParameters
• reset_delta_z1() : protocols::helical_bundle::parameters::BundleParameters
• reset_DMC() : protocols::moves::DualMonteCarlo
• reset_filters() : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::match::output::MatchProcessor
• reset_from_interface() : protocols::dna::DnaInterfaceMinMover
• reset_from_ref() : protocols::scoring::methods::pcs2::PcsTensor
• reset_grid() : protocols::match::Bool3DGrid
• reset_grouper() : protocols::match::output::MatchConsolidator
• reset_move_data() : protocols::environment::ProtectedConformation
• reset_mover_data() : protocols::cyclic_peptide::PeptideStubMover
• reset_node_in_moving_flexseg_count() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• reset_num_connections() : protocols::simple_filters::RegionalConnections
• reset_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• reset_pose() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix
• reset_r1() : protocols::helical_bundle::parameters::BundleParameters
• reset_raw_counter() : protocols::canonical_sampling::SimulatedTempering
• reset_recovery() : protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• reset_scorefxn() : protocols::moves::MonteCarlo
• reset_statistics() : protocols::backrub::BackrubSidechainMover , protocols::noesy_assign::PeakCalibrator
• reset_status() : protocols::moves::Mover
• reset_temp_counter() : protocols::canonical_sampling::TemperingBase
• reset_tensor() : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• reset_timing_stats() : protocols::wum::MPI_WorkUnitManager
• reset_to_original_pose() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• reset_trans_axis() : protocols::rigid::UniformSphereTransMover
• reset_unique_id() : protocols::motifs::IRCollection
• reset_x() : protocols::evaluation::PCA
• ResetBaselineMover() : protocols::simple_moves::ResetBaselineMover
• resfile() : protocols::flxbb::DesignTask , protocols::forge::components::BDR
• resfile_at() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• resfile_general_property() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_name() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::SaveResfileToDiskFilter
• resfile_prefix() : protocols::simple_filters::SaveResfileToDiskFilter
• resfile_suffix() : protocols::simple_filters::SaveResfileToDiskFilter
• ResFileOutputter() : protocols::outputter::ResFileOutputter
• resfiles() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• resi() : protocols::frag_picker::VallResidue
• ResId() : protocols::moves::ResId
• resid() : protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• resid_2_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• ResidualDipolarCouplingEnergyRigidSegments() : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• ResidualDipolarCouplingRigidSegments() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• residue() : protocols::hotspot_hashing::HotspotStub , protocols::sic_dock::NoPoseXYX_Func , protocols::simple_filters::ResidueBurialFilter
• residue_alternative_set() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• residue_alternatives_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• residue_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• residue_conformations_redundant() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• 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() : protocols::fldsgn::potentials::AACompositionEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::SpecialRotamerEnergy
• 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_is_in_h3_loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• residue_list() : protocols::simple_moves::SetTorsion
• residue_name() : protocols::helical_bundle::MakeBundleHelix
• residue_neighbors() : protocols::simple_filters::NonSequentialNeighborsFilter
• residue_num() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• residue_packed() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• residue_pair() : protocols::fldsgn::topology::StrandPairing
• residue_pair_constraint_exists() : protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• residue_pair_energy() : protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::scoring::methods::InterchainPairEnergy
• residue_range_is_protein() : protocols::features::BetaTurnDetection
• residue_set_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_set_numbers_to_decomposition() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• residue_to_constrain() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• residue_type_set() : protocols::forge::build::BuildInstruction , protocols::simple_moves::ExtendedPoseMover
• ResidueAlternativeSet() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• ResidueAlternativeStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• ResidueAlternativeStepWiseSamplerComb() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• ResidueBurialFeatures() : protocols::features::ResidueBurialFeatures
• ResidueBurialFeaturesCreator() : protocols::features::ResidueBurialFeaturesCreator
• ResidueBurialFilter() : protocols::simple_filters::ResidueBurialFilter
• ResidueChunkSelection() : protocols::abinitio::abscript::ResidueChunkSelection
• ResidueConformationFeatures() : protocols::features::ResidueConformationFeatures
• ResidueConformationFeaturesCreator() : protocols::features::ResidueConformationFeaturesCreator
• ResidueConformerFilter() : protocols::enzdes::ResidueConformerFilter
• ResidueContactScreener() : protocols::stepwise::screener::ResidueContactScreener
• ResidueCountFilter() : protocols::simple_filters::ResidueCountFilter
• ResidueDecompositionByChainCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• ResidueDecompositionCalculator() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• ResidueDistanceFilter() : protocols::simple_filters::ResidueDistanceFilter
• ResidueElement() : protocols::environment::claims::ResidueElement
• ResidueFeatureFactory() : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueFeatures() : protocols::features::ResidueFeatures
• ResidueFeaturesCreator() : protocols::features::ResidueFeaturesCreator
• ResidueGridScoresFeatures() : protocols::features::ResidueGridScoresFeatures
• ResidueGridScoresFeaturesCreator() : protocols::features::ResidueGridScoresFeaturesCreator
• ResidueGroupIGEdgeUpweighter() : protocols::toolbox::ResidueGroupIGEdgeUpweighter
• ResidueIEFilter() : protocols::simple_filters::ResidueIEFilter
• ResidueIndexDescription() : protocols::loops::ResidueIndexDescription
• ResidueIndexDescriptionFromFile() : protocols::loops::ResidueIndexDescriptionFromFile
• ResidueKinemageWriter() : protocols::match::output::ResidueKinemageWriter
• ResidueListStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler
• ResidueNetwork() : protocols::toolbox::ResidueNetwork
• ResiduePairJump() : protocols::jumping::ResiduePairJump
• ResiduePairJumpSetup() : protocols::jumping::ResiduePairJumpSetup
• ResiduePairJumpSingle() : protocols::jumping::ResiduePairJumpSingle
• ResidueProbDesignOperation() : protocols::antibody::design::ResidueProbDesignOperation
• residues() : protocols::constraints_additional::SequenceCouplingConstraint , protocols::kinematic_closure::ClosureProblem , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• residues1() : protocols::simple_filters::ShapeComplementarityFilter
• residues2() : protocols::simple_filters::ShapeComplementarityFilter
• residues_are_different() : protocols::dna::PDBOutput
• residues_compatible() : protocols::enzdes::SecondaryMatchProtocol
• residues_for_entity_begin() : protocols::pack_daemon::EntityCorrespondence
• residues_for_entity_end() : protocols::pack_daemon::EntityCorrespondence
• residues_to_mutate() : protocols::ddg::ddGMover
• ResidueScoresFeatures() : protocols::features::ResidueScoresFeatures
• ResidueScoresFeaturesCreator() : protocols::features::ResidueScoresFeaturesCreator
• ResidueSecondaryStructureFeatures() : protocols::features::ResidueSecondaryStructureFeatures
• ResidueSecondaryStructureFeaturesCreator() : protocols::features::ResidueSecondaryStructureFeaturesCreator
• ResidueSelectorLoader() : protocols::jd2::parser::ResidueSelectorLoader
• 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() : protocols::jumping::ResiduePairJumpSingle
• ResidueTypeConstraintMover() : protocols::simple_moves::ResidueTypeConstraintMover
• ResidueTypesFeatures() : protocols::features::ResidueTypesFeatures
• ResidueTypesFeaturesCreator() : protocols::features::ResidueTypesFeaturesCreator
• ResidueVicinityInfo() : protocols::forge::remodel::ResidueVicinityInfo
• ResidueVicinityRCG() : protocols::forge::remodel::ResidueVicinityRCG
• resindex() : protocols::loops::ResidueIndexDescription
• ResInteractions() : protocols::toolbox::match_enzdes_util::ResInteractions
• resize() : protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::SS_Info2 , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frags::TorsionFragmentLibrary , protocols::jumping::JumpSample , protocols::loops::LoopsFileData , protocols::simple_moves::BBGaussianMover
• resize_arrays() : protocols::match::output::UpstreamHitCacher
• resize_espGrid_to_match_pocketGrid() : protocols::pockets::ElectrostaticpotentialGrid
• ResizeArray() : protocols::hybridization::TMalign
• resname() : protocols::contact_map::ContactPartner
• resnum() : protocols::antibody::PDBLandmark , 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::sidechain_moves::SetChiMover
• resnum_exists_in_set() : protocols::antibody::design::ResidueProbDesignOperation
• resnum_map() : protocols::jd2::parser::BluePrint
• resnums() : protocols::simple_filters::ResidueIEFilter
• resnums_allow_design() : protocols::toolbox::task_operations::DesignAroundOperation
• ResolutionSwitcher() : protocols::abinitio::ResolutionSwitcher
• resolve_address_and_assign_tag() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• resolve_as_serialized_loop_from_pose() : protocols::loops::LoopFromFileData
• resolve_as_serialized_loops() : protocols::loops::LoopsFileData
• resolve_index() : protocols::loops::ResidueIndexDescription , protocols::loops::ResidueIndexDescriptionFromFile
• resolve_loop_indices() : protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_mover::LoopMover
• resolve_loop_indices_once() : protocols::loops::GuardedLoopsFromFile
• resolve_loopfile_indices() : protocols::comparative_modeling::LoopRelaxMover
• resolve_loops() : protocols::loops::LoopsFileData
• resolve_sequence_label() : protocols::topology_broker::TopologyBroker
• resolve_symmetry_claims() : protocols::topology_broker::TopologyBroker
• resolve_uncommitted_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• resolved_level_best_rmsd() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• resolver() : protocols::environment::ProtectedConformation
• resonance() : protocols::noesy_assign::PeakAssignment
• Resonance() : protocols::noesy_assign::Resonance
• resonance_id() : protocols::noesy_assign::PeakAssignment
• ResonanceList() : protocols::noesy_assign::ResonanceList
• resonances() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignment
• resonances_at_residue() : protocols::noesy_assign::ResonanceList
• resource_description() : protocols::loops::LoopsFileFallbackConfigurationCreator , protocols::surface_docking::SurfaceVectorFallbackConfigurationCreator
• respect_this_movemap() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• respond_to_peripheral_hitlist_change() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• respond_to_primary_hitlist_change() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• restart() : protocols::frag_picker::quota::TorsionBinPool , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor
• restart_mode() : protocols::forge::components::VarLengthBuild
• restart_simulation() : protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::ThermodynamicObserver
• restore() : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• restore_archive() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• restore_best_exemplars() : protocols::cluster::APCluster
• restore_cter() : protocols::ub_e2c::ubi_e2c_modeler
• restore_from_file() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeCentroid , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• restore_original_cst() : protocols::forge::remodel::RemodelGlobalFrame
• restore_original_foldtree() : protocols::hybridization::FoldTreeHybridize
• restore_phi_psi_omega_over_loop_residues() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• restore_phi_psi_over_loop_residues() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• restore_pose_variants_after_chain_closure() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• restore_status() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeBase , protocols::jd2::archive::ArchiveBase
• restorePSER() : protocols::flexpep_docking::FlexPepDockingAbInitio
• restrain_ligand_chis() : protocols::ligand_docking::LigandDockProtocol
• restrain_ligand_nbr_atom() : protocols::ligand_docking::LigandBaseProtocol
• restrain_protein_Calpha() : protocols::ligand_docking::MinimizeBackbone
• restrain_protein_Calphas() : protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::MinimizeBackbone
• restrict_aatypes_for_selection() : protocols::toolbox::SelectResiduesByLayer
• restrict_identities() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• restrict_only_design_to_loops() : protocols::toolbox::task_operations::RestrictToLoops
• restrict_sequence_profile() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• restrict_to_aligned_segments() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• restrict_to_interfacial_loop_packing() : protocols::ub_e2c::ubi_e2c_modeler
• restrict_to_nbrs() : protocols::ddg::ddGMover
• restrict_to_repacking() : protocols::simple_moves::DesignRepackMover
• 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
• RestrictIdentitiesOperation() : protocols::toolbox::task_operations::RestrictIdentitiesOperation
• RestrictInterGroupVectorOperation() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• RestrictNativeResiduesOperation() : protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• RestrictNonSurfaceToRepackingOperation() : protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
• RestrictOperationsBase() : protocols::toolbox::task_operations::RestrictOperationsBase
• RestrictResiduesToRepackingOperation() : protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• RestrictToAlignedSegmentsOperation() : protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• RestrictToCDRH3Loop() : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• RestrictToInterface() : protocols::toolbox::task_operations::RestrictToInterface
• RestrictToInterfaceOperation() : protocols::toolbox::task_operations::RestrictToInterfaceOperation
• RestrictToInterfaceVectorOperation() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• RestrictToLoops() : protocols::toolbox::task_operations::RestrictToLoops
• RestrictToLoopsAndNeighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• RestrictToMoveMapChiOperation() : protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• RestrictToNeighborhoodOperation() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• RestrictToTerminiOperation() : protocols::toolbox::task_operations::RestrictToTerminiOperation
• restype() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::TargetRotamerCoords , protocols::match::upstream::BuildSet , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• restype_atomno() : protocols::match::downstream::TargetRotamerCoords
• restype_geometry() : protocols::match::upstream::BuildSet
• restype_id_2_collision_check_id() : protocols::toolbox::match_enzdes_util::LigandConformer
• restype_name1() : protocols::motifs::Motif
• restype_name2() : protocols::motifs::Motif
• restype_possible_at_position() : protocols::enzdes::SecondaryMatchProtocol
• restype_set() : protocols::enzdes::EnzdesBaseProtocol
• ResTypeFragmentMover() : protocols::simple_moves::ResTypeFragmentMover
• result() : protocols::environment::EnvClaimBroker
• result_query_string() : protocols::wum::DatabaseEntryWorkUnit
• retag_library() : protocols::mpi_refinement::MPI_Refinement
• retrieve() : protocols::hotspot_hashing::HotspotStubSet
• retrieve_relevant_poses_for_entity() : protocols::pack_daemon::DaemonSet
• retrieve_tensor_from_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• RetrieveStoredTaskOperation() : protocols::toolbox::task_operations::RetrieveStoredTaskOperation
• return_centroid() : protocols::abinitio::Protocol
• return_combine_history() : protocols::simple_moves::CombinePoseMover
• return_key() : protocols::loophash::LoopHashMap
• return_lowest_poses_in_clusters() : protocols::cluster::ClusterBase
• return_pseudo_hits() : protocols::match::output::WriteUpstreamCoordinateKinemage
• return_silent() : protocols::simple_moves::CombinePoseMover
• return_top_poses_in_clusters() : protocols::cluster::ClusterBase
• ReturnSidechainMover() : protocols::simple_moves::ReturnSidechainMover
• reversed() : protocols::features::helixAssembly::HelicalFragment
• Reversion() : protocols::dna::Reversion
• reversion_scan() : protocols::dna::DnaInterfacePacker
• reversion_score() : protocols::dna::Reversion
• Revert() : protocols::protein_interface_design::Revert
• revert_facts_params() : protocols::mpi_refinement::WorkUnit_Sampler
• revert_loops_to_original() : protocols::hybridization::FoldTreeHybridize
• revision_id() : protocols::match::OccupiedSpaceHash
• reweight() : protocols::canonical_sampling::SimulatedTempering
• rg() : protocols::simple_moves::symmetry::SymmetrySlider
• RGFilter() : protocols::simple_filters::RGFilter
• rgstr_shift() : protocols::fldsgn::topology::StrandPairing
• right() : protocols::topology_broker::claims::DofClaim
• right_named_stub_id() : protocols::forge::build::ConnectRight
• right_position() : protocols::forge::build::ConnectRight
• right_stub_atoms() : protocols::forge::build::ConnectRight
• rigid_body_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• rigid_body_trial() : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• rigidbody_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• rigidbody_monte_carlo_minimize() : protocols::flexpep_docking::FlexPepDockingProtocol
• RigidBodyDeterministicSpinMover() : protocols::rigid::RigidBodyDeterministicSpinMover
• RigidBodyDofPerturbMover() : protocols::rigid::RigidBodyDofPerturbMover
• RigidBodyDofRandomizeMover() : protocols::rigid::RigidBodyDofRandomizeMover
• RigidBodyDofRandomTransMover() : protocols::rigid::RigidBodyDofRandomTransMover
• RigidBodyDofSeqPerturbMover() : protocols::rigid::RigidBodyDofSeqPerturbMover
• RigidBodyDofSeqRandomizeMover() : protocols::rigid::RigidBodyDofSeqRandomizeMover
• RigidBodyDofSeqTransMover() : protocols::rigid::RigidBodyDofSeqTransMover
• RigidBodyDofTransMover() : protocols::rigid::RigidBodyDofTransMover
• RigidBodyInfo() : protocols::docking::RigidBodyInfo
• RigidBodyMotionMover() : protocols::rigid::RigidBodyMotionMover
• RigidBodyMoveBaseRSO() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• RigidBodyMover() : protocols::rigid::RigidBodyMover
• RigidBodyMoveRSO() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
• RigidBodyPerturbMover() : protocols::rigid::RigidBodyPerturbMover
• RigidBodyPerturbNoCenterMover() : protocols::rigid::RigidBodyPerturbNoCenterMover
• RigidBodyPerturbRandomJumpMover() : protocols::rigid::RigidBodyPerturbRandomJumpMover
• RigidBodyRandomizeMover() : protocols::rigid::RigidBodyRandomizeMover
• RigidBodyRandomTMHMover() : protocols::topology_broker::RigidBodyRandomTMHMover
• RigidBodySampler() : protocols::stepwise::legacy::modeler::RigidBodySampler
• RigidBodySpinMover() : protocols::rigid::RigidBodySpinMover
• RigidBodyStepWiseSampler() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• RigidBodyStepWiseSamplerValueRange() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• RigidBodyStepWiseSamplerWithResidueAlternatives() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• RigidBodyStepWiseSamplerWithResidueList() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• RigidBodyTransMover() : protocols::rigid::RigidBodyTransMover
• RigidChunkClaimer() : protocols::topology_broker::RigidChunkClaimer
• RigidChunkCM() : protocols::abinitio::abscript::RigidChunkCM
• RigidLigandBuilder() : protocols::match::downstream::RigidLigandBuilder
• RigidSearchMover() : protocols::ligand_docking::RigidSearchMover
• RingConformationMover() : protocols::simple_moves::RingConformationMover
• rise() : protocols::dna::DNABasestep
• rm_virt_phosphate() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• rms() : protocols::optimize_weights::SingleStructureData
• rms_pose_list() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• rmsd() : protocols::pockets::PlaidFingerprint , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::toolbox::DecoySetEvaluation
• rmsd_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• 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_over_alignment_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• rmsd_screen() : protocols::stepwise::options::StepWiseBasicOptions
• RmsdEvaluator() : protocols::simple_filters::RmsdEvaluator
• RmsdEvaluatorCreator() : protocols::simple_filters::RmsdEvaluatorCreator
• RmsdFilter() : protocols::protein_interface_design::filters::RmsdFilter
• RMSDReporter() : protocols::pose_reporters::RMSDReporter
• RmsdSimpleFilter() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• RmsdTargetEvaluatorCreator() : protocols::simple_filters::RmsdTargetEvaluatorCreator
• rmsf() : protocols::toolbox::DecoySetEvaluation
• RMSVallData() : protocols::frags::RMSVallData
• RNA_AddDeleteMonteCarlo() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• RNA_AnalyticLoopCloser() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• RNA_AtrRepChecker() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• RNA_AtrRepScreener() : protocols::stepwise::legacy::screener::RNA_AtrRepScreener
• RNA_BaseCentroidChecker() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• rna_ccd_close() : protocols::farna::RNA_LoopCloser
• RNA_ChainClosableGeometryChecker() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• RNA_ChainClosableGeometryResidueBasedScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener
• RNA_ChainClosableGeometryScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryScreener
• RNA_ChainClosableGeometryStubBasedScreener() : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• RNA_ChainClosureChecker() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• RNA_ChainClosureScreener() : protocols::stepwise::screener::RNA_ChainClosureScreener
• RNA_ChiStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• RNA_ChunkLibrary() : protocols::farna::RNA_ChunkLibrary
• RNA_DeNovoProtocol() : protocols::farna::RNA_DeNovoProtocol
• RNA_FragmentMover() : protocols::farna::RNA_FragmentMover
• RNA_Fragments() : protocols::farna::RNA_Fragments
• RNA_HelixAssembler() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• RNA_JumpLibrary() : protocols::farna::RNA_JumpLibrary
• RNA_KIC_Sampler() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• RNA_KinematicCloser() : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• RNA_LegacyNativeRMSD_Screener() : protocols::stepwise::legacy::screener::RNA_LegacyNativeRMSD_Screener
• RNA_LegacyPoseSelectionScreener() : protocols::stepwise::legacy::screener::RNA_LegacyPoseSelectionScreener
• RNA_LoopCloser() : protocols::farna::RNA_LoopCloser
• RNA_MC_MultiSuite() : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite
• RNA_MC_Sugar() : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• RNA_MC_Suite() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• RNA_Minimizer() : protocols::farna::RNA_Minimizer
• RNA_move_trial() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• RNA_NucleosideStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler
• RNA_O2PrimeMover() : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• RNA_Pairing() : protocols::farna::RNA_Pairing
• RNA_PairingTemplate() : protocols::farna::RNA_PairingTemplate
• RNA_Relaxer() : protocols::farna::RNA_Relaxer
• RNA_SecStructInfo() : protocols::farna::RNA_SecStructInfo
• RNA_StructureParameters() : protocols::farna::RNA_StructureParameters
• RNA_SugarStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• RNA_SuiteStepWiseSampler() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• RNA_TorsionScreener() : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• RNA_VDW_BinChecker() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• roll() : protocols::dna::DNABasestep
• RollMover() : protocols::rigid::RollMover
• root() : protocols::jumping::ResiduePairJumpSetup
• root_expression() : protocols::pack_daemon::SurrogateVariableExpression
• Rose() : protocols::sic_dock::Rose
• rosetta2methyl() : protocols::noesy_assign::MethylNames
• rosetta2nmr() : protocols::noesy_assign::MethylNames
• RosettaScriptsParser() : protocols::rosetta_scripts::RosettaScriptsParser
• rot_center() : protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodySpinMover
• rot_level() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• rot_magnitude() : protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover
• rot_number() : protocols::optimize_weights::PNatAAOptERotamerData
• rot_sets() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• rotamer() : protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_data_begin() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• rotamer_data_end() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• rotamer_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_for_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamer_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::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• rotamer_set_contains_rotamer() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• rotamer_sets() : protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• RotamerBoltzCalculator() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• RotamerBoltzmannWeight() : protocols::simple_filters::RotamerBoltzmannWeight
• RotamerBoltzmannWeightFeatures() : protocols::features::RotamerBoltzmannWeightFeatures
• RotamerBoltzmannWeightFeaturesCreator() : protocols::features::RotamerBoltzmannWeightFeaturesCreator
• RotamerDNAHBondFilter() : protocols::dna::RotamerDNAHBondFilter
• RotamerDumpMover() : protocols::RotamerDump::RotamerDumpMover
• RotamerFeatures() : protocols::features::RotamerFeatures
• RotamerFeaturesCreator() : protocols::features::RotamerFeaturesCreator
• RotamerizeMover() : protocols::simple_moves::RotamerizeMover
• 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_on_same_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• rotamersets() : protocols::multistate_design::PackingState
• RotamerSubsetRepacker() : protocols::pack_daemon::RotamerSubsetRepacker
• RotamerTrialsMinMover() : protocols::simple_moves::RotamerTrialsMinMover
• RotamerTrialsMover() : protocols::simple_moves::RotamerTrialsMover
• 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
• RotationMover() : protocols::membrane::RotationMover
• RotationSearchPattern() : protocols::hotspot_hashing::RotationSearchPattern
• RotData() : protocols::make_rot_lib::RotData
• rotid_on_moltenresidue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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
• round() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::features::strand_assembly::StrandBundleFeatures , protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::quota::TorsionBinPool
• round_expired() : protocols::mpi_refinement::Scheduler
• round_to_Real() : protocols::simple_filters::ResidueCountFilter
• roundtype() : protocols::mpi_refinement::Scheduler
• 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
• RRComparerElecDensDiff() : protocols::rotamer_recovery::RRComparerElecDensDiff
• RRComparerElecDensDiffCreator() : protocols::rotamer_recovery::RRComparerElecDensDiffCreator
• RRComparerRotBins() : protocols::rotamer_recovery::RRComparerRotBins
• RRComparerRotBinsCreator() : protocols::rotamer_recovery::RRComparerRotBinsCreator
• RRProtocolCreator() : protocols::rotamer_recovery::RRProtocolCreator
• RRProtocolMinPack() : protocols::rotamer_recovery::RRProtocolMinPack
• RRProtocolMinPackCreator() : protocols::rotamer_recovery::RRProtocolMinPackCreator
• RRProtocolMover() : protocols::rotamer_recovery::RRProtocolMover
• RRProtocolMoverCreator() : protocols::rotamer_recovery::RRProtocolMoverCreator
• RRProtocolPackRotamers() : protocols::rotamer_recovery::RRProtocolPackRotamers
• RRProtocolPackRotamersCreator() : protocols::rotamer_recovery::RRProtocolPackRotamersCreator
• RRProtocolReferenceStructure() : protocols::rotamer_recovery::RRProtocolReferenceStructure
• RRProtocolReferenceStructureCreator() : protocols::rotamer_recovery::RRProtocolReferenceStructureCreator
• RRProtocolRelax() : protocols::rotamer_recovery::RRProtocolRelax
• RRProtocolRelaxCreator() : protocols::rotamer_recovery::RRProtocolRelaxCreator
• RRProtocolRotamerTrials() : protocols::rotamer_recovery::RRProtocolRotamerTrials
• RRProtocolRotamerTrialsCreator() : protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator
• RRProtocolRTMin() : protocols::rotamer_recovery::RRProtocolRTMin
• RRProtocolRTMinCreator() : protocols::rotamer_recovery::RRProtocolRTMinCreator
• RRReporterCreator() : protocols::rotamer_recovery::RRReporterCreator
• RRReporterHuman() : protocols::rotamer_recovery::RRReporterHuman
• RRReporterHumanCreator() : protocols::rotamer_recovery::RRReporterHumanCreator
• RRReporterSimple() : protocols::rotamer_recovery::RRReporterSimple
• RRReporterSimpleCreator() : protocols::rotamer_recovery::RRReporterSimpleCreator
• RRReporterSQLite() : protocols::rotamer_recovery::RRReporterSQLite
• RRReporterSQLiteCreator() : protocols::rotamer_recovery::RRReporterSQLiteCreator
• rsd() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• rsd_sasa() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• rsigma_dot_initializer() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• rt() : protocols::forge::build::ConnectRight
• rt_min() : protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy
• rt_templates() : protocols::jumping::MembraneJump
• rtmin() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::RelativePoseFilter
• run() : protocols::abinitio::AbrelaxApplication , protocols::dna::DnaInterfaceMultiStateDesign , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::hybridization::DomainAssembly , protocols::jd2::MpiFileBuffer , protocols::loophash::WorkUnit_LoopHash , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Relax , protocols::mpi_refinement::WorkUnit_Sampler , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::relax::WorkUnit_BatchRelax , protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RRProtocol , protocols::rotamer_recovery::RRProtocolMinPack , protocols::rotamer_recovery::RRProtocolMover , protocols::rotamer_recovery::RRProtocolPackRotamers , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRotamerTrials , protocols::rotamer_recovery::RRProtocolRTMin , protocols::rpc::JSON_RPC , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::stepwise::StepWiseSampleAndScreen , protocols::wum2::WorkUnit , protocols::wum2::WorkUnit_ElScripts , protocols::wum2::WorkUnit_Wait , protocols::wum::WorkUnit_MoverWrapper , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnit_Wait , protocols::wum::WorkUnitBase
• run_A_ANN_Prediction() : protocols::sparta::Sparta
• run_basic_mc_algorithm() : protocols::antibody::design::AntibodyGraftDesignMover
• run_calculator() : protocols::forge::remodel::RemodelDesignMover , protocols::toolbox::task_operations::RestrictOperationsBase
• run_cluster() : protocols::forge::remodel::RemodelAccumulator
• run_design_on_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• run_deterministic_graft_algorithm() : protocols::antibody::design::AntibodyGraftDesignMover
• run_domain_assembly() : protocols::hybridization::HybridizeSetup
• run_graft() : protocols::antibody::design::AntibodyGraftDesignMover
• run_mc() : protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• run_motifs() : protocols::motifs::MotifDnaPacker
• run_one_job() : protocols::jd2::JobDistributor
• run_packer() : protocols::multistate_design::PackingState
• run_post_graft_min() : protocols::antibody::design::AntibodyGraftDesignMover
• run_rattle1() : protocols::md::Rattle
• run_rattle2() : protocols::md::Rattle
• run_sa() : protocols::simple_moves::GreenPacker
• running_average_pair() : protocols::make_rot_lib::running_average_pair
• runSpartaANN() : protocols::sparta::ANN
• runtime() : protocols::rpc::JSON_RPC
• RuntimeFeatures() : protocols::features::RuntimeFeatures