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

- e -

• e2_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• e2_d77_jump_ : protocols::ub_e2c::ubi_e2c_modeler
• e2_end_ : protocols::ub_e2c::ubi_e2c_modeler
• e2_k48r_jump_ : protocols::ub_e2c::ubi_e2c_modeler
• e_ : protocols::normalmode::NormalMode
• E_mult_ : protocols::frag_picker::scores::TalosSSSimilarity
• early_exit_check() : protocols::stepwise::StepWiseSampleAndScreen
• eat_signal() : protocols::jd2::MPIFileBufJobDistributor
• echo_metrics_to_jd2() : protocols::antibody::AntibodyModelerProtocol
• eckart_correction() : protocols::normalmode::NormalMode
• eckart_correction_ : protocols::normalmode::NormalMode
• edge1 : protocols::farna::BasePairType , protocols::farna::RNA_Pairing
• edge2 : protocols::farna::BasePairType , protocols::farna::RNA_Pairing
• edge_ : protocols::scoring::methods::pcs2::GridSearchIterator , 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
• edge_connects_flexsegmate() : protocols::flexpack::interaction_graph::FlexbbNode
• edge_connects_flexsegmate_ : protocols::flexpack::interaction_graph::FlexbbNode
• EdgeBase : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• EdgeStandScore() : protocols::sic_dock::EdgeStandScore
• edit_mode : protocols::toolbox::KClusterElement
• ee : protocols::sic_dock::XfoxmScore
• effect_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• egg_and_ext_list_ : protocols::pockets::NonPlaidFingerprint
• EGGSHELL : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• eggshell_CoM_ : protocols::pockets::EggshellGrid
• eggshell_coord_list() : protocols::pockets::EggshellGrid
• eggshell_coord_list_ : protocols::pockets::EggshellGrid
• eggshell_list_ : protocols::pockets::NonPlaidFingerprint
• EGGSHELL_SURROUNDING : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• EggshellGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::EggshellGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• eigsrt() : protocols::normalmode::NormalMode
• eigval_ : protocols::normalmode::NormalMode
• eigvec_ : protocols::evaluation::PCA
• eigvec_cart_ : protocols::normalmode::NormalMode
• eigvec_tor_ : protocols::normalmode::NormalMode
• el : protocols::sic_dock::XfoxmScore
• EL_DISTVIOL : protocols::noesy_assign::CrossPeak
• EL_MAXASSIGN : protocols::noesy_assign::CrossPeak
• EL_MINPEAKVOL : protocols::noesy_assign::CrossPeak
• EL_NETWORK : protocols::noesy_assign::CrossPeak
• elapsed_time() : protocols::jd2::Job
• ElectricField : protocols::sparta::PDB
• ElectrostaticpotentialGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• element_from_string() : protocols::genetic_algorithm::EntityElementFactory
• eliminate_spurious_peaks() : protocols::noesy_assign::CrossPeakList
• eliminate_violated_constraints() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap , protocols::noesy_assign::StructureDependentPeakCalibrator
• eliminated() : protocols::noesy_assign::CrossPeak
• eliminated_ : protocols::noesy_assign::CrossPeak
• eliminated_due_to_dist_violations_ : protocols::noesy_assign::CrossPeak
• elimination_candidate_ : protocols::noesy_assign::CrossPeak
• elimination_comment_ : protocols::noesy_assign::CrossPeak
• elimination_reason() : protocols::noesy_assign::CrossPeak
• EliminationReason : protocols::noesy_assign::CrossPeak
• ellipsoid_is_first_partner_ : protocols::docking::EllipsoidalRandomizationMover
• EllipsoidalRandomizationMover() : protocols::docking::EllipsoidalRandomizationMover
• elongate() : protocols::fldsgn::topology::StrandPairing
• elsefilter_ : protocols::filters::IfThenFilter
• elsevalue_ : protocols::filters::IfThenFilter
• elseweight_ : protocols::filters::IfThenFilter
• Embedding() : protocols::membrane::geometry::Embedding
• embedding() : protocols::membrane::geometry::Embedding
• EmbeddingDef() : protocols::membrane::geometry::EmbeddingDef
• embeddings() : protocols::membrane::geometry::Embedding
• embeddings_ : protocols::membrane::geometry::Embedding , protocols::membrane::visualize::VisualizeEmbeddingMover
• Emin_obj_ : protocols::md::MDBase
• empty() : protocols::antibody::clusters::CDRClusterSet , protocols::dna::DnaChains , protocols::forge::build::BuildManager , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loops::Loops
• EMPTY : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid , protocols::sparta::GDB , protocols::sparta::PDB
• empty() : protocols::wum2::WUQueue
• empty_ : protocols::fldsgn::topology::StrandPairingSet , protocols::rpc::BasicCmdLineInit , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• empty_clone() : protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak
• empty_pose() : protocols::match::output::MatchCollisionFilter
• empty_pose_ : protocols::match::output::MatchCollisionFilter
• empty_pose_data_list() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• empty_sfxn() : protocols::match::output::MatchCollisionFilter
• empty_sfxn_ : protocols::match::output::MatchCollisionFilter
• empty_sugar_modeling_list() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• empty_voxel_color_ : protocols::match::Bool3DGridKinemageWriter
• enable() : protocols::ligand_docking::ResidueTorsionRestraints
• enable_autotemp() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• enable_benchmark_mode() : protocols::antibody::CloseOneCDRLoop , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover
• enable_build_stage() : protocols::loop_modeling::LoopModeler
• enable_centroid_stage() : protocols::loop_modeling::LoopModeler
• enable_constraint_scoreterms() : protocols::enzdes::EnzdesBaseProtocol , protocols::forge::remodel::RemodelEnzdesCstModule
• enable_design_ : protocols::relax::FastRelax
• enable_end_bias_check() : protocols::simple_moves::ClassicFragmentMover
• enable_fullatom_stage() : protocols::loop_modeling::LoopModeler
• enable_graft_h1() : protocols::antibody_legacy::GraftMover
• enable_graft_h2() : protocols::antibody_legacy::GraftMover
• enable_graft_h3() : protocols::antibody_legacy::GraftMover
• enable_graft_l1() : protocols::antibody_legacy::GraftMover
• enable_graft_l2() : protocols::antibody_legacy::GraftMover
• enable_graft_l3() : protocols::antibody_legacy::GraftMover
• enable_ignorefinished() : protocols::jobdist::BaseJobDistributor
• enable_inprogress() : protocols::jobdist::BaseJobDistributor
• enable_ligand_rotamer_packing() : protocols::ligand_docking::HighResDocker
• enable_max_residue_count() : protocols::simple_filters::ResidueCountFilter
• enable_max_residue_count_ : protocols::simple_filters::ResidueCountFilter
• enable_min_residue_count() : protocols::simple_filters::ResidueCountFilter
• enable_min_residue_count_ : protocols::simple_filters::ResidueCountFilter
• enable_output() : protocols::jobdist::BaseJobDistributor
• enabled() : protocols::dna::PDBOutput
• enabled_ : protocols::dna::PDBOutput
• encounter_ : protocols::surface_docking::FullatomRelaxMover
• encounter_cycle_ : protocols::surface_docking::FullatomRelaxMover
• end() : protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::anchored_design::Anchor , protocols::antibody::clusters::CDRCluster , protocols::ddG::ddGData , protocols::dna::DnaChains , protocols::environment::Environment , protocols::features::helixAssembly::HelicalFragment , protocols::filters::CompoundFilter , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelWorkingSet , protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::hotspot_hashing::HotspotStubSet , protocols::jumping::Interval , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::ligand_docking::MinimizeLigand , protocols::loops::Loops , protocols::motifs::MotifLibrary , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::FoldResonance , protocols::noesy_assign::MethylNames , protocols::noesy_assign::ResonanceList , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::TryRotamers , protocols::rbsegment_relax::RBResidueRange , protocols::rosetta_scripts::ParsedProtocol , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• end1() : protocols::fldsgn::topology::StrandPairing
• end1_ : protocols::fldsgn::topology::StrandPairing
• end2() : protocols::fldsgn::topology::StrandPairing
• end2_ : protocols::fldsgn::topology::StrandPairing
• end_ : protocols::anchored_design::Anchor , protocols::antibody::clusters::CDRCluster , protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::fldsgn::topology::SS_Base , protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::jd2::parser::FragmentReader , protocols::jumping::Interval , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::simple_filters::GeometryFilter , protocols::simple_filters::RmsdEvaluator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• end_1_distance : protocols::features::helixAssembly::FragmentPair
• end_2_distance : protocols::features::helixAssembly::FragmentPair
• end_atom_ : protocols::topology_broker::BasicJumpClaimer
• end_atom_list_ : protocols::simple_moves::BBGaussianMover
• end_atomid() : protocols::backrub::BackrubSegment
• end_atomid_ : protocols::backrub::BackrubSegment
• end_atoms1() : protocols::backrub::BackrubSegment
• end_atoms2() : protocols::backrub::BackrubSegment
• end_bias() : protocols::simple_moves::ClassicFragmentMover
• end_bias_ : protocols::simple_moves::ClassicFragmentMover
• end_bias_check() : protocols::simple_moves::ClassicFragmentMover
• end_bias_check_enabled() : protocols::simple_moves::ClassicFragmentMover
• end_bond_angle_key() : protocols::backrub::BackrubSegment
• end_chain_pair() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• end_critical_section() : protocols::jd2::BOINCJobDistributor , protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• end_index_ : protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixMultiFunc
• end_label() : protocols::topology_broker::BasicJumpClaimer
• end_label_ : protocols::topology_broker::BasicJumpClaimer
• end_native_ : protocols::protein_interface_design::filters::RmsdFilter
• end_output_writing() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PoseMatchOutputWriter
• end_pose_ : protocols::protein_interface_design::filters::RmsdFilter
• end_position() : protocols::topology_broker::BasicJumpClaimer
• end_position_ : protocols::topology_broker::BasicJumpClaimer
• end_processing() : protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor
• end_processing_of_match_dspos1_groups() : protocols::match::output::MatchConsolidator
• end_processing_of_regular_match_groups() : protocols::match::output::MatchConsolidator
• end_rep_weight : protocols::relax::ClassicRelax
• end_res() : protocols::docking::DockingEnsemble , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::toolbox::task_operations::DatabaseThread
• end_res_ : protocols::docking::DockingEnsemble , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ReturnSidechainMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::toolbox::task_operations::DatabaseThread
• end_stage() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• end_structure() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• end_weight() : protocols::moves::RampingMover
• end_weights_ : protocols::moves::RampingMover
• EndPoint() : protocols::wum2::EndPoint
• endtime_ : protocols::rpc::JSON_RPC
• EnergiesData() : protocols::toolbox::pose_metric_calculators::EnergiesData
• EnergiesEdge : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesGraph : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesUpperEdgeListConstIter : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesUpperEdgeListIter : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesVertex : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• energy : protocols::simple_filters::nmer_svm_res_data
• energy_ : protocols::make_rot_lib::RotData
• energy_cutoff_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• energy_drop() : protocols::moves::TrialCounter
• energy_drop_counter_ : protocols::moves::TrialCounter
• energy_event_link_ : protocols::viewer::SilentObserver
• energy_gap_counter_ : protocols::simple_moves::GenericMonteCarloMover
• energy_map() : protocols::toolbox::pose_metric_calculators::EnergiesData
• energy_map_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• energy_method_ : protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter
• energy_reduction_factor() : protocols::simple_filters::RotamerBoltzmannWeight
• energy_reduction_factor_ : protocols::simple_filters::RotamerBoltzmannWeight
• energy_sort_cluster() : protocols::mpi_refinement::Clusterer
• energy_terms() : protocols::optimize_weights::OptEData
• energy_terms_ : protocols::optimize_weights::OptEData , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• energy_threshold_ : protocols::enzdes::RepackWithoutLigandFilter
• energy_to_beat : protocols::vip::VIP_Mover
• energy_type() : protocols::moves::PyMolMover
• energy_type_ : protocols::moves::PyMolMover
• energycut : protocols::relax::ClassicRelax
• energycut_ : protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• EnergyCutRotamerTrialsMinMover() : protocols::simple_moves::EnergyCutRotamerTrialsMinMover
• EnergyCutRotamerTrialsMover() : protocols::simple_moves::EnergyCutRotamerTrialsMover
• energyEvent() : protocols::moves::PyMolObserver
• EnergyGraph : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• EnergyMap : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::simple_moves::GreenPacker
• EnergyMethodOP : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator
• EnergyMethodOptions : protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator
• EnergyPerResidueFilter() : protocols::simple_filters::EnergyPerResidueFilter
• EnergyReporter() : protocols::pose_reporters::EnergyReporter
• enforce_bb_contiguity_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• enforce_false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• enforce_minimum_length() : protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::ligand_options::Interface
• enlargen_to_capture_volume_within_radius_of_backbone() : protocols::match::downstream::ActiveSiteGrid
• enlargen_to_capture_volume_within_radius_of_residue() : protocols::match::downstream::ActiveSiteGrid
• enlargen_to_capture_volume_within_radius_of_sidechain() : protocols::match::downstream::ActiveSiteGrid
• enough_connections() : protocols::simple_filters::RegionalConnections
• enqueue() : protocols::moves::CyclicMover
• enrich_Zscore_cut_ : protocols::mpi_refinement::Scheduler
• ensemble1_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingProtocol
• ensemble1_filename_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingProtocol
• ensemble1_mover_ : protocols::docking::DockingLowResEnsemble
• ensemble2_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingProtocol
• ensemble2_filename_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingProtocol
• ensemble2_mover_ : protocols::docking::DockingLowResEnsemble
• ensemble_ : protocols::docking::ConformerSwitchMover
• ensemble_ca_rmsd : protocols::simple_moves::ShakeStructureMover
• ensemble_ca_rmsd_tolerance : protocols::simple_moves::ShakeStructureMover
• ensemble_file_path_ : protocols::docking::DockingEnsemble
• ensemble_list_ : protocols::docking::DockingEnsemble
• ensemble_list_cen_ : protocols::docking::DockingEnsemble
• ensemble_size_ : protocols::docking::DockingEnsemble
• EnsembleConstraints() : protocols::cluster::EnsembleConstraints
• EnsembleConstraints_Simple() : protocols::cluster::EnsembleConstraints_Simple
• EnsembleEnergy() : protocols::scoring::methods::EnsembleEnergy
• ensure_all_fields_are_valid() : protocols::loops::JSONFormattedLoopsFileReader
• ensure_proper_his_tautomers() : protocols::metal_interface::MatchGrafter
• ensure_scofx_cstfication() : protocols::enzdes::EnzRepackMinimize
• ensure_structure_tags_are_ready() : protocols::features::ReportToDB
• ensure_variant_matching_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• EntElemEq : protocols::pack_daemon::PackDaemon
• entities_checkpoint_filename() : protocols::genetic_algorithm::GeneticAlgorithmBase
• Entity() : protocols::genetic_algorithm::Entity , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::TopEntitySet
• entity_aas_ : protocols::pack_daemon::EntityFunc
• entity_cache() : protocols::genetic_algorithm::GeneticAlgorithmBase
• entity_cache_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• entity_for_residue() : protocols::pack_daemon::EntityCorrespondence
• entity_funcs_ : protocols::pack_daemon::DynamicAggregateFunction
• entity_funcs_dec_line_ : protocols::pack_daemon::DynamicAggregateFunction
• entity_id_2_resids_ : protocols::pack_daemon::EntityCorrespondence
• entity_length() : protocols::genetic_algorithm::EntityRandomizer
• entity_length_ : protocols::genetic_algorithm::EntityRandomizer
• entity_randomizer_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• entity_resfile() : protocols::pack_daemon::DaemonSet
• entity_resfile_ : protocols::pack_daemon::DaemonSet
• entity_task() : protocols::pack_daemon::DaemonSet
• entity_task_ : protocols::pack_daemon::DaemonSet
• entity_template() : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase
• entity_template_ : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityAndScore : protocols::pack_daemon::EntityHistoryLT , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• EntityCAP : protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityCAPs : protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityCOP : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityCOPs : protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityCorrespondence() : protocols::pack_daemon::EntityCorrespondence
• EntityElement() : protocols::genetic_algorithm::EntityElement , protocols::pack_daemon::PackDaemon
• EntityElementFactory() : protocols::genetic_algorithm::EntityElementFactory
• EntityElementOP : protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::PosType , protocols::multistate_design::PosTypeCreator , protocols::pack_daemon::PackDaemon
• EntityElementRegistrator() : protocols::genetic_algorithm::EntityElementRegistrator< T >
• EntityElements : protocols::pack_daemon::PackDaemon
• EntityFunc() : protocols::pack_daemon::EntityFunc
• EntityFuncExpressionCreator() : protocols::pack_daemon::EntityFuncExpressionCreator
• EntityHistory : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• EntityOP : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::multistate_design::MultiStateEntity< T > , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::TopEntitySet
• EntityRandomizer() : protocols::genetic_algorithm::EntityRandomizer
• EntityRandomizerOP : protocols::genetic_algorithm::GeneticAlgorithmBase
• EntityToRotamerHash : protocols::pack_daemon::PackDaemon
• Entries : protocols::sparta::GDB
• entries_ : protocols::abinitio::PairingStatistics , protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• EntryList : protocols::sparta::GDB
• EntryMap : protocols::sparta::PDB
• enum_manager_ : protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyNumberingParser
• enum_to_string_ : protocols::antibody::clusters::CDRClusterEnumManager
• enumerate_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• enumerate_ligand_rotamers() : protocols::match::MatcherTask
• enumerate_ligand_rotamers_ : protocols::match::MatcherTask
• ENUMERATION : protocols::abinitio::IterativeBase
• env_ : protocols::environment::EnvClaimBroker , protocols::environment::EnvMover , protocols::environment::ProtectedConformation
• env_destruction() : protocols::environment::ProtectedConformation
• env_potential_ : protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy
• EnvClaim() : protocols::environment::claims::EnvClaim
• EnvClaimBroker : protocols::environment::ClientMover , protocols::environment::EnvClaimBroker , protocols::environment::ProtectedConformation
• EnvClaims : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::loops::loop_mover::LoopCM , protocols::rigid::UniformRigidBodyCM
• Environment : protocols::environment::ClientMover , protocols::environment::Environment , protocols::environment::ProtectedConformation
• environment() : protocols::environment::ProtectedConformation
• environment_exists_ : protocols::environment::ProtectedConformation
• EnvLabelSelector() : protocols::environment::claims::EnvLabelSelector
• EnvMover() : protocols::environment::EnvMover
• enz_cst_params() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• enz_cst_params_missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• enz_cst_params_size() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• enz_cst_template_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• enz_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• enz_input_data() : protocols::match::MatcherTask
• enz_input_data_ : protocols::match::MatcherTask
• enz_io() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• enz_io_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• enz_io_param_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• enz_loop_info() : protocols::enzdes::EnzdesFlexibleRegion
• enz_loops_file() : protocols::enzdes::EnzdesFlexBBProtocol
• enz_loops_file_ : protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesJobInputter , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• enz_scofile_ : protocols::enzdes::EnzdesJobOutputter
• enz_template_res_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• EnzConstraintIO() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• EnzConstraintParameters() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• enzcst_io() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• enzcst_io_ : protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::fldsgn::BluePrintBDR , protocols::forge::constraints::InvrotTreeRCG , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• EnzCstTemplateRes() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• EnzCstTemplateResCache() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• enzdes_loops_file() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• enzdes_pack() : protocols::enzdes::EnzdesBaseProtocol
• enzdes_protocol_ : protocols::enzdes::EnzdesFlexibleRegion
• EnzdesBaseProtocol() : protocols::enzdes::EnzdesBaseProtocol
• EnzdesCacheableObserver() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• EnzdesConstraintReporter() : protocols::enzdes::EnzdesConstraintReporter
• EnzdesCstCache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• EnzdesCstParamCache() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• EnzdesFixBBProtocol() : protocols::enzdes::EnzdesFixBBProtocol
• EnzdesFlexBBProtocol() : protocols::enzdes::EnzdesFlexBBProtocol
• EnzdesFlexibleRegion() : protocols::enzdes::EnzdesFlexibleRegion
• EnzdesJobInputter() : protocols::enzdes::EnzdesJobInputter
• EnzdesJobOutputter() : protocols::enzdes::EnzdesJobOutputter
• EnzdesLoopInfo() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• EnzdesLoopsFile() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• EnzdesScorefileFilter() : protocols::enzdes::EnzdesScorefileFilter
• EnzdesSeqRecoveryCache() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• enzloops_ : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• EnzRepackMinimize() : protocols::enzdes::EnzRepackMinimize
• EnzScoreFilter() : protocols::enzdes::EnzScoreFilter
• ep_cutoff_ : protocols::simple_filters::NMerSVMEnergyFilter
• epitope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• eps_ : protocols::make_rot_lib::MakeRotLibJob
• eps_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• epsilon() : protocols::dna::DNABase
• epsilon_ : protocols::dna::DNABase , protocols::make_rot_lib::RotData
• epsilon_0_ : protocols::qsar::scoring_grid::ChargeGrid
• equal_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• EQUALS : protocols::enzdes::ValueEvaluator
• equals() : protocols::membrane::geometry::EmbeddingDef
• erase() : protocols::cluster::Cluster , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• erase_decoy() : protocols::abinitio::IterativeCentroid , protocols::jd2::archive::ArchiveBase
• erase_hit() : protocols::match::Matcher
• erase_rigid_body_confs_for_lig() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• erraser() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• erraser_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• error() : protocols::noesy_assign::Resonance
• error_ : protocols::noesy_assign::Resonance
• esp_dim_ : protocols::pockets::NonPlaidFingerprint
• esp_mid_ : protocols::pockets::NonPlaidFingerprint
• esp_spacing_ : protocols::pockets::NonPlaidFingerprint
• espGrid_ : protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::NonPlaidFingerprint
• espGrid_dim_ : protocols::pockets::ElectrostaticpotentialGrid
• espGrid_mid_ : protocols::pockets::ElectrostaticpotentialGrid
• espGrid_point_list() : protocols::pockets::ElectrostaticpotentialGrid
• espGrid_points_list_ : protocols::pockets::ElectrostaticpotentialGrid
• espGrid_spacing_ : protocols::pockets::ElectrostaticpotentialGrid
• estimate_membrane_center() : protocols::rigid::MovePoseToMembraneCenterMover
• etable_energy() : protocols::match::output::MatchCollisionFilter
• etable_energy_ : protocols::match::output::MatchCollisionFilter
• etable_evaluator_ : protocols::ligand_docking::rdf::RDFEtableFunction
• euclidean_bin_widths() : protocols::match::MatcherTask
• euclidean_bin_widths_ : protocols::match::Matcher , protocols::match::MatcherTask
• euler_alpha : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• euler_alpha_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_alpha_values_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_max_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_min_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_angle_bin_size_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_bin_halfwidths_ : protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• euler_bin_widths() : protocols::match::MatcherTask
• euler_bin_widths_ : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• euler_gamma : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• euler_gamma_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_gamma_values_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• euler_z_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_bin_max_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_bin_min_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_bin_size_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• euler_z_values_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• EulerAngles() : protocols::stepwise::sampler::rigid_body::EulerAngles
• ev_objective_function() : protocols::loophash::MPI_LoopHashRefine_Master
• eval() : protocols::evaluation::PCA , protocols::jumping::SameStrand
• eval_ : protocols::stepwise::screener::PartitionContactScreener
• eval_cd_1b() : protocols::flexpack::OtherContextScoreFunction
• eval_cd_2b() : protocols::flexpack::OtherContextScoreFunction
• eval_cd_2b_residues() : protocols::match::downstream::ScoringSecMatchRPE
• eval_cd_intrares_energy() : protocols::flexpack::OtherContextScoreFunction
• eval_dipolar() : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• eval_dof_derivative() : protocols::scoring::methods::SpecialRotamerEnergy
• eval_filters() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• eval_intrares_energy() : protocols::scoring::methods::InterchainPairEnergy
• eval_longRange_2b_residue() : protocols::match::downstream::ScoringSecMatchRPE
• eval_lowest_score_pose() : protocols::moves::MonteCarlo
• eval_non_residue_pair_energy() : protocols::constraints_additional::MaxSeqSepConstraintSet
• evalGradient() : protocols::viewer::triangleIterator
• evals_ : protocols::simple_filters::EvaluatedTrialMover
• evaluate() : protocols::branch_angle::BranchCoef1 , protocols::branch_angle::BranchCoef2 , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::genetic_algorithm::FitnessFunction , protocols::jd2::JobOutputter , protocols::multistate_design::MetricCalculatorFitnessFunction , protocols::multistate_design::MultiStateAggregateFunction , protocols::multistate_design::MultiStateFitnessFunction , protocols::multistate_design::MultiStatePacker , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::multistate_design::SingleStateFitnessFunction , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction
• evaluate_and_add() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• evaluate_constraint_energy() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• evaluate_constraints() : protocols::metal_interface::AddZincSiteConstraints
• evaluate_contact_score() : protocols::scoring::InterchainPotential
• evaluate_convergence_checks() : protocols::moves::MonteCarlo
• evaluate_core() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• evaluate_env_score() : protocols::scoring::InterchainPotential
• evaluate_fitnesses() : protocols::genetic_algorithm::GeneticAlgorithm
• evaluate_local() : protocols::jd2::archive::EvaluatedArchive
• evaluate_native() : protocols::ub_e2c::ubi_e2c_modeler
• evaluate_pair_and_vdw_score() : protocols::scoring::InterchainPotential
• evaluate_pddf_energy() : protocols::scoring::methods::saxs::PDDFEnergy
• evaluate_pose() : protocols::abinitio::Protocol , protocols::jd2::archive::EvaluatedArchive
• evaluate_positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• evaluate_residues() : protocols::match::downstream::AtomAngleSecMatchRPE , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::ScoringSecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• evaluate_silent_struct() : protocols::jd2::archive::EvaluatedArchive
• evaluate_stub_bumps_() : protocols::hotspot_hashing::HotspotStubSet
• evaluate_stub_self_energy_() : protocols::hotspot_hashing::HotspotStubSet
• EvaluatedArchive() : protocols::jd2::archive::EvaluatedArchive
• EvaluatedTrialMover() : protocols::simple_filters::EvaluatedTrialMover
• evaluator() : protocols::abinitio::Protocol
• evaluator_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Protocol , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::match::output::MatchProcessor , protocols::simple_filters::EvaluatedTrialMover
• evaluator_map_ : protocols::enzdes::EnzdesScorefileFilter
• Evaluator_MCFI_ID_Pair : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• evaluator_name() : protocols::match::MatcherTask
• evaluator_name_ : protocols::match::MatcherTask
• EvaluatorCreator() : protocols::evaluation::EvaluatorCreator
• EvaluatorCreatorMap : protocols::evaluation::EvaluatorFactory
• EvaluatorFactory() : protocols::evaluation::EvaluatorFactory
• EvaluatorList : protocols::evaluation::MetaPoseEvaluator
• EvaluatorMap : protocols::jd2::archive::EvaluatedArchive
• EvaluatorRegistrator() : protocols::evaluation::EvaluatorRegistrator< T >
• evaluators() : protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• evaluators_ : protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• EvaluatorSet : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• evolve_next_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• ex_level_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::task_operations::InteractingRotamerExplosion
• ex_level_from_flags() : protocols::match::upstream::FullChiSampleSet
• exact_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• examine_new_loopconf() : protocols::enzdes::EnzdesFlexibleRegion
• examine_pose() : protocols::enzdes::EnzdesScorefileFilter
• exchange_accepts_ : protocols::canonical_sampling::ParallelTempering
• exchange_attempts_ : protocols::canonical_sampling::ParallelTempering
• exchange_grid_ : protocols::canonical_sampling::HamiltonianExchange
• exchange_grid_dim() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::TemperatureController
• exchange_grid_dimension_ : protocols::canonical_sampling::HamiltonianExchange
• exchange_ligands_in_pose() : protocols::enzdes::EnzdesBaseProtocol
• exchange_requests_ : protocols::canonical_sampling::AsyncMPITemperingBase
• exchange_schedule : protocols::moves::ReplicaExchangeMC
• exchange_schedule_file_ : protocols::canonical_sampling::HamiltonianExchange
• exchange_schedules_ : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering
• ExchangeRequest() : protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest
• ExchangeRequestMap : protocols::canonical_sampling::AsyncMPITemperingBase
• ExchangeSchedule : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering
• exclude_aatypes_for_selection() : protocols::toolbox::SelectResiduesByLayer
• exclude_clusters() : protocols::antibody::CDRSetOptions
• exclude_clusters_ : protocols::antibody::CDRSetOptions
• exclude_clusters_add() : protocols::antibody::CDRSetOptions
• exclude_clusters_clear() : protocols::antibody::CDRSetOptions
• exclude_cys_peptides : protocols::frags::RMSVallData
• exclude_desinated_pdbs_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_germlines() : protocols::antibody::CDRSetOptions
• exclude_germlines_ : protocols::antibody::CDRSetOptions
• exclude_germlines_add() : protocols::antibody::CDRSetOptions
• exclude_germlines_clear() : protocols::antibody::CDRSetOptions
• exclude_gly : protocols::frags::RMSVallData
• exclude_list_ : protocols::simple_filters::TruncatedScoreEvaluator
• exclude_ncaas() : protocols::flxbb::LayerDesignOperation
• exclude_pdb_ids_ : protocols::antibody::CDRSetOptions
• exclude_pdbs() : protocols::antibody::CDRSetOptions
• exclude_pdbs_add() : protocols::antibody::CDRSetOptions
• exclude_pdbs_clear() : protocols::antibody::CDRSetOptions
• exclude_pro : protocols::frags::RMSVallData
• exclude_protein_protein_fa_elec_ : protocols::enzdes::EnzdesBaseProtocol
• exclude_radius_ : protocols::toolbox::task_operations::InteractingRotamerExplosion
• exclude_residues_vector_is_current() : 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
• exclude_sandwich_that_has_near_backbone_atoms_between_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_has_non_canonical_LR_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_has_non_canonical_properties_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_has_non_canonical_shortest_dis_between_facing_aro_in_sw_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_is_linked_w_same_direction_strand_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_is_suspected_to_have_not_facing_2_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_with_SS_bond_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_species() : protocols::antibody::CDRSetOptions
• exclude_species_ : protocols::antibody::CDRSetOptions
• exclude_species_add() : protocols::antibody::CDRSetOptions
• exclude_species_clear() : protocols::antibody::CDRSetOptions
• EXCLUDED : protocols::sparta::Sparta::SpartaLib
• excluded_aatypes_for_selection_ : protocols::toolbox::SelectResiduesByLayer
• excluded_positions : protocols::vip::VIP_Mover
• excluded_positions_ : protocols::helix_capper::HelixNCapperMover
• excluded_residues_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• exclusions_ : protocols::mpi_refinement::Scheduler
• EXCLUSIVE : protocols::environment::claims::ClaimStrength , protocols::topology_broker::claims::DofClaim
• exclusive() : protocols::topology_broker::claims::DofClaim
• EXCN_Archive() : protocols::jd2::archive::EXCN_Archive
• EXCN_AssignmentNotFound() : protocols::noesy_assign::EXCN_AssignmentNotFound
• EXCN_bbdb_Merge_Failed() : protocols::loophash::EXCN_bbdb_Merge_Failed
• EXCN_Converged() : protocols::moves::EXCN_Converged
• EXCN_DB_IO_Failed() : protocols::loophash::EXCN_DB_IO_Failed
• EXCN_Env_Passport() : protocols::environment::EXCN_Env_Passport
• EXCN_Env_Security_Exception() : protocols::environment::EXCN_Env_Security_Exception
• EXCN_FailedBroking() : protocols::topology_broker::EXCN_FailedBroking
• EXCN_FileFormat() : protocols::noesy_assign::EXCN_FileFormat
• EXCN_FilterFailed() : protocols::topology_broker::EXCN_FilterFailed
• EXCN_Input() : protocols::topology_broker::EXCN_Input
• EXCN_Invalid_Hashmap() : protocols::loophash::EXCN_Invalid_Hashmap
• EXCN_Loop_not_closed() : protocols::loops::EXCN_Loop_not_closed
• EXCN_No_Extra_Data_To_Write() : protocols::loophash::EXCN_No_Extra_Data_To_Write
• EXCN_NoesyAssign() : protocols::noesy_assign::EXCN_NoesyAssign
• EXCN_TopologyBroker() : protocols::topology_broker::EXCN_TopologyBroker
• EXCN_Unknown() : protocols::topology_broker::EXCN_Unknown
• EXCN_UnknownAtomname() : protocols::noesy_assign::EXCN_UnknownAtomname
• EXCN_UnknownResonance() : protocols::noesy_assign::EXCN_UnknownResonance
• EXCN_Wrong_DB_Format() : protocols::loophash::EXCN_Wrong_DB_Format
• execute_one_search() : protocols::hotspot_hashing::movers::PlaceProbeMover
• ExecutionMode : protocols::hotspot_hashing::movers::PlaceProbeMover
• Exemplar() : protocols::cluster::Exemplar
• exemplarRestriction_ : protocols::pockets::PocketGrid
• exgeom_ids_ : protocols::match::downstream::ClassicMatchAlgorithm
• existing_data_ : protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell
• existing_residue_ : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• exit_gracefully() : protocols::optimize_weights::IterativeOptEDriver
• exit_on_fail_ : protocols::stepwise::legacy::screener::RNA_AtrRepScreener
• exp_hash() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo
• exp_hash_ : protocols::noesy_assign::CrossPeakInfo
• expand() : protocols::hotspot_hashing::SearchPatternExpansion
• expand_domains_to_full_length() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• expand_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• expand_loop_takeoff_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• expand_motifs() : protocols::motifs::MotifDnaPacker
• expand_motifs_ : protocols::motifs::MotifDnaPacker
• expand_non_dunbrack_chi() : protocols::match::upstream::FullChiSampleSet
• expand_samples_by_ex_behavior() : protocols::match::upstream::FullChiSampleSet
• expand_samples_by_steps_wi_sdrange() : protocols::match::upstream::FullChiSampleSet
• expand_samples_for_nrchi_wi_nrchi_bin() : protocols::match::upstream::FullChiSampleSet
• expdbno_ : protocols::pockets::PocketGrid
• experimental : protocols::ddG::ddGData
• experimental_ddG_ : protocols::optimize_weights::DDGMutationOptEData
• experimental_ddG_bind_ : protocols::optimize_weights::DDGBindOptEData
• ExpExpression() : protocols::pack_daemon::ExpExpression
• expire_after_rounds_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• ExpiryFilter() : protocols::simple_filters::ExpiryFilter
• explicit_constructor_ : protocols::analysis::InterfaceAnalyzerMover
• explicit_ramp_constraints() : protocols::relax::RelaxProtocolBase
• explicit_ramp_constraints_ : protocols::relax::RelaxProtocolBase
• explosion_ : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::TryRotamers
• export_only_low() : protocols::cluster::ClusterBase
• export_only_low_ : protocols::cluster::ClusterBase
• expose_counts() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• expose_data() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• ExposedHydrophobicsFilter() : protocols::denovo_design::filters::ExposedHydrophobicsFilter
• Expression : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• expression_ : protocols::pack_daemon::IterativeVectorExpression
• expression_evaluation_order_ : protocols::pack_daemon::EntityFunc
• expression_evaluation_order_by_name_ : protocols::pack_daemon::DynamicAggregateFunction
• ExpressionCOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::PowExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VectorExpressionCreator , protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction
• ExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• ExpressionValues : protocols::pack_daemon::DynamicAggregateFunction
• extend : protocols::flexpep_docking::FlexPepDockingFlags
• extend_barcode_regions_if_chain_break() : protocols::LoopRebuild
• extend_CDR() : protocols::antibody::design::AntibodyDesignModeler
• extend_cterm : protocols::seeded_abinitio::GrowPeptides
• extend_h3_ : protocols::antibody::ModelCDRH3
• extend_h3_before_modeling_ : protocols::antibody::AntibodyModelerProtocol
• extend_inside_ : protocols::seeded_abinitio::SegmentHybridizer
• extend_loops : protocols::LoopRebuild
• extend_nterm : protocols::seeded_abinitio::GrowPeptides
• extend_outside_ : protocols::seeded_abinitio::SegmentHybridizer
• extend_peptide() : protocols::flexpep_docking::FlexPepDockingProtocol
• extend_unaligned() : protocols::star::Extender
• extended() : protocols::loops::LoopFromFileData , protocols::loops::SerializedLoop
• extended_ : protocols::antibody_legacy::Antibody , protocols::loops::Loop , protocols::loops::LoopFromFileData
• extended_loop() : protocols::LoopRebuild
• extended_loops_ : protocols::abinitio::DoubleLayerKinematicAbinitio
• extended_mm_ : protocols::seeded_abinitio::SegmentHybridizer
• extended_name() : protocols::jd2::PDBJobOutputter
• ExtendedPoseMover() : protocols::simple_moves::ExtendedPoseMover
• Extender() : protocols::star::Extender
• extending_ : protocols::simple_moves::SetTorsion
• extension_ : protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter
• extension_window_ : protocols::ligand_docking::InterfaceBuilder
• external_geom_id() : protocols::match::Hit , protocols::match::upstream_hit
• external_sampler() : protocols::match::downstream::ClassicMatchAlgorithm
• external_samplers_ : protocols::match::downstream::ClassicMatchAlgorithm
• external_score() : protocols::abinitio::Template
• ExternalEvaluator() : protocols::simple_filters::ExternalEvaluator
• ExternalGeomSampler() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• extra() : protocols::jd2::parser::BluePrint
• extra_ : protocols::jd2::parser::BluePrint , protocols::loophash::BackboneDB , protocols::loophash::LoopHashLibrary
• extra_beta_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• extra_broker_files() : protocols::jd2::archive::Batch
• extra_chi() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• extra_chi_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• extra_coord_list() : protocols::pockets::EggshellGrid
• extra_coord_list_ : protocols::pockets::EggshellGrid
• extra_data_ : protocols::jobdist::BasicJob , protocols::loophash::BackboneDB
• extra_data_1() : protocols::wum::WorkUnitBase
• extra_data_1_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_2() : protocols::wum::WorkUnitBase
• extra_data_2_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_3() : protocols::wum::WorkUnitBase
• extra_data_3_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_4_ : protocols::wum::WorkUnitBase::WU_Header
• extra_epsilon_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• extra_key : protocols::loophash::BBData
• extra_loose_rep_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• extra_min_ : protocols::seeded_abinitio::SegmentHybridizer
• extra_minimize_chi_res_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer
• extra_minimize_res_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• extra_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• extra_residues_ : protocols::comparative_modeling::ThreadingJobInputter
• extra_residues_to_steal() : protocols::comparative_modeling::ThreadingJob
• extra_residues_to_steal_ : protocols::comparative_modeling::ThreadingJob
• extra_size() : protocols::loophash::BackboneDB
• extra_tag_ : protocols::stepwise::screener::TagDefinition
• extract_cartesian_coordinates() : protocols::kinematic_closure::ClosureProblem
• extract_collective_var() : protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::WTEBiasEnergy
• extract_data_from_Job() : protocols::jd2::PDBJobOutputter
• extract_data_from_pose() : protocols::loophash::LoopHashLibrary
• extract_extra_scores() : protocols::jd2::PDBJobOutputter
• extract_Hbond_atoms_from_protein_rna_complex() : protocols::pockets::GenPharmacophore
• extract_internal_coordinates() : protocols::kinematic_closure::ClosureProblem
• extract_lig_designability_score() : protocols::enzdes::EnzdesFlexibleRegion
• extract_native_only_ : protocols::features::strand_assembly::StrandBundleFeatures
• extract_rna_rings_from_protein_rna_complex() : protocols::pockets::GenPharmacophore
• extract_rt() : protocols::forge::build::ConnectRight
• extract_sandwich_ : protocols::features::strand_assembly::SandwichFeatures
• extract_scores() : protocols::jd2::PDBJobOutputter
• ExtractAsymmetricPoseMover() : protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover
• ExtractAsymmetricUnitMover() : protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover
• ExtractSubposeMover() : protocols::matdes::ExtractSubposeMover
• extrapolate_mode() : protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::TorsionNormalModeMover
• ExtraResidues : protocols::comparative_modeling::ThreadingJobInputter
• ExtraRotSample : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::SampleStrategyData
• extras_ : protocols::matdes::ExtractSubposeMover
• ExtraScoreEvaluatorCreator() : protocols::simple_filters::ExtraScoreEvaluatorCreator
• ExtraThreadingMover() : protocols::comparative_modeling::ExtraThreadingMover
• extreme_value_removal() : protocols::simple_filters::DdgFilter
• extreme_value_removal_ : protocols::simple_filters::DdgFilter
• extshell_list_ : protocols::pockets::NonPlaidFingerprint