- 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
• 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
• edit_mode : protocols::toolbox::KClusterElement
• ee : protocols::sic_dock::XfoxmScore
• egg_and_ext_list_ : protocols::pockets::NonPlaidFingerprint
• eggshell_CoM_ : protocols::pockets::EggshellGrid
• eggshell_coord_list_ : protocols::pockets::EggshellGrid
• eggshell_list_ : protocols::pockets::NonPlaidFingerprint
• eigval_ : protocols::normalmode::NormalMode
• eigvec_ : protocols::evaluation::PCA
• eigvec_cart_ : protocols::normalmode::NormalMode
• eigvec_tor_ : protocols::normalmode::NormalMode
• el : protocols::sic_dock::XfoxmScore
• ElectricField : protocols::sparta::PDB
• 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
• ellipsoid_is_first_partner_ : protocols::docking::EllipsoidalRandomizationMover
• elsefilter_ : protocols::filters::IfThenFilter
• elsevalue_ : protocols::filters::IfThenFilter
• elseweight_ : protocols::filters::IfThenFilter
• Emin_obj_ : protocols::md::MDBase
• EMPTY : protocols::sparta::GDB , protocols::sparta::PDB
• empty_ : protocols::fldsgn::topology::StrandPairingSet , protocols::rpc::BasicCmdLineInit , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• empty_pose_ : protocols::match::output::MatchCollisionFilter
• empty_sfxn_ : protocols::match::output::MatchCollisionFilter
• empty_voxel_color_ : protocols::match::Bool3DGridKinemageWriter
• enable_max_residue_count_ : protocols::simple_filters::ResidueCountFilter
• enable_min_residue_count_ : protocols::simple_filters::ResidueCountFilter
• enabled_ : protocols::dna::PDBOutput
• encounter_ : protocols::surface_docking::FullatomRelaxMover
• encounter_cycle_ : protocols::surface_docking::FullatomRelaxMover
• end : protocols::forge::remodel::RemodelWorkingSet
• end1_ : 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::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::BBG8T3AMover
• end_atomid_ : protocols::backrub::BackrubSegment
• end_bias_ : protocols::simple_moves::ClassicFragmentMover
• end_label_ : protocols::topology_broker::BasicJumpClaimer
• end_native_ : protocols::protein_interface_design::filters::RmsdFilter
• end_pose_ : protocols::protein_interface_design::filters::RmsdFilter
• end_position_ : protocols::topology_broker::BasicJumpClaimer
• end_rep_weight : protocols::relax::ClassicRelax
• end_res_ : protocols::docking::DockingEnsemble , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::simple_moves::ReturnSidechainMover , protocols::stepwise::sampling::protein::StepWiseProteinLoopBridger , protocols::toolbox::task_operations::DatabaseThread
• end_weights_ : protocols::moves::RampingMover
• endtime_ : protocols::rpc::JSON_RPC
• energy : protocols::simple_filters::nmer_svm_res_data
• energy_ : protocols::MakeRotLib::RotData
• energy_cutoff_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• 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_method_ : protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter
• energy_reduction_factor_ : protocols::simple_filters::RotamerBoltzmannWeight
• 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
• energycut : protocols::relax::ClassicRelax
• energycut_ : protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• enforce_bb_contiguity_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• 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
• ensure_variant_matching_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• entity_aas_ : protocols::pack_daemon::EntityFunc
• entity_cache_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• 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_randomizer_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• entity_resfile_ : protocols::pack_daemon::DaemonSet
• entity_task_ : protocols::pack_daemon::DaemonSet
• entity_template_ : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase
• Entries : protocols::sparta::GDB
• entries_ : protocols::abinitio::PairingStatistics , protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• enum_manager_ : protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyNumberingParser
• enum_to_string_ : protocols::antibody::clusters::CDRClusterEnumManager
• enumerate_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo
• enumerate_ligand_rotamers_ : protocols::match::MatcherTask
• env_ : protocols::environment::EnvBeginMover , protocols::environment::EnvEndMover , protocols::environment::ProtectedConformation
• environment_exists_ : protocols::environment::ProtectedConformation
• enz_input_data_ : protocols::match::MatcherTask
• enz_io_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• enz_io_param_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• 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
• 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
• enzdes_protocol_ : protocols::enzdes::EnzdesFlexibleRegion
• enzloops_ : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• ep_cutoff_ : protocols::simple_filters::NMerSVMEnergyFilter
• epsilon_ : protocols::dna::DNABase , protocols::MakeRotLib::RotData , protocols::qsar::scoring_grid::ChargeGrid , protocols::toolbox::InteratomicVarianceMatrix
• epsilon_0_ : protocols::qsar::scoring_grid::ChargeGrid
• erraser_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions
• error_ : protocols::noesy_assign::Resonance
• esp_grid_point_list_ : protocols::pockets::DelphiElectrostatics
• etable_energy_ : protocols::match::output::MatchCollisionFilter
• etable_evaluator_ : protocols::ligand_docking::rdf::RDFEtableFunction
• euclidean_bin_widths_ : protocols::match::Matcher , protocols::match::MatcherTask
• euler_alpha : protocols::stepwise::sampling::rna::rigid_body::BaseBin
• euler_alpha_values_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange
• euler_angle_bin_max_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_angle_bin_min_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_angle_bin_size_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_bin_halfwidths_ : protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• 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::sampling::rna::rigid_body::BaseBin
• euler_gamma_values_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange
• euler_z : protocols::stepwise::sampling::rna::rigid_body::BaseBin
• euler_z_bin_max_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_z_bin_min_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_z_bin_size_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler
• euler_z_values_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange
• evals_ : protocols::simple_filters::EvaluatedTrialMover
• evaluator_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Protocol , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::match::output::MatchProcessor , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_filters::MinValueEvaluator< T >
• evaluator_map_ : protocols::enzdes::EnzdesScorefileFilter
• evaluator_name_ : protocols::match::MatcherTask
• evaluators_ : protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• ex1_ : protocols::motif_hash::Xfrag
• ex2_ : protocols::motif_hash::Xfrag
• ex3_ : protocols::motif_hash::Xfrag
• ex4_ : protocols::motif_hash::Xfrag
• exact_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• exchange_accepts_ : protocols::canonical_sampling::MpiParallelTempering
• exchange_attempts_ : protocols::canonical_sampling::MpiParallelTempering
• exchange_grid_ : protocols::canonical_sampling::MpiHamiltonianExchange
• exchange_grid_dimension_ : protocols::canonical_sampling::MpiHamiltonianExchange
• exchange_schedule : protocols::moves::ReplicaExchangeMC
• exchange_schedules_ : protocols::canonical_sampling::MpiHamiltonianExchange , protocols::canonical_sampling::MpiParallelTempering
• exclude_cys_peptides : protocols::frags::RMSVallData
• exclude_desinated_pdbs_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_gly : protocols::frags::RMSVallData
• exclude_list_ : protocols::simple_filters::TruncatedScoreEvaluator
• exclude_pro : protocols::frags::RMSVallData
• exclude_protein_protein_fa_elec_ : protocols::enzdes::EnzdesBaseProtocol
• exclude_sandwich_that_has_near_backbone_atoms_between_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• exclude_sandwich_that_is_linked_w_same_direction_strand_ : protocols::features::strand_assembly::SandwichFeatures
• EXCLUDED : protocols::sparta::Sparta::SpartaLib
• excluded_aatypes_for_selection_ : protocols::toolbox::SelectResiduesByLayer
• excluded_positions : protocols::vip::VIP_Mover
• excluded_residues_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• 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_on_fail_ : protocols::stepwise::screener::AtrRepScreener
• exp_hash_ : protocols::noesy_assign::CrossPeakInfo
• expand_loop_takeoff_ : protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler , protocols::stepwise::sampling::protein::StepWiseProteinModelerOptions
• expand_motifs_ : protocols::motifs::MotifDnaPacker
• expdbno_ : protocols::pockets::PocketGrid
• experimental : protocols::ddG::ddGData
• experimental_ddG_ : protocols::optimize_weights::DDGMutationOptEData
• experimental_ddG_bind_ : protocols::optimize_weights::DDGBindOptEData
• expire_after_rounds_ : protocols::loophash::MPI_LoopHashRefine_Master
• explicit_constructor_ : protocols::analysis::InterfaceAnalyzerMover
• 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
• expression_ : protocols::pack_daemon::IterativeVectorExpression
• expression_evaluation_order_ : protocols::pack_daemon::EntityFunc
• expression_evaluation_order_by_name_ : protocols::pack_daemon::DynamicAggregateFunction
• extend : protocols::flexpep_docking::FlexPepDockingFlags
• 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_native_cdrs_ : protocols::antibody::design::AntibodyGraftDesigner
• extend_nterm : protocols::seeded_abinitio::GrowPeptides
• extend_outside_ : protocols::seeded_abinitio::SegmentHybridizer
• extended : protocols::loops::SerializedLoop
• extended_ : protocols::antibody_legacy::Antibody , protocols::loops::Loop , protocols::loops::LoopFromFileData
• extended_loops_ : protocols::abinitio::DoubleLayerKinematicAbinitio
• extended_mm_ : protocols::seeded_abinitio::SegmentHybridizer
• extension_ : protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter
• extension_window_ : protocols::ligand_docking::InterfaceBuilder
• external_samplers_ : protocols::match::downstream::ClassicMatchAlgorithm
• extra_ : protocols::jd2::parser::BluePrint , protocols::loophash::BackboneDB , protocols::loophash::LoopHashLibrary
• extra_beta_ : protocols::rotamer_sampler::rna::RNA_SuiteRotamer
• extra_chi_ : protocols::rotamer_sampler::rna::RNA_ChiRotamer , protocols::rotamer_sampler::rna::RNA_KicSampler , protocols::rotamer_sampler::rna::RNA_NucleosideRotamer , protocols::rotamer_sampler::rna::RNA_SuiteRotamer , protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
• extra_coord_list_ : protocols::pockets::EggshellGrid
• extra_data_ : protocols::jobdist::BasicJob , protocols::loophash::BackboneDB
• extra_data_1_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_2_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_3_ : protocols::wum::WorkUnitBase::WU_Header
• extra_data_4_ : protocols::wum::WorkUnitBase::WU_Header
• extra_epsilon_ : protocols::rotamer_sampler::rna::RNA_KicSampler , protocols::rotamer_sampler::rna::RNA_SuiteRotamer
• extra_key : protocols::loophash::BBData
• extra_loose_rep_cutoff_ : protocols::stepwise::sampling::rna::checker::AtrRepChecker
• extra_min_ : protocols::seeded_abinitio::SegmentHybridizer
• extra_minimize_res_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer , protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions , protocols::stepwise::sampling::protein::StepWisePoseSetup , protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer
• extra_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• extra_residues_ : protocols::comparative_modeling::ThreadingJobInputter
• extra_residues_to_steal_ : protocols::comparative_modeling::ThreadingJob
• extra_tag_ : protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler , protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler , protocols::stepwise::screener::TagDefinition
• extract_native_only_ : protocols::features::strand_assembly::StrandBundleFeatures
• extract_sandwich_ : protocols::features::strand_assembly::SandwichFeatures
• extshell_list_ : protocols::pockets::NonPlaidFingerprint