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_ : core::scoring::methods::carbohydrates::SugarBackboneEnergy
• e_ : protocols::normalmode::NormalMode
• e_1 : core::chemical::ElectronConfiguration
• e_2 : core::chemical::ElectronConfiguration
• e_3 : core::chemical::ElectronConfiguration
• e_4 : core::chemical::ElectronConfiguration
• e_5 : core::chemical::ElectronConfiguration
• e_6 : core::chemical::ElectronConfiguration
• e_7 : core::chemical::ElectronConfiguration
• e_D : core::chemical::ElectronConfiguration
• E_elec() : core::scoring::FACTSResidueInfo
• E_elec_ : core::scoring::FACTSResidueInfo
• e_F : core::chemical::ElectronConfiguration
• E_mult_ : protocols::frag_picker::scores::TalosSSSimilarity
• e_P : core::chemical::ElectronConfiguration
• e_S : core::chemical::ElectronConfiguration
• E_solv() : core::scoring::FACTSResidueInfo
• E_solv_ : core::scoring::FACTSResidueInfo
• E_solv_pair() : core::scoring::FACTSResidueInfo
• E_solv_pair_ : core::scoring::FACTSResidueInfo
• E_solv_self() : core::scoring::FACTSResidueInfo
• E_solv_self_ : core::scoring::FACTSResidueInfo
• early_exit_check() : protocols::stepwise::StepWiseSampleAndScreen
• eat_signal() : protocols::jd2::MPIFileBufJobDistributor
• eat_until_delimiter() : core::chemical::sdf::SDFParser
• EC : core::io::HeaderInformation
• echo_metrics_to_jd2() : protocols::antibody::AntibodyModelerProtocol
• eckart_correction() : protocols::normalmode::NormalMode
• eckart_correction_ : protocols::normalmode::NormalMode
• Edge() : core::graph::Edge
• edge() : core::graph::EdgeListElement
• Edge : core::graph::Graph , core::kinematics::Edge , core::scoring::constraints::ConstraintEdge
• edge() : core::scoring::rna::data::RNA_Datum
• edge1() : core::pose::rna::BasePair , protocols::farna::libraries::BasePairType
• edge1_ : core::pose::rna::BasePair
• edge2() : core::pose::rna::BasePair , protocols::farna::libraries::BasePairType
• edge2_ : core::pose::rna::BasePair
• edge_ : core::graph::EdgeListElement , core::scoring::rna::data::RNA_Datum , 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
• edge_count : core::kinematics::FoldTree
• edge_exists() : core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E >
• edge_file_ : protocols::sewing::AssemblyMover
• edge_index_ : core::pack::interaction_graph::DoubleLazyEdge
• edge_iter_ : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator
• edge_label() : core::kinematics::FoldTree
• edge_list_ : core::graph::Graph , core::kinematics::FoldTree , core::pack::interaction_graph::BackgroundNode< V, E, G >
• edge_list_begin() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::NodeBase
• edge_list_element_pool() : core::graph::Graph
• edge_list_element_pool_ : core::graph::EdgeList , core::graph::Graph
• edge_list_end() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::NodeBase
• edge_list_iterator_at_end() : core::pack::interaction_graph::InteractionGraphBase
• edge_matrix_ptrs_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• edge_path_ : protocols::sewing::Assembly
• edge_pool_ : core::graph::Graph
• edge_reweighters_ : core::pack::task::IGEdgeReweightContainer
• edge_vector_ : core::pack::interaction_graph::BackgroundNode< V, E, G >
• edge_vector_up_to_date_ : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• edge_weight() : core::pack::interaction_graph::EdgeBase
• edge_weight_ : core::pack::interaction_graph::EdgeBase
• EdgeBase() : core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• EdgeClass : core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E >
• EdgeList : core::environment::FoldTreeSketch::Node , core::graph::EdgeList , core::graph::EdgeListConstIterator , core::graph::EdgeListElement , core::graph::EdgeListIterator , core::kinematics::FoldTree , core::kinematics::ShortestPathInFoldTree
• edgeList() : core::sequence::SequenceCoupling
• edgeList_ : core::sequence::SequenceCoupling
• EdgeListConstIter : core::graph::Graph , core::graph::Node , core::scoring::constraints::CstResNeighbConstIterator
• EdgeListConstIterator() : core::graph::EdgeListConstIterator , core::graph::EdgeListIterator
• EdgeListElement() : core::graph::EdgeListElement
• EdgeListIter : core::graph::Edge , core::graph::Graph , core::graph::Node , core::scoring::constraints::CstResNeighbIterator
• EdgeListIterator() : core::graph::EdgeListIterator
• edgePotBetween() : core::sequence::SequenceCoupling
• edgePots() : core::sequence::SequenceCoupling
• edgePots_ : core::sequence::SequenceCoupling
• edges() : protocols::sewing::Assembly
• edges_match() : core::chemical::AutomorphismIterator
• EdgeStandScore() : protocols::sic_dock::EdgeStandScore
• edit_mode : protocols::toolbox::KClusterElement
• ee : protocols::sic_dock::XfoxmScore
• eeval_ : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• effect_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• effective_sequence_separation() : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint
• effectiveB : core::scoring::electron_density::ElectronDensity
• Efield_fixed() : core::scoring::MultipoleElecResidueInfo
• Efield_fixed_ : core::scoring::MultipoleElecResidueInfo
• Efield_induced() : core::scoring::MultipoleElecResidueInfo
• Efield_induced_ : core::scoring::MultipoleElecResidueInfo
• Efield_rf_fixed() : core::scoring::MultipoleElecResidueInfo
• Efield_rf_fixed_ : core::scoring::MultipoleElecResidueInfo
• Efield_rf_induced() : core::scoring::MultipoleElecResidueInfo
• Efield_rf_induced_ : core::scoring::MultipoleElecResidueInfo
• egen_ : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• 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
• Ei() : core::scoring::FACTSResidueInfo
• Ei_ : core::scoring::FACTSResidueInfo
• EIG_ : core::scoring::ResidualDipolarCoupling
• eigsrt() : protocols::normalmode::NormalMode
• eigval_ : protocols::normalmode::NormalMode
• eigvec_ : protocols::evaluation::PCA
• eigvec_cart_ : protocols::normalmode::NormalMode
• eigvec_tor_ : protocols::normalmode::NormalMode
• eit_ : core::fragment::ConstantLengthFragSetIterator_
• EItem() : core::optimization::EItem
• 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
• elec_die() : core::scoring::methods::EnergyMethodOptions
• elec_die_ : core::scoring::methods::EnergyMethodOptions
• elec_group_file() : core::scoring::methods::EnergyMethodOptions
• elec_group_file_ : core::scoring::methods::EnergyMethodOptions
• elec_max_dis() : core::scoring::methods::EnergyMethodOptions
• elec_max_dis_ : core::scoring::methods::EnergyMethodOptions
• elec_min_dis : core::init::pre_talaris_2013_behavior_settings , core::scoring::methods::EnergyMethodOptions
• elec_min_dis_ : core::scoring::methods::EnergyMethodOptions
• elec_no_dis_dep_die() : core::scoring::methods::EnergyMethodOptions
• elec_no_dis_dep_die_ : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_D0_ : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_D_ : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_die() : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_die_ : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_die_params() : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_S_ : core::scoring::methods::EnergyMethodOptions
• elec_weight() : core::scoring::elec::FA_ElecEnergy
• ElecAtom() : core::scoring::elec::ElecAtom
• ElecDensAllAtomCenEnergy() : core::scoring::electron_density::ElecDensAllAtomCenEnergy
• ElecDensAtomwiseEnergy() : core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• ElecDensCenEnergy() : core::scoring::electron_density::ElecDensCenEnergy
• ElecDensEnergy() : core::scoring::electron_density::ElecDensEnergy
• elecF2() : core::scoring::FACTSResidueInfo
• elecF2_ : core::scoring::FACTSResidueInfo
• ElectricField : protocols::sparta::PDB
• electron_configuration_ : core::chemical::Element
• ELECTRON_CRYSTALLOGRAPHY : core::io::HeaderInformation
• ELECTRON_DEFRACTION : core::io::HeaderInformation
• ELECTRON_MICROSCOPY : core::io::HeaderInformation
• ElectronConfiguration() : core::chemical::ElectronConfiguration
• ElectronDensity() : core::scoring::electron_density::ElectronDensity
• ElectronDensityAtomwise() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• ElectronDensityLoader() : core::scoring::electron_density::ElectronDensityLoader
• ElectronDensityLoaderCreator() : core::scoring::electron_density::ElectronDensityLoaderCreator
• ElectronDensityOptions() : core::scoring::electron_density::ElectronDensityOptions
• ElectronDensityOptionsCreator() : core::scoring::electron_density::ElectronDensityOptionsCreator
• electrons_ : core::chemical::ElectronConfiguration
• ElectrostaticpotentialGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• elem_length() : protocols::denovo_design::components::Segment
• element() : core::chemical::Atom , core::chemical::AtomType , core::chemical::Element
• Element() : core::chemical::Element
• element() : core::chemical::ElementSet , core::chemical::sdf::MolFileIOAtom , core::io::AtomInformation
• element_ : core::chemical::Atom , core::chemical::AtomType , core::chemical::Element , core::chemical::sdf::MolFileIOAtom , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator
• element_from_string() : protocols::genetic_algorithm::EntityElementFactory
• element_index() : core::chemical::ElementSet
• element_index_ : core::chemical::ElementSet
• element_set() : core::chemical::ChemicalManager , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::ResidueType , core::chemical::ResidueTypeSet
• element_set_ : core::chemical::gasteiger::GasteigerAtomTypeSet
• element_set_ptr() : core::chemical::ResidueType
• element_set_tag() : core::chemical::ResidueLoaderOptions
• element_set_tag_ : core::chemical::ResidueLoaderOptions
• element_sets_ : core::chemical::ChemicalManager
• element_type : boost::unordered_object_pool< T, UserAllocator > , core::chemical::Atom
• element_type_ : core::chemical::gasteiger::GasteigerAtomTypeData
• elements_ : core::chemical::ElementSet , core::chemical::ResidueType , core::chemical::ResidueTypeSet
• ElementSet() : core::chemical::ElementSet
• ElementSets : core::chemical::ChemicalManager
• eliminate_background_ : protocols::simple_moves::StructProfileMover
• 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
• elt_ : core::scoring::electron_density::poseCoord
• emap() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• emap_ : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• EMapVector() : core::scoring::EMapVector
• 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
• emergency_rotamer() : core::pack::rotamers::SingleResidueRotamerLibrary
• Emin_obj_ : protocols::md::MDBase
• empty() : core::conformation::Conformation
• EMPTY : core::conformation::signals::ConnectionEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent
• empty() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet , core::graph::ArrayPool< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::ResidueCoordinateChangeList , core::pose::Pose , core::pose::reference_pose::ReferencePoseSet , core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer , 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::fldsgn::topology::StrandPairingSet , protocols::rpc::BasicCmdLineInit , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• empty_clone() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::MultiConstraint , protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak
• empty_list : core::conformation::symmetry::SymmetryInfo
• empty_list_ : core::chemical::AutomorphismIterator
• empty_pose() : protocols::match::output::MatchCollisionFilter
• empty_pose_ : protocols::match::output::MatchCollisionFilter
• empty_pose_data_list() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• empty_record() : core::pose::PDBInfo
• empty_rsdcst_ : core::scoring::constraints::ConstraintSet
• empty_sfxn() : protocols::match::output::MatchCollisionFilter
• empty_sfxn_ : protocols::match::output::MatchCollisionFilter
• empty_sugar_modeling_list() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• empty_voxel_color_ : protocols::match::Bool3DGridKinemageWriter
• enable() : protocols::ligand_docking::ResidueTorsionRestraints
• enable_adapt_graft_cartesian_ : protocols::antibody::design::AntibodyDesignMover
• 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_custom_variant_types() : core::chemical::ResidueProperties , core::chemical::ResidueType
• enable_design_ : protocols::relax::FastRelax
• enable_end_bias_check() : protocols::simple_moves::ClassicFragmentMover
• enable_full_protocol_atom_pair_cst_ : protocols::antibody::design::AntibodyDesignMover
• 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
• encode_aa_string() : core::scoring::methods::NMerSVMEnergy
• encode_nmer() : core::scoring::methods::NMerSVMEnergy
• encode_wtd_avg_aa_string() : core::scoring::methods::NMerSVMEnergy
• encounter_ : protocols::surface_docking::FullatomRelaxMover
• encounter_cycle_ : protocols::surface_docking::FullatomRelaxMover
• end() : core::conformation::membrane::Span , core::environment::DofPassport , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::Frame , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Library< Books > , core::graph::EdgeList , core::io::pdb::Field , core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets , core::pack::task::TaskFactory , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , core::scoring::packstat::trace , 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::features::Segment , 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::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() : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• end1_ : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• end2() : protocols::fldsgn::topology::StrandPairing
• end2_ : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• end_ : core::conformation::membrane::Span , core::fragment::Frame , core::graph::EdgeList , core::io::serialization::BUFFER , core::scoring::ResRangePredicate , 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::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_checkpointing() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• end_const() : core::io::raw_data::RawFileData
• 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_receptor_partner_pair() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• end_rep_weight : protocols::relax::ClassicRelax
• end_res() : protocols::docking::DockingEnsemble , protocols::indel::IndelOptimizationMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::toolbox::task_operations::DatabaseThread
• end_res_ : protocols::docking::DockingEnsemble , protocols::indel::IndelOptimizationMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::sewing::AddStartnodeFragments , 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_time() : protocols::jd2::Job
• end_time_ : protocols::jd2::Job
• end_timing() : protocols::jd2::Job
• end_weight() : protocols::moves::RampingMover
• end_weights_ : protocols::moves::RampingMover
• ending_node() : protocols::sewing::Assembly
• endtime_ : protocols::rpc::JSON_RPC
• energies() : core::io::silent::SilentStruct , core::pose::Pose
• Energies() : core::scoring::Energies , core::scoring::MinimizationGraph
• energies_ : core::pose::Pose
• energies_are_outdated_ : core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricContainer
• energies_from_pose() : core::io::silent::SilentStruct
• energies_into_pose() : core::io::silent::SilentStruct
• energies_not_yet_computed() : core::scoring::EnergyEdge
• energies_not_yet_computed_ : core::scoring::EnergyEdge
• energies_updated() : core::scoring::Energies
• energies_updated_since_last_prep_for_simA_ : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge
• EnergiesData() : protocols::toolbox::pose_metric_calculators::EnergiesData
• EnergiesEdge : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesGraph : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesIterator : core::scoring::MinimizationGraph
• EnergiesUpperEdgeListConstIter : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesUpperEdgeListIter : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• EnergiesVertex : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• energy() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::scmin::SidechainStateAssignment , core::scoring::constraints::Constraints , core::scoring::hbonds::HBond , protocols::simple_filters::nmer_svm_res_data
• energy_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::scmin::SidechainStateAssignment , core::scoring::hbonds::HBond , protocols::make_rot_lib::RotData
• energy_array_pool_ : core::scoring::EnergyGraph
• energy_computed() : core::scoring::constraints::ConstraintEdge , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• energy_computed_ : core::scoring::constraints::ConstraintEdge
• energy_cut() : core::import_pose::pose_stream::SilentFilePoseInputStream
• energy_cut_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• energy_cutoff() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• energy_cutoff_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• ENERGY_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• energy_drop() : protocols::moves::TrialCounter
• energy_drop_counter_ : protocols::moves::TrialCounter
• energy_edge_pool_ : core::scoring::EnergyGraph
• energy_event_link_ : protocols::moves::PyMolObserver , protocols::viewer::SilentObserver
• energy_gap_counter_ : protocols::simple_moves::GenericMonteCarloMover
• energy_graph() : core::scoring::Energies
• energy_graph_ : core::scoring::Energies
• energy_graph_no_state_check() : core::scoring::Energies
• energy_map() : protocols::toolbox::pose_metric_calculators::EnergiesData
• energy_map_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• energy_method() : core::scoring::ScoringManager
• energy_method_ : protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter
• energy_method_options() : core::scoring::ScoreFunction
• energy_method_options_ : core::scoring::methods::FreeDOF_Energy , core::scoring::ScoreFunction , core::scoring::ScoreFunctionInfo
• energy_minima_conformers_ : core::chemical::rings::RingConformerSet
• energy_minimum_conformer_ : core::chemical::rings::RingConformerSet
• energy_names() : core::io::silent::EnergyNames , core::io::silent::SilentStruct
• energy_names_ : core::io::silent::EnergyNames
• energy_obs_hub_ : core::pose::Pose
• energy_observer : protocols::moves::PyMolObserver
• energy_reduction_factor() : protocols::simple_filters::RotamerBoltzmannWeight
• energy_reduction_factor_ : protocols::simple_filters::RotamerBoltzmannWeight
• energy_sort_cluster() : protocols::mpi_refinement::Clusterer
• energy_state_ : core::scoring::Energies , core::scoring::methods::PBLifetimeCache
• energy_sum_group_membership_ : core::pack::interaction_graph::InteractionGraphBase
• 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_top_ : core::pack::annealer::MultiCoolAnnealer
• 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
• EnergyDependentCalculator() : core::pose::metrics::EnergyDependentCalculator
• EnergyEdge() : core::scoring::EnergyEdge
• EnergyEval() : core::fragment::picking_old::vall::eval::EnergyEval
• EnergyEvent : core::pose::Pose , core::pose::signals::EnergyEvent
• energyEvent() : protocols::moves::PyMolObserver
• EnergyGraph : core::scoring::Energies , core::scoring::EnergyGraph , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• EnergyMap : core::scoring::constraints::SequenceProfileConstraint , core::scoring::Energies , core::scoring::EnergyEdge , 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
• EnergyMethod() : core::scoring::methods::EnergyMethod
• EnergyMethodOP : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator
• EnergyMethodOptions() : core::scoring::methods::EnergyMethodOptions , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator
• EnergyMethodRegistrator() : core::scoring::methods::EnergyMethodRegistrator< T >
• EnergyNames() : core::io::silent::EnergyNames
• EnergyNode() : core::scoring::EnergyNode
• EnergyPerResidueFilter() : protocols::simple_filters::EnergyPerResidueFilter
• EnergyReporter() : protocols::pose_reporters::EnergyReporter
• EnergyState : core::scoring::Energies
• EnergyVector : core::scoring::mm::MMLJEnergyTable
• 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
• ENGINEERED : core::io::HeaderInformation
• engulf_leading_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• engulf_trailing_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• enlarge_h_lj_wdepth : core::scoring::etable::EtableOptions
• enlarge_h_lj_wdepth_ : core::scoring::etable::Etable
• 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
• EnsembleJobInputter() : protocols::jd2::EnsembleJobInputter
• ensure_all_fields_are_valid() : protocols::loops::JSONFormattedLoopsFileReader
• ensure_lrenergy_container_is_up_to_date() : core::scoring::disulfides::FullatomDisulfideEnergy
• ensure_proper_his_tautomers() : protocols::metal_interface::MatchGrafter
• ensure_scofx_cstfication() : protocols::enzdes::EnzRepackMinimize
• ensure_size() : core::optimization::Particle
• 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
• entropy() : core::pack::dunbrack::RotamerLibraryScratchSpace
• entropy_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamerLibraryScratchSpace , core::scoring::methods::ProQ_Energy
• entropy_feature() : core::scoring::methods::ProQ_Energy
• entry_2_resid_ : core::scoring::trie::CPDataCorrespondence
• EntryList : protocols::sparta::GDB
• EntryMap : protocols::sparta::PDB
• Enum : core::pose::datacache::CacheableDataType , core::pose::datacache::CacheableObserverType
• enum2name_() : core::pose::datacache::CacheableDataType
• enum_manager_ : protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyNumberingParser
• enum_to_string_ : protocols::antibody::clusters::CDRClusterEnumManager
• enumerate() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• enumerate_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• enumerate_chi_sets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• enumerate_ligand_rotamers() : protocols::match::MatcherTask
• enumerate_ligand_rotamers_ : protocols::match::MatcherTask
• EnumerateAssemblyMover() : protocols::sewing::EnumerateAssemblyMover
• ENUMERATION : protocols::abinitio::IterativeBase
• enumeration_shell() : core::scoring::FACTSResidueInfo
• enumeration_shell_ : core::scoring::FACTSResidueInfo
• env() : protocols::environment::EnvMover
• env_ : core::scoring::SmoothEnvPairPotential , protocols::environment::EnvClaimBroker , protocols::environment::EnvMover , protocols::environment::ProtectedConformation
• env_dep_low_nneigh_ : core::scoring::elec::FA_ElecEnergy
• env_dep_low_scale_ : core::scoring::elec::FA_ElecEnergy
• env_destruction() : protocols::environment::ProtectedConformation
• env_id() : core::environment::DofPassport
• env_id_ : core::environment::DofPassport
• env_log_ : core::scoring::EnvPairPotential
• env_pair_potential_ : core::scoring::ScoringManager
• env_potential_ : protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy
• env_stats_ : core::scoring::dna::DNA_EnvPairPotential
• 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
• EnvCore() : core::environment::EnvCore
• envdata_ : core::scoring::methods::EnvSmoothEnergy
• EnvEnergy() : core::scoring::methods::EnvEnergy
• 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
• EnvPairPotential() : core::scoring::EnvPairPotential
• envsmooth_zero_negatives() : core::scoring::methods::EnergyMethodOptions
• envsmooth_zero_negatives_ : core::scoring::methods::EnergyMethodOptions
• EnvSmoothEnergy() : core::scoring::methods::EnvSmoothEnergy
• envsplines_ : core::scoring::CenRotEnvPairPotential
• 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_OBSERVER : core::pose::datacache::CacheableObserverType
• 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 : core::scoring::GenBornPotential , core::scoring::MultipoleElecPotential
• ep_cutoff_ : protocols::simple_filters::NMerSVMEnergyFilter
• ep_sasa_for_djs_node_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• epitope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover
• eps : core::optimization::DFPMinConvergedFractional
• eps_ : protocols::make_rot_lib::MakeRotLibJob
• eps_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• epsilon() : core::pose::Pose , core::scoring::etable::Etable , protocols::dna::DNABase
• epsilon_ : core::scoring::etable::Etable , core::scoring::methods::PoissonBoltzmannEnergy , protocols::dna::DNABase , protocols::make_rot_lib::RotData
• epsilon_0_ : protocols::qsar::scoring_grid::ChargeGrid
• epsilon_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• epsilon_atom_names_ : core::scoring::dna::DNATorsionPotential
• epsilon_components() : core::scoring::dna::DNATorsionPotential
• epsilon_components_ : core::scoring::dna::DNATorsionPotential
• epsilon_north() : core::chemical::rna::RNA_FittedTorsionInfo
• epsilon_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• epsilon_south() : core::chemical::rna::RNA_FittedTorsionInfo
• epsilon_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• epsilonmax : core::pose::rna::RNA_SuiteName
• epsilonmin : core::pose::rna::RNA_SuiteName
• eq_type_ : core::scoring::FACTSPotential
• equal_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• equalBase() : core::grid::CartGrid< T >
• equalDimensions() : core::grid::CartGrid< T >
• EQUALS : protocols::enzdes::ValueEvaluator
• equals() : protocols::membrane::geometry::EmbeddingDef
• equivalent_residue_on_subunit() : core::conformation::symmetry::SymmetryInfo
• erase() : core::graph::EdgeList , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , protocols::cluster::Cluster , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::jd2::JobsContainer , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• erase_comment() : core::io::silent::SilentStruct
• erase_decoy() : protocols::abinitio::IterativeCentroid , protocols::jd2::archive::ArchiveBase
• erase_hit() : protocols::match::Matcher
• erase_random_seed_info() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• erase_rigid_body_confs_for_lig() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• erase_segments() : protocols::sewing::SegmentGraph
• erraser() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• erraser_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• error : core::scoring::sc::ShapeComplementarityCalculatorException , protocols::noesy_assign::Resonance
• error_ : protocols::noesy_assign::Resonance
• error_out_on_complex_cycles_ : core::scoring::loop_graph::LoopGraph
• esEnergy : core::scoring::APBSResult
• esolvE() : core::scoring::FACTSResidueInfo
• esolvE_ : core::scoring::FACTSResidueInfo
• 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_dfunc() : core::scoring::func::Func
• estimate_membrane_center() : protocols::rigid::MovePoseToMembraneCenterMover
• etable() : core::scoring::etable::BaseEtableEnergy< Derived >
• Etable() : core::scoring::etable::Etable
• etable() : core::scoring::ScoringManager
• etable_ : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::lkball::LK_BallEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack , core::scoring::rna::RNA_LJ_BaseEnergy
• etable_bins_per_A2_ : core::scoring::etable::TableLookupEvaluator , core::scoring::lkball::LK_BallEnergy
• etable_disbins() : core::scoring::etable::Etable
• etable_disbins_ : core::scoring::etable::Etable
• etable_energy() : protocols::match::output::MatchCollisionFilter
• etable_energy_ : protocols::match::output::MatchCollisionFilter
• etable_evaluator_ : core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , protocols::ligand_docking::rdf::RDFEtableFunction
• etable_options() : core::scoring::methods::EnergyMethodOptions
• etable_options_ : core::scoring::methods::EnergyMethodOptions
• etable_type : core::scoring::etable::EtableOptions , core::scoring::methods::EnergyMethodOptions
• EtableAtom() : core::scoring::etable::etrie::EtableAtom
• EtableEvaluator() : core::scoring::etable::EtableEvaluator
• EtableFunc() : core::scoring::func::EtableFunc
• EtableOptions() : core::scoring::etable::EtableOptions
• EtableParamsOnePair() : core::scoring::etable::EtableParamsOnePair
• etables_by_options_ : core::scoring::ScoringManager
• etables_by_string_ : core::scoring::ScoringManager
• 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_ : core::scoring::ResidualDipolarCoupling
• ev_objective_function() : protocols::loophash::MPI_LoopHashRefine_Master
• eval() : protocols::evaluation::PCA , protocols::jumping::SameStrand
• eval_ : protocols::stepwise::screener::PartitionContactScreener
• eval_atom_atom_fa_elecE() : core::scoring::etable::coulomb::Coulomb
• eval_atom_derivative() : core::scoring::constraints::ConstraintsEnergy , core::scoring::cryst::XtalMLEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::GenBornPotential , core::scoring::hackaro::HackAroEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::vdwaals::VDW_Energy
• eval_atom_derivative_aro_aro() : core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::hackaro::HackAroEnergy
• eval_atom_derivative_base_base() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_intra_RNA() : core::scoring::methods::LK_PolarNonPolarEnergy
• eval_atom_derivative_RNA() : core::scoring::elec::RNA_FA_ElecEnergy
• eval_atom_derivative_rna_backbone_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_rna_base_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_rna_repulsive() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_energy() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• eval_atom_nonpolar_derivative() : core::scoring::FACTSPotential
• eval_atom_polar_derivative() : core::scoring::FACTSPotential
• eval_base_pair_derivative() : core::scoring::dna::DNA_BasePotential
• eval_base_pair_Z_scores() : core::scoring::dna::DNA_BasePotential
• eval_base_step_derivative() : core::scoring::dna::DNA_BasePotential
• eval_base_step_Z_scores() : core::scoring::dna::DNA_BasePotential
• eval_cd_1b() : core::scoring::ScoreFunction , protocols::flexpack::OtherContextScoreFunction
• eval_cd_2b() : core::scoring::ScoreFunction , protocols::flexpack::OtherContextScoreFunction
• eval_cd_2b_bb_bb() : core::scoring::ScoreFunction
• eval_cd_2b_bb_sc() : core::scoring::ScoreFunction
• eval_cd_2b_residues() : protocols::match::downstream::ScoringSecMatchRPE
• eval_cd_2b_sc_sc() : core::scoring::ScoreFunction
• eval_cd_intrares_energy() : core::scoring::ScoreFunction , protocols::flexpack::OtherContextScoreFunction
• eval_ci_1b() : core::scoring::ScoreFunction
• eval_ci_2b() : core::scoring::ScoreFunction
• eval_ci_2b_bb_bb() : core::scoring::ScoreFunction
• eval_ci_2b_bb_sc() : core::scoring::ScoreFunction
• eval_ci_2b_sc_sc() : core::scoring::ScoreFunction
• eval_ci_intrares_energy() : core::scoring::ScoreFunction
• eval_context_derivatives() : core::scoring::elec::FA_GrpElecEnergy
• eval_csa() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• eval_cubic_polynomial() : core::scoring::etable::Etable
• eval_d_lk_fraction_dr_over_r() : core::scoring::lkball::LK_BallEnergy
• eval_dc() : core::scoring::methods::DipolarCouplingEnergy
• eval_dE_dR_over_r() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
• eval_dE_dR_over_r_() : core::scoring::etable::BaseEtableEnergy< Derived >
• eval_dE_dR_over_r_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• eval_desolvation_derivs_no_count_pair() : core::scoring::lkball::LK_BallEnergy
• eval_dfa_elecE_dr_over_r() : core::scoring::etable::coulomb::Coulomb
• eval_dfire_pair_energy() : core::scoring::methods::dfire::DFIRE_Potential
• eval_dipolar() : core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• eval_dna_bform_bb_torsion_score_residue() : core::scoring::dna::DNABFormPotential
• eval_dna_bform_chi_torsion_score_residue() : core::scoring::dna::DNABFormPotential
• eval_dof_derivative() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::pHEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction , protocols::scoring::methods::SpecialRotamerEnergy
• eval_fa_mbenv() : core::scoring::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy
• eval_filters() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• eval_grp_trunc() : core::scoring::elec::GroupElec
• eval_harmonic_backbone_torsion_score_and_deriv() : core::scoring::dna::DNA_DihedralPotential
• eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv() : core::scoring::dna::DNA_DihedralPotential
• eval_impl() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• eval_improper_torsion_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_improper_torsions() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_derivs_two_from_rsd1() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_derivs_two_from_rsd2() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_energies_two_from_rsd1() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_energies_two_from_rsd2() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_bond_energy() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_bond_length_derivs() : core::scoring::methods::CartesianBondedEnergy
• eval_intrares_atom_derivative() : core::scoring::constraints::Constraints
• eval_intrares_derivatives() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy
• eval_intrares_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy , protocols::scoring::methods::InterchainPairEnergy
• eval_intrares_energy_ext() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy
• eval_intraresidue_dof_derivative() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::TwoBodyEnergy
• eval_likelihood_potential() : core::scoring::rna::RNA_SuitePotential
• eval_lj() : core::scoring::rna::RNA_LJ_BaseEnergy
• eval_lk() : core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_PolarNonPolarEnergy
• eval_lk_ball_fraction_deriv() : core::scoring::lkball::LK_BallEnergy
• eval_lk_efficient() : core::scoring::methods::LK_PolarNonPolarEnergy
• eval_lk_fraction() : core::scoring::lkball::LK_BallEnergy
• eval_long_range_twobody_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_longRange_2b_residue() : protocols::match::downstream::ScoringSecMatchRPE
• eval_lowest_score_pose() : protocols::moves::MonteCarlo
• eval_mg_interaction() : core::scoring::magnesium::MgEnergy
• eval_mg_residue_pair_derivatives() : core::scoring::magnesium::MgEnergy
• eval_multibody_atom_derivative() : core::scoring::constraints::ConstraintSet
• eval_n() : core::scoring::elec::FA_GrpElecEnergy
• eval_non_residue_pair_energy() : core::scoring::constraints::ConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• eval_npd_atom_derivative() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_omega_score_all() : core::scoring::OmegaTether
• eval_omega_score_residue() : core::scoring::OmegaTether
• eval_onebody_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_PB_energy_residue() : core::scoring::PoissonBoltzmannPotential
• eval_rama_score_all() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• eval_rama_score_residue() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• eval_rama_score_residue_nonstandard_connection() : core::scoring::Ramachandran
• eval_res() : core::scoring::methods::GoapEnergy
• eval_res_ : core::scoring::methods::GoapEnergy
• eval_residue_derivatives() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::RingClosureEnergy , core::scoring::methods::SmoothEnvEnergy
• eval_residue_dof_derivative() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::YHHPlanarityEnergy
• eval_residue_pair() : core::scoring::magnesium::MgEnergy
• eval_residue_pair_derivatives() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::MultipoleElecPotential , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_SuiteEnergy , core::scoring::VdWTinkerPotential
• eval_residue_pair_derivatives_one_way() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• eval_residue_pair_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_respair_atom_derivative() : core::scoring::constraints::Constraints
• eval_respair_group_coulomb() : core::scoring::elec::GroupElec
• eval_respair_group_derivatives() : core::scoring::elec::GroupElec
• eval_rna_base_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• eval_rna_base_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• eval_rotameric_energy_bb_dof_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• eval_rotameric_energy_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• eval_rpp_rama_score() : core::scoring::RamaPrePro
• eval_score() : core::scoring::methods::CartesianBondedEnergy , core::scoring::rna::RNA_SuitePotential
• eval_singleres_angle_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_angle_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_energy() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_improper_torsion_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_improper_torsions_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_length_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_length_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_torsion_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_torsion_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_standard_coulomb() : core::scoring::elec::GroupElec
• eval_sugar_torsion_score_and_deriv() : core::scoring::dna::DNA_DihedralPotential
• eval_suiteness_bonus() : core::scoring::rna::RNA_SuitePotential
• eval_tuple() : core::scoring::hbonds::HBond
• eval_tuple_ : core::scoring::hbonds::HBond
• eval_twobody_neighbor_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_type() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBond
• eval_type_ : core::scoring::hbonds::HBEvalTuple
• eval_types_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• eval_ws_atom_derivative() : core::scoring::constraints::Constraints
• evalGradient() : protocols::viewer::triangleIterator
• evals_ : protocols::simple_filters::EvaluatedTrialMover
• evaluate() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential , core::scoring::rna::data::RNA_DMS_Potential , core::scoring::saxs::SinXOverX , 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_cbeta() : core::scoring::MembranePotential
• evaluate_cen_rot_env_and_cbeta_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_env_and_cbeta_score() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_orientation_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_orientation_score() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_score() : core::scoring::CenRotEnvPairPotential
• evaluate_constraint_energy() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• evaluate_constraints() : protocols::metal_interface::AddZincSiteConstraints
• evaluate_contact_score() : protocols::scoring::InterchainPotential
• evaluate_context_change_for_packing() : core::scoring::FACTSPotential
• evaluate_convergence_checks() : protocols::moves::MonteCarlo
• evaluate_core() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• evaluate_derivative() : core::scoring::carbohydrates::CHIEnergyFunction
• evaluate_distance_closure() : protocols::pose_length_moves::PossibleLoop
• evaluate_env() : core::scoring::MembranePotential
• evaluate_env_and_cbeta_deriv() : core::scoring::SmoothEnvPairPotential
• evaluate_env_and_cbeta_scores() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• evaluate_env_score() : protocols::scoring::InterchainPotential
• evaluate_extent() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• evaluate_fitnesses() : protocols::genetic_algorithm::GeneticAlgorithm
• evaluate_function() : core::scoring::carbohydrates::CHIEnergyFunction
• evaluate_local() : protocols::jd2::archive::EvaluatedArchive
• evaluate_native() : protocols::ub_e2c::ubi_e2c_modeler
• evaluate_nonpolar_energy() : core::scoring::FACTSPotential
• evaluate_pair() : core::scoring::MembranePotential
• evaluate_pair_and_cenpack_deriv() : core::scoring::SmoothEnvPairPotential
• evaluate_pair_and_cenpack_score() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• evaluate_pair_and_vdw_score() : protocols::scoring::InterchainPotential
• evaluate_pddf_energy() : protocols::scoring::methods::saxs::PDDFEnergy
• evaluate_polar_energy() : core::scoring::FACTSPotential
• evaluate_polar_otf_energy() : core::scoring::FACTSPotential
• 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_rotamer_background_energies() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_background_energy_maps() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy
• evaluate_rotamer_intrares_energies() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_intrares_energy_maps() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_pair_energies() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::ScoreFunction , core::scoring::vdwaals::VDW_Energy
• evaluate_silent_struct() : protocols::jd2::archive::EvaluatedArchive
• evaluate_stub_bumps_() : protocols::hotspot_hashing::HotspotStubSet
• evaluate_stub_self_energy_() : protocols::hotspot_hashing::HotspotStubSet
• evaluate_term() : core::scoring::carbohydrates::CHIEnergyFunction
• EvaluatedArchive() : protocols::jd2::archive::EvaluatedArchive
• EvaluatedTrialMover() : protocols::simple_filters::EvaluatedTrialMover
• evaluation_score_fxn_ : protocols::residue_optimization::MetapatchEnumeration
• Evaluator : core::scoring::etable::AnalyticEtableEnergy
• evaluator() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• Evaluator : core::scoring::etable::TableLookupEtableEnergy
• evaluator() : protocols::abinitio::Protocol
• evaluator_ : core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , 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
• evdw : core::scoring::packstat::CavityBall
• Event() : core::scoring::packstat::Event
• events() : core::pose::datacache::LengthEventCollector
• events_ : core::scoring::packstat::Slice
• evolve_next_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• Ew : core::scoring::GenBornPotential , core::scoring::MultipoleElecPotential
• ex1() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex1_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex1_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex1aro() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex1aro_exposed() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_exposed_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex1aro_exposed_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_exposed_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex1aro_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex2() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex2_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex2_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex2aro() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex2aro_exposed() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_exposed_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex2aro_exposed_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_exposed_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex2aro_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex3() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex3_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex3_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex3_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex4() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex4_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex4_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex4_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• ex_chi_steps : core::pack::dunbrack::ChiSet
• ex_cutoff_ : core::pack::task::EX_CUTOFF
• 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
• exact_occ_include_Hbond_contribution_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• exact_occ_pairwise_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• exact_occ_pairwise_by_res_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• exact_occ_self_res_occ_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• exact_occ_skip_Hbonders_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• exact_occ_split_between_res_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• ExactOccludedHbondSolEnergy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• examine_edge() : core::chemical::RigidDistanceVisitor
• examine_new_loopconf() : protocols::enzdes::EnzdesFlexibleRegion
• examine_pose() : protocols::enzdes::EnzdesScorefileFilter
• examine_vertex() : core::chemical::RigidDistanceVisitor
• 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
• excise_mini_pose() : protocols::magnesium::MgHydrater , protocols::magnesium::MgWaterHydrogenPacker
• excise_mini_pose_ : protocols::magnesium::MgHydrater , protocols::magnesium::MgWaterHydrogenPacker
• exclude_aatypes_for_selection() : core::select::util::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_DNA_DNA() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• exclude_DNA_DNA_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::VdWTinkerEnergy
• 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_intra_res_protein() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• exclude_intra_res_protein_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• exclude_intra_res_RNA() : core::scoring::hbonds::HBondOptions
• exclude_intra_res_RNA_ : core::scoring::hbonds::HBondOptions
• exclude_list_ : protocols::simple_filters::TruncatedScoreEvaluator
• exclude_monomer_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy
• exclude_monomer_fa_elec() : core::scoring::methods::EnergyMethodOptions
• exclude_monomer_fa_elec_ : core::scoring::methods::EnergyMethodOptions
• 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_polar_all_in_hsasa_ : core::scoring::sasa::SasaCalc
• exclude_pro : protocols::frags::RMSVallData
• exclude_protein_protein_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy
• exclude_protein_protein_fa_elec() : core::scoring::methods::EnergyMethodOptions
• exclude_protein_protein_fa_elec_ : core::scoring::methods::EnergyMethodOptions , protocols::enzdes::EnzdesBaseProtocol
• exclude_radius_ : protocols::toolbox::task_operations::InteractingRotamerExplosion
• exclude_residues() : protocols::hybridization::FragmentBiasAssigner
• exclude_residues_ : protocols::hybridization::CartesianSampler
• 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_self_hbonds() : core::scoring::hbonds::HBondOptions
• exclude_self_hbonds_ : core::scoring::hbonds::HBondOptions
• exclude_species() : protocols::antibody::CDRSetOptions
• exclude_species_ : protocols::antibody::CDRSetOptions
• exclude_species_add() : protocols::antibody::CDRSetOptions
• exclude_species_clear() : protocols::antibody::CDRSetOptions
• exclude_variants() : core::chemical::ResidueTypeSelector
• EXCLUDED : protocols::sparta::Sparta::SpartaLib
• excluded_ : core::scoring::ExcludedResPredicate
• excluded_aatypes_for_selection_ : core::select::util::SelectResiduesByLayer
• excluded_positions : protocols::vip::VIP_Mover
• excluded_positions_ : protocols::helix_capper::HelixNCapperMover
• excluded_properties_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• excluded_residues_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• excluded_types_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• ExcludedResPredicate() : core::scoring::ExcludedResPredicate
• exclusions_ : protocols::mpi_refinement::Scheduler
• EXCLUSIVE : protocols::environment::claims::ClaimStrength
• exclusive() : protocols::topology_broker::claims::DofClaim
• EXCLUSIVE : protocols::topology_broker::claims::DofClaim
• EXCN_Apply() : protocols::denovo_design::components::EXCN_Apply
• EXCN_Archive() : protocols::jd2::archive::EXCN_Archive
• EXCN_AssignmentNotFound() : protocols::noesy_assign::EXCN_AssignmentNotFound
• EXCN_AtomNotFound() : core::id::EXCN_AtomNotFound
• EXCN_bbdb_Merge_Failed() : protocols::loophash::EXCN_bbdb_Merge_Failed
• EXCN_Build() : protocols::denovo_design::components::EXCN_Build
• EXCN_ConnectionFailed() : protocols::denovo_design::connection::EXCN_ConnectionFailed
• EXCN_Converged() : protocols::moves::EXCN_Converged
• EXCN_DB_IO_Failed() : protocols::loophash::EXCN_DB_IO_Failed
• EXCN_Env_Exception() : core::environment::EXCN_Env_Exception
• 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_FTSketchGraph() : core::environment::EXCN_FTSketchGraph
• EXCN_Illegal_Arguments() : core::conformation::membrane::EXCN_Illegal_Arguments
• EXCN_Input() : protocols::topology_broker::EXCN_Input
• EXCN_Invalid_Hashmap() : protocols::loophash::EXCN_Invalid_Hashmap
• EXCN_InvalidFoldTree() : core::kinematics::EXCN_InvalidFoldTree
• EXCN_Loop_not_closed() : protocols::loops::EXCN_Loop_not_closed
• EXCN_Membrane() : core::conformation::membrane::EXCN_Membrane
• EXCN_Membrane_Bounds() : core::conformation::membrane::EXCN_Membrane_Bounds
• EXCN_MembraneFoldTree() : core::conformation::membrane::EXCN_MembraneFoldTree
• EXCN_No_Extra_Data_To_Write() : protocols::loophash::EXCN_No_Extra_Data_To_Write
• EXCN_NoesyAssign() : protocols::noesy_assign::EXCN_NoesyAssign
• EXCN_NonMembrane() : core::conformation::membrane::EXCN_NonMembrane
• EXCN_PoseInconsistent() : protocols::denovo_design::components::EXCN_PoseInconsistent
• EXCN_PreFilterFailed() : protocols::denovo_design::components::EXCN_PreFilterFailed
• EXCN_Process() : protocols::denovo_design::components::EXCN_Process
• EXCN_RemoveCstsFailed() : protocols::moves::EXCN_RemoveCstsFailed
• EXCN_Resource_Definition() : core::conformation::membrane::EXCN_Resource_Definition
• EXCN_Setup() : protocols::denovo_design::components::EXCN_Setup
• 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_UnknownSubtag() : protocols::denovo_design::connection::EXCN_UnknownSubtag
• EXCN_VirtualRsd() : core::conformation::membrane::EXCN_VirtualRsd
• EXCN_Wrong_DB_Format() : protocols::loophash::EXCN_Wrong_DB_Format
• exdna_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• exdna_sample_level_ : core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• exec() : core::scoring::APBSWrapper
• 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
• exhphobe_index_ : core::pack::interaction_graph::exposed_hydrophobic_data
• 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_if_missing_heavy_atoms() : core::io::StructFileRepOptions
• exit_if_missing_heavy_atoms_ : core::io::StructFileRepOptions
• exit_on_fail_ : protocols::stepwise::legacy::screener::RNA_AtrRepScreener
• EXP_chem_shift_data_list_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• exp_hash() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo
• exp_hash_ : protocols::noesy_assign::CrossPeakInfo
• exp_param_ : core::scoring::func::MixtureFunc
• exp_shift : core::scoring::rna::chemical_shift::ChemicalShiftData
• exp_val_ : core::scoring::func::SplineFunc
• expand() : core::grid::CartGrid< T > , protocols::hotspot_hashing::SearchPatternExpansion
• expand_job_list() : protocols::jd3::StandardJobQueen
• 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_node_labels_partial_by_contig() : core::kinematics::TreeVizBuilder
• expand_non_dunbrack_chi() : protocols::match::upstream::FullChiSampleSet
• expand_pattern_to_fit() : protocols::ncbb::SecStructFinder
• expand_proton_chis() : core::pack::rotamers::SingleResidueRotamerLibrary
• 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
• expand_st_chi2sampling : core::init::pre_talaris_2013_behavior_settings
• expandToUnitCell() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• expdbno_ : protocols::pockets::PocketGrid
• expected_by_properties_absolute() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• expected_by_properties_absolute_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• expected_by_properties_fraction() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• expected_by_properties_fraction_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• experimental : protocols::ddG::ddGData
• experimental_ddG_ : protocols::optimize_weights::DDGMutationOptEData
• experimental_ddG_bind_ : protocols::optimize_weights::DDGBindOptEData
• experimental_technique_in_progress() : core::io::HeaderInformation
• experimental_technique_in_progress_ : core::io::HeaderInformation
• experimental_technique_to_string() : core::io::HeaderInformation
• experimental_techniques() : core::io::HeaderInformation
• experimental_techniques_ : core::io::HeaderInformation
• ExperimentalTechnique : core::io::HeaderInformation
• ExperimentalTechnique_max : core::io::HeaderInformation
• ExperimentalTechnique_max_current : core::io::HeaderInformation
• ExperimentalTechniques : core::io::HeaderInformation
• ExpExpression() : protocols::pack_daemon::ExpExpression
• expid() : core::scoring::RDC
• expid_ : core::scoring::RDC
• 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_radii_set_ : core::scoring::sasa::SasaCalc
• 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 >
• exposed_hydrophobic_data() : core::pack::interaction_graph::exposed_hydrophobic_data
• exposed_radius : core::scoring::packstat::CavityBall
• ExposedHydrophobicsFilter() : protocols::denovo_design::filters::ExposedHydrophobicsFilter
• exprdc_ : core::scoring::ResidualDipolarCoupling
• 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() : core::fragment::SecondaryStructure , core::scoring::dssp::StrandPairing , core::scoring::TMscore , protocols::flexpep_docking::FlexPepDockingFlags
• extend_barcode_regions_if_chain_break() : protocols::LoopRebuild
• extend_CDR() : protocols::antibody::design::GeneralAntibodyModeler
• 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_ss_ : protocols::denovo_design::connection::Connection
• extend_to() : core::scoring::dssp::StrandPairing
• extend_unaligned() : protocols::star::Extender
• ExtendChain() : protocols::denovo_design::connection::ExtendChain
• 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
• ExtendedPoseInputStream() : core::import_pose::pose_stream::ExtendedPoseInputStream
• ExtendedPoseMover() : protocols::simple_moves::ExtendedPoseMover
• Extender() : protocols::star::Extender
• extending_ : protocols::simple_moves::SetTorsion
• extendRegion() : protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_length_moves::PossibleLoop
• extension_ : protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter
• extension_window_ : protocols::ligand_docking::InterfaceBuilder
• Extent : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen
• extent_begin : core::fragment::picking_old::vall::scores::VallFragmentScore
• extent_end : core::fragment::picking_old::vall::scores::VallFragmentScore
• extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• ExtentEvalCOP : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• ExtentEvalOP : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• ExtentEvalOPs : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• ExtentGenCOP : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• ExtentGenOP : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• ExtentGenOPs : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• external_coordinate_residues_changed_ : core::kinematics::AtomTree
• 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
• externally_required_context_graphs_ : core::scoring::Energies
• 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_cdf_ : core::scoring::Ramachandran
• 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_cut_off_interaction_ : core::scoring::FACTSPotential
• extra_cut_off_self_ : core::scoring::FACTSPotential
• 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::options::RNA_MinimizerOptions
• extra_minimize_chi_res_ : protocols::farna::options::RNA_MinimizerOptions
• extra_minimize_res() : core::pose::full_model_info::FullModelInfo , protocols::farna::options::RNA_MinimizerOptions
• extra_minimize_res_ : protocols::farna::options::RNA_MinimizerOptions , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• extra_parameter() : core::chemical::AtomType
• extra_parameter_index() : core::chemical::AtomTypeSet
• extra_parameter_indices() : core::chemical::AtomTypeSet
• extra_parameter_indices_ : core::chemical::AtomTypeSet
• extra_parameters_ : core::chemical::AtomType
• extra_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• extra_ram_counts_ : core::scoring::Ramachandran
• extra_ram_energ_ : core::scoring::Ramachandran
• extra_ram_probabil_ : core::scoring::Ramachandran
• 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
• extrachi_cutoff() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• extrachi_cutoff_ : core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraRotamerSamplingData , core::pack::task::ResidueLevelTask_
• extrachi_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ExtraChiCutoff() : core::pack::task::operation::ExtraChiCutoff
• ExtraChiCutoffRLT() : core::pack::task::operation::ExtraChiCutoffRLT
• 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_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_pose_balls() : core::pose::xyzStripeHashPose
• extract_rna_rings_from_protein_rna_complex() : protocols::pockets::GenPharmacophore
• extract_rt() : protocols::forge::build::ConnectRight
• extract_sandwich_ : protocols::features::strand_assembly::SandwichFeatures
• extract_writeable_cacheable_data() : core::io::silent::SilentStruct
• ExtractAsymmetricPoseMover() : protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover
• ExtractAsymmetricUnitMover() : protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover
• ExtractSubposeMover() : protocols::matdes::ExtractSubposeMover
• extrapolate_mode() : protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::TorsionNormalModeMover
• extrapolated_slope : core::scoring::etable::ExtraQuadraticRepulsion
• ExtraQuadraticRepulsion() : core::scoring::etable::ExtraQuadraticRepulsion
• ExtraResidues : protocols::comparative_modeling::ThreadingJobInputter
• ExtraRotamers() : core::pack::task::operation::ExtraRotamers
• ExtraRotamerSamplingData() : core::pack::task::operation::ExtraRotamerSamplingData
• ExtraRotamersGeneric() : core::pack::task::operation::ExtraRotamersGeneric
• ExtraRotamersGenericRLT() : core::pack::task::operation::ExtraRotamersGenericRLT
• ExtraRotSample : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::SampleStrategyData
• extras_ : protocols::matdes::ExtractSubposeMover
• extrasamples_ : core::chemical::AddProtonChi
• 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