- l -

• L1ScoringScheme() : core::sequence::L1ScoringScheme
• label() : core::kinematics::Edge , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::topology_broker::ClaimerMessage , core::kinematics::Edge , protocols::noesy_assign::CrossPeak3D , protocols::topology_broker::SequenceClaim , protocols::topology_broker::TopologyClaimer , protocols::noesy_assign::CrossPeak3D
• label_atom() : protocols::noesy_assign::PeakAssignment
• label_atom_name() : protocols::noesy_assign::CrossPeakInfo
• label_atom_type() : protocols::noesy_assign::CrossPeakInfo
• label_resonance_id() : protocols::noesy_assign::PeakAssignment
• label_tolerance() : protocols::noesy_assign::CrossPeakInfo
• LAMBEGO_IO() : protocols::frag_picker::LAMBEGO_IO
• LAMBEGO_Similarity() : protocols::frag_picker::scores::LAMBEGO_Similarity
• LargeFragWeight() : protocols::topology_broker::weights::LargeFragWeight
• largest_possible_sequence_sep() : protocols::constraints_additional::MaxSeqSepConstraintSet
• largestTargetPocketVolume() : protocols::pockets::PocketGrid
• last() : core::graph::EdgeList
• last_accept() : protocols::moves::MonteCarlo
• last_accepted() : protocols::canonical_sampling::MetropolisHastingsMover
• last_accepted_pose() : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• last_accepted_score() : protocols::simple_moves::GenericMonteCarloMover , protocols::moves::MonteCarlo
• last_angle() : protocols::backrub::BackrubMover
• last_assignment() : protocols::pack_daemon::PackDaemon
• last_attempted_mover_idx() : protocols::rosetta_scripts::ParsedProtocol
• last_backbone_atom() : core::chemical::ResidueType , core::conformation::Residue
• last_batch_id() : protocols::jd2::archive::ArchiveManager
• last_considered_backbone_sub_unresolved() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_backbone_sub_valid() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_substitution_kept_backbone_fixed() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_substitution_moved_the_backbone() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_substitution_unresolved() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_controlling_chi() : core::chemical::ResidueType
• last_end_atom_name() : protocols::backrub::BackrubMover
• last_inner_score_temperature_delta() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• last_key() : protocols::noesy_assign::ResonanceList
• last_move() : protocols::canonical_sampling::MetropolisHastingsMover
• last_move_succeeded() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• last_mutation() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_nchi() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_nonempty_bin() : core::scoring::saxs::DistanceHistogram
• last_proposal_density_ratio() : protocols::canonical_sampling::ThermodynamicMover , protocols::moves::Mover , protocols::moves::RandomMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• last_received_from() : protocols::wum::WorkUnitBase
• last_residue() : protocols::topology_broker::SequenceClaim
• last_section() : core::fragment::picking_old::vall::VallLibrary
• last_segment_id() : protocols::backrub::BackrubMover
• last_start_atom_name() : protocols::backrub::BackrubMover
• last_uniform() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_withinrot() : protocols::simple_moves::sidechain_moves::SidechainMover
• launch_atom() : protocols::match::downstream::ClassicMatchAlgorithm
• layer() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• LayerDesignOperation() : protocols::flxbb::LayerDesignOperation
• LayerOperations() : protocols::toolbox::task_operations::LayerOperations
• lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• lazy_sort() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• LazyEdge() : core::pack::interaction_graph::LazyEdge
• LazyInteractionGraph() : core::pack::interaction_graph::LazyInteractionGraph
• LazyNode() : core::pack::interaction_graph::LazyNode
• LazySilentFileJobInputter() : protocols::jd2::LazySilentFileJobInputter
• LazySilentFilePoseInputStream() : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• LazySortedVector1() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• lb() : core::scoring::constraints::BoundFunc
• lbfgs() : core::optimization::Minimizer
• leaves_of_jump() : core::conformation::symmetry::SymmData
• LeeRichards() : core::scoring::packstat::LeeRichards
• left_handed() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• left_named_stub_id() : protocols::forge::build::ConnectRight
• left_position() : protocols::forge::build::ConnectRight
• left_stub_atoms() : protocols::forge::build::ConnectRight
• length() : core::fragment::Frame , core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::fldsgn::topology::SS_Base , protocols::forge::build::Interval , protocols::jd2::SingleFileBuffer , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::rbsegment_relax::RBResidueRange
• length_obs_link() : protocols::forge::build::BuildInstruction
• length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• LengthEvent() : core::conformation::signals::LengthEvent
• LengthEventCollector() : core::pose::datacache::LengthEventCollector
• LengthGen() : core::fragment::picking_old::vall::gen::LengthGen
• less_than() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• let_neighboring_chis_minimize() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• level_find() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• level_radius() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• level_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• LHRepulsiveRamp() : protocols::antibody2::LHRepulsiveRamp
• LHRepulsiveRampLegacy() : protocols::antibody2::LHRepulsiveRampLegacy
• LHSnugFitLegacy() : protocols::antibody2::LHSnugFitLegacy
• lib() : protocols::sparta::Sparta
• lib_full_path() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Librarian() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• library() : protocols::motifs::MotifLibrary
• Library() : core::fragment::picking_old::concepts::Library< Books >
• library_central() : protocols::loophash::MPI_LoopHashRefine
• library_size() : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• lig_rigid_body_confs() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• ligand_calculate() : protocols::scoring::Interface
• Ligand_info() : protocols::ligand_docking::Ligand_info
• ligand_resno() : protocols::enzdes::EnzdesConstraintReporter
• LigandArea() : protocols::ligand_docking::LigandArea
• LigandAreaLoader() : protocols::ligand_docking::LigandAreaLoader
• LigandBaseProtocol() : protocols::ligand_docking::LigandBaseProtocol
• LigandConformer() : protocols::toolbox::match_enzdes_util::LigandConformer
• LigandConformerBuilder() : protocols::match::downstream::LigandConformerBuilder
• LigandDesign() : protocols::ligand_docking::LigandDesign
• LigandDockMain() : protocols::ligand_docking::LigandDockMain
• LigandDockProtocol() : protocols::ligand_docking::LigandDockProtocol
• LigandMotifSearch() : protocols::motifs::LigandMotifSearch
• LigBurialFilter() : protocols::enzdes::LigBurialFilter
• LigDSasaFilter() : protocols::enzdes::LigDSasaFilter
• LigInterfaceEnergyFilter() : protocols::enzdes::LigInterfaceEnergyFilter
• limit() : core::scoring::constraints::TopOutFunc , protocols::simple_moves::symmetry::SetupNCSMover , protocols::wum::SilentStructStore
• limit_aroma_chi2() : protocols::relax::RelaxProtocolBase
• limit_groups() : protocols::cluster::ClusterBase
• limit_groupsize() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• limit_library() : protocols::loophash::MPI_LoopHashRefine
• limit_total_structures() : protocols::cluster::ClusterBase
• LimitAromaChi2_RotamerSetOperation() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• LimitAromaChi2Operation() : protocols::toolbox::task_operations::LimitAromaChi2Operation
• LimitHitsPerRotamerFilter() : protocols::match::output::LimitHitsPerRotamerFilter
• Line() : core::util::Line
• LinearChainbreakEnergy() : core::scoring::methods::LinearChainbreakEnergy
• LinearMemEdge() : core::pack::interaction_graph::LinearMemEdge
• LinearMemNode() : core::pack::interaction_graph::LinearMemNode
• LinearMemoryInteractionGraph() : core::pack::interaction_graph::LinearMemoryInteractionGraph
• LinearPenaltyFunction() : core::scoring::constraints::LinearPenaltyFunction
• LineMinimizationAlgorithm() : core::optimization::LineMinimizationAlgorithm
• linenum() : protocols::loops::ResidueIndexDescriptionFromFile
• link_cache() : protocols::wum2::WorkUnit
• link_torsion_vectors() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• link_vectors() : core::optimization::DOF_Node
• LinkerScore() : protocols::sic_dock::LinkerScore
• linmem_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• linmin() : core::optimization::Minimizer
• LipidBurial() : core::scoring::MembraneTopology
• LipidExposure() : core::scoring::MembraneTopology
• LipoDefined() : core::scoring::MembraneTopology
• list() : core::scoring::Hairpins
• list_pools() : protocols::frag_picker::quota::QuotaCollector
• listen_wu_sendrecv() : protocols::wum2::EndPoint
• lj_cutoff() : protocols::match::output::MatchCollisionFilter
• lj_radius() : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lj_three_bond_radius() : core::chemical::MMAtomType
• lj_three_bond_wdepth() : core::chemical::MMAtomType
• lj_wdepth() : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable
• ljatr() : core::scoring::etable::Etable
• ljrep() : core::scoring::etable::Etable
• LK_BallEnergy() : core::scoring::methods::LK_BallEnergy
• LK_CosThetaEnergy() : core::scoring::methods::LK_CosThetaEnergy
• lk_dgfree() : core::scoring::etable::MembEtable , core::chemical::AtomType , core::scoring::etable::Etable
• lk_dgrefce() : core::scoring::etable::MembEtable
• LK_hack() : core::scoring::methods::LK_hack
• lk_lambda() : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• LK_SigmoidalFunc() : core::scoring::methods::LK_SigmoidalFunc
• lk_volume() : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• LKB_ResidueInfo() : core::scoring::methods::LKB_ResidueInfo
• LKB_ResiduesInfo() : core::scoring::methods::LKB_ResiduesInfo
• LnExpression() : protocols::pack_daemon::LnExpression
• load_APBS_potential() : core::scoring::PoissonBoltzmannPotential
• load_binary() : protocols::cluster::APCluster
• load_chain_endings() : protocols::features::PoseConformationFeatures
• load_conformation() : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• load_data() : protocols::jd2::parser::DataLoader , protocols::jd2::parser::FragSetLoader , protocols::jd2::parser::MonteCarloLoader , protocols::jd2::parser::ScoreFunctionLoader , protocols::jd2::parser::TaskOperationLoader , protocols::ligand_docking::InterfaceBuilderLoader , protocols::ligand_docking::MoveMapBuilderLoader , protocols::ligand_docking::LigandAreaLoader , protocols::loops::loops_definers::LoopsDefinerLoader , protocols::qsar::scoring_grid::ScoringGridLoader
• load_database_table() : protocols::noesy_assign::MethylNameLibrary
• load_db() : protocols::loophash::LoopHashLibrary
• load_dist_table() : protocols::noesy_assign::CovalentCompliance
• load_dotscore_bins() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• load_ensemble() : protocols::docking::DockingEnsemble
• load_ff() : core::scoring::saxs::FormFactorManager
• load_ff_from_db() : core::scoring::saxs::FormFactorManager
• load_fold_tree() : protocols::features::PoseConformationFeatures
• load_from_checkpoint() : protocols::protein_interface_design::movers::Splice
• load_into_pose() : protocols::features::FeaturesReporter , protocols::features::JobDataFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures , protocols::features::StructureFeatures
• load_jumps() : protocols::features::PoseConformationFeatures
• load_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• load_mergeddb() : protocols::loophash::LoopHashLibrary
• load_new_batch() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• load_options_from_option_system() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• load_pdb_id_from_file() : protocols::frag_picker::PdbIdChunkFilter
• load_pdb_segments_from_pose_comments() : protocols::protein_interface_design::movers::Splice
• load_phi_theta_bins() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• load_pool() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• load_pose() : protocols::features::ProteinSilentReport , protocols::optimize_weights::IterativeOptEDriver
• load_pose_allocate_memory() : protocols::hybridization::TMalign
• load_pose_into_job() : protocols::jd2::JobInputter
• load_pssm_data() : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• load_residue_pdb_confidence() : protocols::features::PdbDataFeatures
• load_residue_pdb_identification() : protocols::features::PdbDataFeatures
• load_sample_weight() : protocols::loophash::MPI_LoopHashRefine_Master
• load_score_tables() : core::scoring::dna::DNA_BasePotential
• load_sequence() : protocols::features::PoseConformationFeatures
• load_silent_file() : protocols::toolbox::KClusterData
• load_silent_files() : protocols::toolbox::KClusterData
• load_state() : protocols::loophash::MPI_LoopHashRefine
• load_string_data() : protocols::features::JobDataFeatures
• load_string_real_data() : protocols::features::JobDataFeatures
• load_string_string_data() : protocols::features::JobDataFeatures
• load_structures_from_cmdline_into_library() : protocols::loophash::MPI_LoopHashRefine
• load_tag() : protocols::features::StructureFeatures
• load_templates_from_pdbs() : protocols::antibody2::Ab_TemplateInfo
• load_trial_number_from_checkpoint() : protocols::simple_moves::GenericMonteCarloMover
• load_weights_file() : core::scoring::ScoreFunctionFactory
• loader_type() : core::chemical::ResidueLoaderCreator , core::conformation::symmetry::SymmDataLoaderCreator , core::import_pose::PoseFromPDBLoaderCreator , core::io::silent::SilentFileLoaderCreator , core::scoring::electron_density::ElectronDensityLoaderCreator , protocols::loops::LoopsFileLoaderCreator
• loadGDB() : protocols::sparta::GDB
• loadPDB() : protocols::sparta::PDB
• loadPDB_Entry() : protocols::sparta::PDB
• LoadPDBMover() : protocols::simple_moves::LoadPDBMover
• LoadUnboundRotMover() : protocols::simple_moves::LoadUnboundRotMover
• loadWeightBias3() : protocols::sparta::ANN
• loadWeights() : protocols::sparta::ANN
• local2global() : core::kinematics::Stub
• local_minimize_at_chainbreaks() : protocols::rna::RNA_LoopCloser
• local_rotid_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_rotid_for_rotamer_on_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_rotid_start_for_moltenres_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_variable() : protocols::pack_daemon::IterativeVectorExpression
• LocalCoordinateConstraint() : core::scoring::constraints::LocalCoordinateConstraint
• LocalCoordinateConstraintCreator() : core::scoring::constraints::LocalCoordinateConstraintCreator
• LocalInserter() : protocols::loophash::LocalInserter
• LocalInserter_SimpleMin() : protocols::loophash::LocalInserter_SimpleMin
• locate_anchor_loop() : protocols::anchored_design::AnchorMoversData
• locate_command() : core::pack::task::ResfileContents
• locate_resid() : core::pack::task::ResfileContents
• location_in_parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• locked_res() : protocols::protein_interface_design::movers::Splice
• locked_res_id() : protocols::protein_interface_design::movers::Splice
• log() : protocols::frag_picker::QuotaDebug
• LoggedFragmentMover() : protocols::simple_moves::LoggedFragmentMover
• long_range_container() : core::scoring::Energies
• long_range_energies_begin() : core::scoring::ScoreFunction
• long_range_energies_end() : core::scoring::ScoreFunction
• long_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• long_range_type() : core::scoring::methods::dfire::DFIRE_Energy , core::scoring::electron_density::FastDensEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::sym_e::symEnergy
• long_string_rep() : protocols::contact_map::Contact
• longestSide() : core::grid::CartGrid< T >
• LongRangeTwoBodyEnergy() : core::scoring::methods::LongRangeTwoBodyEnergy
• lookup() : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::fldsgn::NcontactsCalculator , core::scoring::mm::MMLJLibrary , core::pose::metrics::simple_calculators::SasaCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::StructureDependentCalculator , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMLJLibrary , core::scoring::mm::MMTorsionLibrary , protocols::loophash::LoopHashMap , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• lookup_angle() : core::scoring::methods::IdealParametersDatabase
• lookup_angle_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_bondangle_buildideal() : core::scoring::methods::IdealParametersDatabase
• lookup_bondlength_buildideal() : core::scoring::methods::IdealParametersDatabase
• lookup_length() : core::scoring::methods::IdealParametersDatabase
• lookup_length_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_stored_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• lookup_three_bond() : core::scoring::mm::MMLJLibrary
• lookup_torsion() : core::scoring::methods::IdealParametersDatabase
• lookup_torsion_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_withkey() : protocols::loophash::LoopHashMap
• Loop() : protocols::fldsgn::topology::Loop , protocols::loops::Loop
• loop() : core::optimization::GA_Minimizer , protocols::anchored_design::AnchorMoversData , protocols::fldsgn::topology::SS_Info2 , protocols::loops::loop_closure::ccd::LoopClosure
• loop_ang() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• loop_begin() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• loop_centroid_relax() : protocols::antibody2::RefineOneCDRLoopCentroid , protocols::antibody::CDRH3Modeler
• loop_dbase_file_name() : protocols::protein_interface_design::movers::Splice
• loop_dih() : protocols::toolbox::match_enzdes_util::ResInteractions , protocols::forge::remodel::ResidueVicinityInfo
• loop_end() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::protein_interface_design::movers::LoopLengthChange
• loop_fa_relax() : protocols::antibody::CDRH3Modeler
• loop_file_name() : protocols::loops::Loops
• loop_fraction() : core::fragment::SecondaryStructure
• loop_frags() : protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer , protocols::topology_broker::LoopFragmentClaimer
• loop_id() : protocols::fldsgn::topology::SS_Info2
• loop_incident() : core::graph::Node
• loop_index_of_residue() : protocols::loops::Loops
• loop_info() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• loop_length() : protocols::protein_interface_design::movers::PlaceOnLoop
• loop_model() : protocols::LoopRebuild
• loop_mover() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• loop_mover_fold_tree_constant() : protocols::forge::components::VarLengthBuild
• loop_mover_instance() : protocols::forge::components::VarLengthBuild
• loop_mover_str() : protocols::forge::components::VarLengthBuild , protocols::fldsgn::BluePrintBDR
• loop_of_residue() : protocols::loops::Loops
• loop_pdb_source() : protocols::protein_interface_design::movers::Splice
• loop_size() : protocols::loops::Loops
• loop_sizes() : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashDiversifier
• loop_start() : protocols::protein_interface_design::movers::LoopLengthChange
• loop_str() : protocols::loops::FoldTreeFromLoops
• LoopAnalyzerMover() : protocols::analysis::LoopAnalyzerMover
• LoopAnchorFeatures() : protocols::features::LoopAnchorFeatures
• LoopAnchorFeaturesCreator() : protocols::features::LoopAnchorFeaturesCreator
• LoopBuildMover() : protocols::loop_build::LoopBuildMover
• LoopClosure() : protocols::loops::loop_closure::ccd::LoopClosure
• loopclosure_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• loopdb_range() : protocols::loophash::LoopHashLibrary
• LoopFinder() : protocols::protein_interface_design::movers::LoopFinder
• LoopFragmentClaimer() : protocols::topology_broker::LoopFragmentClaimer
• LoopFromFileData() : protocols::loops::LoopFromFileData
• loophash_cycles() : protocols::forge::remodel::RemodelLoopMover
• loophash_stage() : protocols::forge::remodel::RemodelLoopMover
• LoopHashDiversifier() : protocols::loophash::LoopHashDiversifier
• LoopHashLibrary() : protocols::loophash::LoopHashLibrary
• LoopHashMap() : protocols::loophash::LoopHashMap
• LoopHashMoverWrapper() : protocols::loophash::LoopHashMoverWrapper
• LoopHashRelaxProtocol() : protocols::loophash::LoopHashRelaxProtocol
• LoopHashSampler() : protocols::loophash::LoopHashSampler
• LoopJumpFoldCst() : protocols::abinitio::LoopJumpFoldCst
• LoopLengthChange() : protocols::protein_interface_design::movers::LoopLengthChange
• LoopMover() : protocols::loops::loop_mover::LoopMover
• LoopMover_Perturb_CCD() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD
• LoopMover_Perturb_KIC() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• LoopMover_Perturb_KICCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator
• LoopMover_Perturb_QuickCCD() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• LoopMover_Perturb_QuickCCD_Moves() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
• LoopMover_Perturb_QuickCCD_MovesCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator
• LoopMover_Perturb_QuickCCDCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator
• LoopMover_Refine_Backrub() : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub
• LoopMover_Refine_CCD() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• LoopMover_Refine_KIC() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• LoopMover_Refine_KICCreator() : protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator
• LoopMover_SlidingWindow() : protocols::loop_build::LoopMover_SlidingWindow
• LoopMover_SlidingWindowCreator() : protocols::loop_build::LoopMover_SlidingWindowCreator
• LoopMoverFactory() : protocols::loops::LoopMoverFactory
• LoopMoverFromCommandLine() : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• LoopOver() : protocols::protein_interface_design::movers::LoopOver
• LoopRebuild() : protocols::LoopRebuild
• LoopRefine() : protocols::LoopRefine
• LoopRefineInnerCycle() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• LoopRefineInnerCycleContainer() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• LoopRefineInnerCycleContainerCreator() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator
• LoopRefineInnerCycleFactory() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• LoopRelaxMover() : protocols::comparative_modeling::LoopRelaxMover
• LoopRelaxThreadingMover() : protocols::comparative_modeling::LoopRelaxThreadingMover
• LoopRemodel() : protocols::protein_interface_design::movers::LoopRemodel
• loopres_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base2_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• LoopRlxMover() : protocols::antibody::LoopRlxMover
• LoopRmsdEvaluator() : protocols::simple_filters::LoopRmsdEvaluator
• loops() : protocols::loops::loop_mover::LoopMover , protocols::forge::remodel::RemodelLoopMover , protocols::loops::GuardedLoopsFromFile , protocols::comparative_modeling::ThreadingJob
• Loops() : protocols::loops::Loops
• loops() : protocols::loops::loop_mover::LoopMover , protocols::forge::remodel::RemodelLoopMover , protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_mover::LoopMover , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::loops::GuardedLoopsFromFile
• Loops() : protocols::loops::Loops
• loops() : protocols::loops::FoldTreeFromLoops , protocols::anchored_design::AnchorMoversData , protocols::comparative_modeling::LoopRelaxMover , protocols::fldsgn::topology::SS_Info2 , protocols::loops::loop_mover::LoopMover
• Loops() : protocols::loops::Loops
• loops() : protocols::loops::Loops
• Loops() : protocols::loops::Loops
• loops_buns_polar_calc_name() : protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR
• loops_file_data() : protocols::comparative_modeling::LoopRelaxMover , protocols::loops::GuardedLoopsFromFile
• LoopsDatabaseDefiner() : protocols::loops::loops_definers::LoopsDatabaseDefiner
• LoopsDatabaseDefinerCreator() : protocols::loops::loops_definers::LoopsDatabaseDefinerCreator
• LoopsDefinerCreator() : protocols::loops::loops_definers::LoopsDefinerCreator
• LoopsDefinerFactory() : protocols::loops::loops_definers::LoopsDefinerFactory
• LoopsDefinerLoader() : protocols::loops::loops_definers::LoopsDefinerLoader
• LoopsDefinerRegistrator() : protocols::loops::loops_definers::LoopsDefinerRegistrator< T >
• LoopsExplicitDefiner() : protocols::loops::loops_definers::LoopsExplicitDefiner
• LoopsExplicitDefinerCreator() : protocols::loops::loops_definers::LoopsExplicitDefinerCreator
• LoopsFileDefiner() : protocols::loops::loops_definers::LoopsFileDefiner
• LoopsFileDefinerCreator() : protocols::loops::loops_definers::LoopsFileDefinerCreator
• LoopsFileFallbackConfiguration() : protocols::loops::LoopsFileFallbackConfiguration
• LoopsFileIO() : protocols::loops::LoopsFileIO
• LoopsFileLoader() : protocols::loops::LoopsFileLoader
• LoopsFileOptions() : protocols::loops::LoopsFileOptions
• lores_monte_carlo() : protocols::rna::RNA_Relaxer
• low_temp() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::PackerTask
• lower() : protocols::simple_filters::DeltaFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter , protocols::protein_interface_design::filters::Torsion
• lower_bound() : core::scoring::PoissonBoltzmannPotential
• lower_chain() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• lower_connect() : core::chemical::ResidueType , core::conformation::Residue
• lower_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• lower_connect_atom() : core::chemical::ResidueType , core::conformation::Residue
• lower_connect_id() : core::chemical::ResidueType
• lower_edge_list_begin() : core::graph::Node
• lower_edge_list_end() : core::graph::Node
• lower_neighbor_id() : core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::constraints::CstResNeighbIterator , core::scoring::ResidueNeighborIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::DenseNeighborIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• lower_threshold() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• lowest_score() : protocols::simple_moves::GenericMonteCarloMover , protocols::moves::MonteCarlo
• lowest_score_pose() : protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::moves::MonteCarlo
• lowres_reference_energy() : protocols::docking::DockingEnsemble
• lowval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• lr() : core::conformation::PseudoBond
• LR_AtomData() : core::scoring::packstat::LR_AtomData
• lr_conn_id() : core::conformation::PseudoBond
• LR_MP_AtomData() : core::scoring::packstat::LR_MP_AtomData
• lr_resconnid() : core::conformation::PseudoBond
• LSMSearchPattern() : protocols::hotspot_hashing::LSMSearchPattern
• lstart() : protocols::forge::remodel::ResidueVicinityRCG
• lstop() : protocols::forge::remodel::ResidueVicinityRCG
• lt_dih() : protocols::toolbox::match_enzdes_util::ResInteractions , protocols::forge::remodel::ResidueVicinityInfo