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

- l -

• l : core::scoring::fiber_diffraction::Hankel
• L1_t_name_ : protocols::antibody::Ab_TemplateInfo
• L1_t_pose_ : protocols::antibody::Ab_TemplateInfo
• L1ScoringScheme() : core::sequence::L1ScoringScheme
• L2_t_name_ : protocols::antibody::Ab_TemplateInfo
• L2_t_pose_ : protocols::antibody::Ab_TemplateInfo
• L3_t_name_ : protocols::antibody::Ab_TemplateInfo
• L3_t_pose_ : protocols::antibody::Ab_TemplateInfo
• l_ : core::environment::LengthChecker
• L_ : core::io::nmr::ParaIon
• l_ : core::scoring::hbonds::SSWeightParameters
• l_aa_set() : core::io::NomenclatureManager
• l_aa_set_ : core::io::NomenclatureManager
• L_alpha_comp_file_exists_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• L_beta_comp_file_exists_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• L_chain_ : protocols::antibody::AntibodyInfo
• L_ini_ : core::scoring::TMscore
• L_mult_ : protocols::frag_picker::scores::TalosSSSimilarity
• l_to_d_mapping() : core::chemical::ResidueTypeSet
• l_to_d_mapping_ : core::chemical::ResidueTypeSet
• label() : core::environment::LocalPosition , core::kinematics::Edge , core::pose::PDBInfo::ResidueRecord , core::scoring::epr_deer::EPRSpinLabel , protocols::abinitio::abscript::StructPerturberCM , protocols::environment::claims::JumpClaim , protocols::environment::claims::JumpElement , protocols::environment::claims::ResidueElement , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::FragmentContainer , protocols::topology_broker::TopologyClaimer
• label1_ : protocols::noesy_assign::CrossPeak3D
• label2_ : protocols::noesy_assign::CrossPeak4D
• label_ : core::environment::LocalPosition , core::kinematics::Edge , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , protocols::abinitio::abscript::StructPerturberCM , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::JumpClaim , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::noesy_assign::Resonance , protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4 , protocols::simple_moves::AddResidueLabelMover , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::FragmentContainer , protocols::topology_broker::TopologyClaimer
• label_atom() : protocols::noesy_assign::PeakAssignment
• label_atom_name() : protocols::noesy_assign::CrossPeakInfo
• label_atom_type() : protocols::noesy_assign::CrossPeakInfo
• label_atom_type_ : protocols::noesy_assign::CrossPeakInfo
• label_energy() : protocols::moves::PyMOLMover
• label_insertion() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• label_insertion_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• label_resonance() : protocols::noesy_assign::PeakAssignment
• label_resonance_id() : protocols::noesy_assign::PeakAssignment
• label_to_pose_numbers_ : core::environment::SequenceAnnotation
• label_tolerance() : protocols::noesy_assign::CrossPeakInfo
• label_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• label_type_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy
• labeled_residues() : core::scoring::epr_deer::DEERDataCache
• labeled_residues_ : core::scoring::epr_deer::DEERDataCache
• LabelPoseFromResidueSelectorMover() : protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover
• LabelResonance() : protocols::noesy_assign::LabelResonance
• labels() : core::scoring::epr_deer::DEERDataCache , core::scoring::packstat::PosePackData
• lambda_ : protocols::cyclic_peptide_predict::PNearCalculator
• lambda_memory() : protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField
• lambda_memory_ : protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField
• lambda_sq_ : protocols::toolbox::MulliganPNearEvaluator
• LAMBEGO_IO() : protocols::frag_picker::LAMBEGO_IO
• LAMBEGO_Similarity() : protocols::frag_picker::scores::LAMBEGO_Similarity
• landing_atom_id_ : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator
• landing_domain() : core::scoring::loop_graph::Loop
• landing_domain_ : core::scoring::loop_graph::Loop
• landing_pos() : core::scoring::loop_graph::Loop
• landing_pos_ : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator , core::scoring::loop_graph::Loop
• laplacian_offset_ : protocols::electron_density::DockIntoDensityMover
• large_ : protocols::fold_from_loops::utils::Nub
• large_cluster_pose_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• large_cutoff_square_ : 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
• large_frag_file_ : protocols::struct_fragment::StructFragmentMover
• large_frag_size_ : protocols::struct_fragment::StructFragmentMover
• large_fragments() : protocols::fold_from_loops::utils::Nub
• largeF_ : protocols::struct_fragment::StructFragmentMover
• LargeFragWeight() : protocols::topology_broker::weights::LargeFragWeight
• LargeNstructJobInputter() : protocols::jd2::LargeNstructJobInputter
• LARGER : protocols::enzdes::ValueEvaluator
• largest_chunk_size_ : protocols::frag_picker::VallProvider
• largest_fragment_ : protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::PCS_FragDistance
• largest_possible_sequence_sep() : protocols::constraints_additional::MaxSeqSepConstraintSet
• largestTargetPocketVolume() : protocols::pockets::PocketGrid
• lariat_sidechain_index_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• larmord_beta_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• larmord_distance_cutoff_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• larval_job_counter_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• LarvalJob() : protocols::jd3::LarvalJob
• last_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• last_accept() : protocols::moves::MonteCarlo
• last_accept_ : protocols::moves::MonteCarlo
• last_accepted() : protocols::canonical_sampling::MetropolisHastingsMover
• last_accepted_ : protocols::canonical_sampling::MetropolisHastingsMover
• last_accepted_decoys_in_idle_ : protocols::abinitio::IterativeBase
• last_accepted_energy : protocols::boinc::BoincSharedMemory
• last_accepted_ligand_residues_ : protocols::ligand_docking::TransformEnsemble
• last_accepted_pose() : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::rational_mc::RationalMonteCarlo
• last_accepted_pose_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo
• last_accepted_pose_buf : protocols::boinc::BoincSharedMemory
• last_accepted_pose_exists : protocols::boinc::BoincSharedMemory
• last_accepted_pose_non_const() : protocols::moves::MonteCarlo
• last_accepted_reference_residues_ : protocols::ligand_docking::TransformEnsemble
• last_accepted_score() : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo
• last_accepted_score_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo
• last_accepted_scores() : protocols::monte_carlo::GenericMonteCarloMover
• last_accepted_scores_ : protocols::monte_carlo::GenericMonteCarloMover
• last_angle() : protocols::backrub::BackrubMover
• last_angle_ : protocols::backrub::BackrubMover
• last_append_res_ : protocols::stepwise::screener::ResidueContactScreener
• last_apply_failed() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundleHelix
• last_apply_failed_ : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundleHelix
• last_assignment() : protocols::pack_daemon::PackDaemon
• last_assignment_ : protocols::pack_daemon::PackDaemon
• last_attempted_mover_idx() : protocols::rosetta_scripts::ParsedProtocol
• last_attempted_mover_idx_ : protocols::rosetta_scripts::ParsedProtocol
• last_backbone_atom() : core::chemical::ResidueType , core::conformation::Residue
• last_batch_id() : protocols::jd2::archive::BaseArchiveManager
• last_carbon_in_ring() : core::chemical::carbohydrates::CarbohydrateInfo
• LAST_CENTROID_START : protocols::abinitio::IterativeBase
• last_change_ : protocols::sewing::data_storage::SmartAssembly
• last_change_was_n_terminal_ : protocols::sewing::data_storage::SmartAssembly
• last_channel_ : protocols::jd2::MpiFileBuffer
• last_check_ : protocols::moves::MonteCarlo
• last_chi1_post_ : protocols::backrub::BackrubSidechainMover
• last_chi1_pre_ : protocols::backrub::BackrubSidechainMover
• last_chi_angles_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• last_chimaera_ : protocols::sewing::data_storage::SmartAssembly
• last_chimaera_deleted_ : protocols::sewing::data_storage::SmartAssembly
• last_closure_cycles() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• last_closure_success() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• last_completed_job_ : protocols::jd2::JobDistributor
• last_considered_backbone_sub_unresolved() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_backbone_sub_unresolved_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_backbone_sub_valid() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_backbone_sub_valid_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_fixedbb_sub_unresolved_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_considered_substitution_accepted_ : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• 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_constructed_selector_ : core::select::residue_selector::SelectorLogicParser
• last_contact_added_ : protocols::sewing::hashing::LigandBindingResPlacer
• last_controlling_chi() : core::chemical::ResidueType
• last_controlling_chi_ : core::chemical::ResidueType
• last_dG_ : protocols::monte_carlo::MonteCarloInterface
• last_dim_ : core::scoring::epr_deer::FittingInfo
• last_end_atom_name() : protocols::backrub::BackrubMover
• last_end_atom_name_ : protocols::backrub::BackrubMover
• last_energies_ : protocols::canonical_sampling::ParallelTempering
• last_energylist : protocols::moves::ReplicaExchangeMC
• last_entity_ : protocols::pack_daemon::PackDaemon
• last_exchange_schedule_ : protocols::canonical_sampling::ParallelTempering
• last_flush_ : protocols::canonical_sampling::MetricRecorder
• last_garbage_collection_ : protocols::jd2::MpiFileBuffer
• last_generated_scoretable_ : protocols::mainchain_potential::GenerateMainchainPotential
• last_generated_scoretables_by_scoreterm_ : protocols::mainchain_potential::GenerateMainchainPotential
• last_ind_assigned() : protocols::mean_field::ResHashMap
• last_ind_assigned_ : protocols::mean_field::ResHashMap
• last_indep_residue_ : core::conformation::symmetry::SymmetryInfo
• last_independent_residue() : core::conformation::symmetry::SymmetryInfo
• last_inner_score_delta_over_temperature() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• last_input_pose_ : protocols::forge::remodel::RemodelMover
• last_inserted_frag_begin() : protocols::frags::TorsionFragmentMover
• last_inserted_frag_begin_ : protocols::frags::TorsionFragmentMover
• last_job_for_input_pose_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• last_job_for_input_source_ : protocols::jd3::JobTracker
• last_job_for_input_source_id() : protocols::jd3::JobTracker
• last_jobs_for_inputs_sources() : protocols::jd3::JobTracker
• last_key() : protocols::noesy_assign::ResonanceList
• last_loop_transform_ : protocols::loop_modeler::perturbers::LoopHashPerturber
• last_mod_depth_ : core::scoring::epr_deer::FittingInfo
• last_move() : protocols::canonical_sampling::MetropolisHastingsMover
• last_move_ : protocols::abinitio::hConvergenceCheck , protocols::canonical_sampling::MetropolisHastingsMover , protocols::hybridization::hConvergenceCheck , protocols::rbsegment_relax::SequenceShiftMover
• last_move_succeeded() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• last_move_succeeded_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• last_mover_ : protocols::rosetta_scripts::ParsedProtocol
• last_mutation() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_mutation_ : protocols::simple_moves::sidechain_moves::SidechainMover
• last_nbr_ : core::optimization::ParticleSwarmMinimizer
• last_nchi() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_nchi_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• last_node_added_ : protocols::legacy_sewing::SewGraph
• last_nonempty_bin() : core::scoring::saxs::DistanceHistogram
• last_nonempty_bin_ : core::scoring::saxs::DistanceHistogram
• last_packet_sent_time_ : protocols::moves::PyMOLMover
• last_pertrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• last_prepend_res_ : protocols::stepwise::screener::ResidueContactScreener
• last_proposal_density_ratio() : protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , 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_proposal_density_ratio_ : protocols::moves::RandomMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• last_received_from() : protocols::wum::WorkUnitBase
• last_received_from_ : protocols::wum::WorkUnitBase
• last_ref_pose_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• last_ref_tag_ : protocols::jd2::AtomTreeDiffJobOutputter
• last_res_ : protocols::simple_moves::RepeatPropagationMover
• last_residue() : core::conformation::parametric::Parameters , protocols::kinematic_closure::ClosureProblem , protocols::topology_broker::claims::DofClaim
• last_residue_index() : core::conformation::parametric::Parameters
• last_residue_index_ : protocols::frag_picker::PhiPsiTalosIO
• last_residue_was_recognized() : core::io::pose_from_sfr::PoseFromSFRBuilder
• last_reverted_parent_chimaera_ : protocols::sewing::data_storage::SmartAssembly
• last_run_successful() : protocols::generalized_kinematic_closure::GeneralizedKIC
• last_run_successful_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• last_sampled_ligand_ : protocols::sewing::data_storage::SmartAssembly
• last_save_state_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• last_scaffold_build_point_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• last_score : protocols::electron_density::SetupForDensityScoringMover , protocols::moves::MonteCarlo
• last_score_ : protocols::monte_carlo::MonteCarloInterface , protocols::moves::MonteCarlo , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer
• last_section() : core::fragment::picking_old::vall::VallLibrary
• last_seen_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• last_seen_restype_index_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• last_segment_id() : protocols::backrub::BackrubMover
• last_segment_id_ : protocols::backrub::BackrubMover
• last_slide_good() : protocols::rigid::RigidBodyDofTransMover
• last_slide_good_ : protocols::rigid::RigidBodyDofTransMover
• last_slope_ : core::scoring::epr_deer::FittingInfo
• last_start_atom_name() : protocols::backrub::BackrubMover
• last_start_atom_name_ : protocols::backrub::BackrubMover
• last_stats_ : protocols::wum::MPI_WorkUnitManager
• last_status_ : protocols::moves::Mover
• last_struct_id_ : protocols::features::ReportToDB
• last_sub_attempted_backbone_move_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• last_symmetry_mirror() : protocols::cyclic_peptide::SymmetricCycpepAlign
• last_symmetry_mirror_ : protocols::cyclic_peptide::SymmetricCycpepAlign
• last_symmetry_repeats() : protocols::cyclic_peptide::SymmetricCycpepAlign
• last_symmetry_repeats_ : protocols::cyclic_peptide::SymmetricCycpepAlign
• last_temp_ : protocols::antibody::H3RefineCCD
• last_tested_scores() : protocols::monte_carlo::GenericMonteCarloMover
• last_tested_scores_ : protocols::monte_carlo::GenericMonteCarloMover
• last_uniform() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• last_valid_segment_index_ : protocols::backrub::BackrubSidechainMover
• last_withinrot() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• lastcol : core::scoring::packstat::SimplePDB_Atom
• lastRes : protocols::sparta::Sparta::SpartaLib
• lastRes_ : core::scoring::methods::RG_LocalEnergy
• lastResidue_ : protocols::pose_length_moves::FixAllLoopsMover
• late_factory_ : protocols::anchored_design::AnchorMoversData
• lattice_mag_ : protocols::cryst::DockLatticeMover
• launch_atom() : protocols::match::downstream::ClassicMatchAlgorithm
• launch_points_ : protocols::match::downstream::ClassicMatchAlgorithm
• layer() : core::select::util::SelectResiduesByLayer
• Layer : protocols::flxbb::LayerDesignOperation
• layer_lines_I : core::scoring::fiber_diffraction::FiberDiffraction
• layer_lines_R : core::scoring::fiber_diffraction::FiberDiffraction
• layer_mode_ : protocols::flxbb::FlxbbDesign
• layer_operation_ : protocols::flxbb::LayerDesignOperation
• layer_residues() : protocols::flxbb::LayerDesignOperation
• layer_residues_ : protocols::flxbb::LayerDesignOperation
• layer_size_ : protocols::carbohydrates::GlycanTreeModeler
• layer_specification_ : protocols::flxbb::LayerDesignOperation
• LayerDefinition : protocols::flxbb::LayerDesignOperation
• LayerDefinitions : protocols::flxbb::LayerDesignOperation
• LayerDesignOperation() : protocols::flxbb::LayerDesignOperation
• LayerOperationType : protocols::flxbb::LayerDesignOperation
• LayerResidues : protocols::flxbb::LayerDesignOperation
• LayerSelector() : core::select::residue_selector::LayerSelector
• LayerSpecificationType : protocols::flxbb::LayerDesignOperation
• lazy_ : protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::task_operations::SetIGTypeOperation
• lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• lazy_ig_ : core::pack::task::PackerTask_
• lazy_load_base_type_already_write_locked() : core::chemical::GlobalResidueTypeSet , core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• 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
• lb_ : core::kinematics::TreeVizBuilder , core::scoring::constraints::BoundFunc
• lbfgs() : core::optimization::Minimizer
• lbuf : protocols::sparta::Sparta::SpartaLib
• LD_types : protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet
• ldsrbb_high_scale_ : core::scoring::hbonds::HBondOptions
• ldsrbb_low_scale_ : core::scoring::hbonds::HBondOptions
• ldsrbb_maxlength_ : core::scoring::hbonds::HBondOptions
• ldsrbb_minlength_ : core::scoring::hbonds::HBondOptions
• LeastNativeLike9merFilter() : protocols::simple_filters::LeastNativeLike9merFilter
• leave_as_is() : protocols::task_operations::DatabaseThread
• leave_as_is_ : protocols::task_operations::DatabaseThread
• leave_coord_csts_after_placement_ : protocols::protein_interface_design::movers::PlaceStubMover
• leaves_of_jump() : core::conformation::symmetry::SymmData
• lec_order : core::scoring::fiber_diffraction::Hankel
• LeeRichards() : core::scoring::packstat::LeeRichards
• left : protocols::forge::build::Interval
• left_ : core::pack::dunbrack::BBIndNRChiSample< P > , core::scoring::interface_::DDPlookup
• left_cdf() : core::scoring::Ramachandran2B
• left_cdf_ : core::scoring::Ramachandran2B
• left_cdf_by_torsion_bin_ : core::scoring::Ramachandran2B
• left_cdf_for_torsion_bin() : core::scoring::Ramachandran2B
• left_handed() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• left_handed_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet , protocols::forge::remodel::RemodelGlobalFrame
• left_named_stub_id() : protocols::forge::build::ConnectRight
• left_position() : protocols::forge::build::ConnectRight
• left_position_ : protocols::forge::build::ConnectRight
• left_ram_probabil_ : core::scoring::Ramachandran2B
• left_skip : protocols::forge::build::CountFromLeft
• left_stub_atoms() : protocols::forge::build::ConnectRight
• left_stub_atoms_ : protocols::forge::build::ConnectRight
• legacy() : protocols::hbnet::UnsatSelector
• legacy_ : protocols::hbnet::UnsatSelector
• legacy_assembly_mover_ct_namer() : protocols::legacy_sewing::LegacyAssemblyMover
• legacy_command_line_post_processing() : core::chemical::AtomTypeSet
• legacy_counting_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• legacy_dof_allow_move_ : protocols::simple_moves::ConstrainToIdealMover
• legacy_global_requirements_ct_namer() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• legacy_global_requirements_group_name() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• legacy_intra_segment_requirements_ct_namer() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• legacy_intra_segment_requirements_group_name() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• legacy_mode_ : protocols::rigid::RollMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• legacy_options_ : protocols::simple_filters::BuriedUnsatHbondFilter
• legacy_turner_mode() : protocols::recces::options::RECCES_Options
• legacy_turner_mode_ : protocols::recces::options::RECCES_Options
• LegacyAddStartnodeFragments() : protocols::legacy_sewing::LegacyAddStartnodeFragments
• LegacyAppendAssemblyMover() : protocols::legacy_sewing::LegacyAppendAssemblyMover
• LegacyAssemblyConstraintsMover() : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• LegacyAssemblyMover() : protocols::legacy_sewing::LegacyAssemblyMover
• LegacyAssemblyScorer() : protocols::legacy_sewing::scoring::LegacyAssemblyScorer
• LegacyBlosumScorer() : protocols::legacy_sewing::scoring::LegacyBlosumScorer
• LegacyCalciumMotifScorer() : protocols::legacy_sewing::scoring::LegacyCalciumMotifScorer
• LegacyClashScorer() : protocols::legacy_sewing::scoring::LegacyClashScorer
• LegacyEnumerateAssemblyMover() : protocols::legacy_sewing::LegacyEnumerateAssemblyMover
• LegacyGivenPathAssemblyMover() : protocols::legacy_sewing::LegacyGivenPathAssemblyMover
• LegacyGlobalLengthRequirement() : protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement
• LegacyGlobalRequirementCreator() : protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirementCreator
• LegacyGlobalRequirementCreatorMap : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• LegacyGreedyAssemblyMover() : protocols::legacy_sewing::LegacyGreedyAssemblyMover
• LegacyInterModelMotifScorer() : protocols::legacy_sewing::scoring::LegacyInterModelMotifScorer
• LegacyIntraSegmentRequirementCreator() : protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirementCreator
• LegacyIntraSegmentRequirementCreatorMap : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• LegacyIntraSegmentRequirementsMap : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• LegacyKicSampler() : protocols::loop_modeling::samplers::LegacyKicSampler
• LegacyMonteCarloAssemblyMover() : protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• LegacyMotifScorer() : protocols::legacy_sewing::scoring::LegacyMotifScorer
• LegacyPartnerMotifScorer() : protocols::legacy_sewing::scoring::LegacyPartnerMotifScorer
• LegacyReadNativeRotamersFile() : protocols::legacy_sewing::LegacyReadNativeRotamersFile
• LegacyReadRepeatNativeRotamersFile() : protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile
• LegacyRepeatAssemblyMover() : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• LegacyRequirementFactory() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• LegacyRequirementRegistrator() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementRegistrator< T >
• LegacyRequirementSet() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• LegacyResidueRetentionRequirement() : protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement
• LegacyRootClaim() : protocols::topology_broker::claims::LegacyRootClaim
• LegacySegmentDsspRequirement() : protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirement
• LegacySegmentLengthRequirement() : protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement
• LeGrandSasa() : core::scoring::sasa::LeGrandSasa
• len_ : protocols::frag_picker::scores::JCoupling
• len_h_ : core::scoring::hbonds::SSWeightParameters
• len_l_ : core::scoring::hbonds::SSWeightParameters
• lenex_ : core::scoring::ResidualDipolarCoupling
• length() : core::environment::SequenceAnnotation , core::fragment::Frame , core::io::HELIXInformation , core::io::LinkInformation , core::io::SSBondInformation , core::sequence::AnnotatedSequence , core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::antibody::clusters::ClusterData , protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , 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 , protocols::topology_broker::claims::SequenceClaim
• length_ : core::environment::SequenceAnnotation , core::sequence::AnnotatedSequence , protocols::denovo_design::components::StructureData , protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol , protocols::sewing::data_storage::SmartAssembly , protocols::sewing::data_storage::SmartSegment , protocols::sewing::requirements::LengthInResiduesRequirement
• length_based_CDRDBPose_indexes_ : protocols::antibody::design::AntibodyDesignMover
• length_change : core::conformation::signals::LengthEvent
• length_dependent_srbb() : core::scoring::hbonds::HBondOptions
• length_dependent_srbb_ : core::scoring::hbonds::HBondOptions
• length_dependent_srbb_highscale() : core::scoring::hbonds::HBondOptions
• length_dependent_srbb_lowscale() : core::scoring::hbonds::HBondOptions
• length_dependent_srbb_maxlength() : core::scoring::hbonds::HBondOptions
• length_dependent_srbb_minlength() : core::scoring::hbonds::HBondOptions
• length_event_link_ : core::conformation::carbohydrates::GlycanTreeSetObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::denovo_design::components::StructureDataObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• length_events_ : core::pose::datacache::LengthEventCollector
• length_normalized_distance() : protocols::antibody::clusters::CDRCluster
• length_obs_hub_ : core::conformation::Conformation
• length_obs_link() : protocols::forge::build::BuildInstruction
• length_obs_link_ : protocols::forge::build::BuildInstruction
• length_parameter : core::scoring::methods::ResidueCartBondedParameters
• length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• length_params_ : core::scoring::methods::ResidueCartBondedParameters
• length_type() : protocols::antibody::CDRSetOptions
• length_types_ : protocols::antibody::CDRSetOptions
• LengthChecker() : core::environment::LengthChecker
• LengthEvent : core::conformation::Conformation , core::conformation::signals::LengthEvent , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• LengthEventCollector() : core::pose::datacache::LengthEventCollector
• LengthGen() : core::fragment::picking_old::vall::gen::LengthGen
• LengthInResiduesRequirement() : protocols::sewing::requirements::LengthInResiduesRequirement
• LengthInResiduesRequirementCreator() : protocols::sewing::requirements::LengthInResiduesRequirementCreator
• lengths() : protocols::denovo_design::connection::ConnectionArchitect
• Lengths : protocols::denovo_design::connection::ConnectionArchitect
• lengths_ : protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::StrandArchitect
• lengths_shifts() : protocols::denovo_design::components::SheetDB
• LengthSet : protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::components::IdealAbegoGenerator , protocols::denovo_design::connection::ConnectionArchitect
• less_than() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• let_neighboring_chis_minimize() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• let_neighboring_side_chains_minimize() : protocols::stepwise::modeler::StepWiseMinimizer
• level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• level_ : core::pack::task::operation::ExtraRotamers , protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• level_2_grid_coord() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::TemperatureController
• 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
• lfd_ : protocols::loops::loops_definers::LoopsFileDefiner
• lfr_ : protocols::antibody_legacy::Antibody
• Lfr_t_name_ : protocols::antibody::Ab_TemplateInfo
• lg1x_ : core::scoring::motif::ResPairMotif
• lg1y_ : core::scoring::motif::ResPairMotif
• lg1z_ : core::scoring::motif::ResPairMotif
• lg2x_ : core::scoring::motif::ResPairMotif
• lg2y_ : core::scoring::motif::ResPairMotif
• lg2z_ : core::scoring::motif::ResPairMotif
• lg_angles_ : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• lg_masks_ : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• LH_dock_jump_ : protocols::antibody::RefineBetaBarrel
• lh_library_ : protocols::loop_modeler::perturbers::LoopHashPerturber
• LH_repulsive_ramp_ : protocols::antibody::AntibodyModelerProtocol
• lh_repulsive_ramp_ : protocols::antibody::RefineBetaBarrel
• lh_snugfit_ : protocols::antibody::RefineBetaBarrel
• lhlibrary_ : protocols::loophash::FastGapMover
• LHRepulsiveRamp() : protocols::antibody::LHRepulsiveRamp
• LHRepulsiveRampLegacy() : protocols::antibody::LHRepulsiveRampLegacy
• lhsampler_ : protocols::loophash::FastGapMover
• LHSnugFitLegacy() : protocols::antibody::LHSnugFitLegacy
• lib() : protocols::sparta::Sparta
• lib_chi_val_ : protocols::make_rot_lib::RotData
• lib_full_path() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• lib_instance_ : protocols::sparta::Sparta
• Librarian() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• Library() : core::fragment::picking_old::concepts::Library< Books >
• library() : protocols::frags::FragLib , protocols::motifs::MotifLibrary
• library_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::loop_grower::LoopGrower , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::LoopHashSampler , protocols::loophash::Mover_LoopHashRefine , protocols::loophash::WorkUnit_LoopHash , protocols::motifs::MotifLibrary , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::nonlocal::SingleFragmentMover , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::SegmentHybridizer
• library_central() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• library_central_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• library_expiry_time_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• library_iterator : core::pack::dunbrack::RotamerLibrary
• library_map_ : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• library_name() : core::chemical::rotamers::BasicRotamerLibrarySpecification , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::chemical::rotamers::NCAARotamerLibrarySpecification , core::chemical::rotamers::PDBRotamerLibrarySpecification , core::chemical::rotamers::StoredRotamerLibrarySpecification
• library_ref() : protocols::mpi_refinement::MPI_Refinement
• library_ref_ : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• library_size() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• lig_chain : protocols::ligand_docking::ProtLigPair_info
• lig_com_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• lig_conformer_builder_ : protocols::enzdes::ResidueConformerFilter
• lig_conformers_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• lig_id_ : protocols::enzdes::LigBurialFilter
• lig_min_stddev_ : protocols::enzdes::EnzdesBaseProtocol
• lig_num_unsatisfied : protocols::hbnet::HBondNetStruct
• lig_packer_weight_ : protocols::enzdes::ProteinLigandInterfaceUpweighter
• lig_potential_acc_sp2_ : core::scoring::PointWaterPotential
• lig_potential_acc_sp3_ : core::scoring::PointWaterPotential
• lig_potential_don_ : core::scoring::PointWaterPotential
• lig_rigid_body_confs() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• lig_rigid_body_confs_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• lig_seqpos_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• lig_state_list : protocols::hbnet::HBondNetStruct
• lig_superposition_file_read_ : protocols::enzdes::EnzdesBaseProtocol
• LIGAND : protocols::denovo_design::components::SegmentCounts
• ligand() : protocols::hbnet::HBNet
• LIGAND : protocols::pockets::ComparisonGrid
• ligand_ : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid , protocols::sewing::hashing::LigandBindingResPlacer , protocols::topology_broker::MetalloClaimer
• ligand_area_ct_namer() : protocols::ligand_docking::LigandAreaLoader
• ligand_areas_ : protocols::ligand_docking::InterfaceBuilder
• ligand_atom : protocols::ligand_docking::rdf::AtomPairData , protocols::sewing::data_storage::LigandContact , protocols::sewing::hashing::IdealContact
• ligand_atom_charge : protocols::ligand_docking::rdf::AtomPairData
• ligand_atom_coords : protocols::ligand_docking::rdf::AtomPairData
• ligand_atom_id : protocols::ligand_docking::rdf::AtomPairData
• ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• ligand_atom_index : protocols::sewing::hashing::LigandCoordInfo
• ligand_atom_name : protocols::sewing::data_storage::ContactDescription
• ligand_atom_name_ : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::metal_interface::MetalSiteResidue
• ligand_atom_num : protocols::sewing::data_storage::ContactDescription
• ligand_atom_type : protocols::ligand_docking::rdf::AtomPairData
• ligand_atom_xyz_ : protocols::metal_interface::MetalSiteResidue
• ligand_calculate() : protocols::scoring::Interface
• ligand_chain_ : protocols::analysis::InterfaceAnalyzerMover , protocols::ligand_docking::ComputeLigandRDF , protocols::simple_moves::AddJobPairData
• ligand_chi_stddev_deg_ : protocols::ligand_docking::LigandDockProtocol
• ligand_conformers_ : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::sewing::data_storage::SmartAssembly
• ligand_contacts : protocols::sewing::data_storage::LigandDescription
• ligand_contacts_ : protocols::sewing::data_storage::LigandSegment
• ligand_coord_files : protocols::sewing::data_storage::LigandDescription
• ligand_coords : protocols::sewing::data_storage::LigandDescription
• ligand_crystal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_discrim_data_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_id() : protocols::ligand_docking::ga_ligand_dock::LigandConformer , protocols::sewing::data_storage::LigandDescription
• ligand_id_ : protocols::sewing::data_storage::LigandResidue
• ligand_indices_ : protocols::comparative_modeling::StealLigandMover
• Ligand_info() : protocols::ligand_docking::Ligand_info
• ligand_jump_id_ : protocols::simple_moves::CoupledMover
• ligand_local_coords_ : protocols::sewing::hashing::LigandBindingResPlacer
• ligand_mode_ : protocols::coupled_moves::CoupledMovesProtocol
• ligand_native_decoy_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_natoms_elstscalc_ : protocols::pockets::DarcParticleSwarmMinimizer
• ligand_natoms_shapecalc_ : protocols::pockets::DarcParticleSwarmMinimizer
• ligand_prob_ : protocols::coupled_moves::CoupledMovesProtocol
• ligand_protein_rdf() : protocols::ligand_docking::ComputeLigandRDF
• ligand_protonation_ : protocols::ligand_docking::LigandDockProtocol
• ligand_repack_native_poses_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_repack_pdbs_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_requirements_ : protocols::sewing::movers::LigandBindingAssemblyMover
• ligand_residue() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligand_residues_ : protocols::ligand_docking::TransformEnsemble , protocols::sewing::data_storage::LigandSegment
• ligand_resno() : protocols::enzdes::EnzdesConstraintReporter
• ligand_resnum : protocols::sewing::data_storage::LigandDescription
• ligand_resnum_ : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• ligand_resnum_string : protocols::sewing::data_storage::LigandDescription
• ligand_resnum_string_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ligand_resnums_ : protocols::coupled_moves::CoupledMovesProtocol
• ligand_restype_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ligand_rg() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligand_rot() : protocols::simple_moves::WaterRotsDB
• ligand_rots_ : protocols::simple_moves::WaterRotsDB
• ligand_selector : protocols::sewing::data_storage::LigandDescription
• ligand_selector_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ligand_seqpos_ : protocols::enzdes::EnzdesConstraintReporter , protocols::membrane::AddMPLigandMover
• ligand_shear_moves_ : protocols::ligand_docking::LigandDockProtocol
• ligand_subset_ : protocols::denovo_design::components::SegmentCounts
• ligand_subtag_ct_namer() : protocols::sewing::hashing::LigandBindingResPlacer
• ligand_tether_ : protocols::ligand_docking::TetherLigand
• ligand_tether_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• ligand_torsion_restraints_ : protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MinimizeLigand
• ligand_typename() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligand_typename_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligand_weight_ : protocols::coupled_moves::CoupledMovesProtocol , protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• ligand_xyz() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• LigandAligner() : protocols::ligand_docking::ga_ligand_dock::LigandAligner
• LigandArea() : protocols::ligand_docking::LigandArea
• LigandAreaLoader() : protocols::ligand_docking::LigandAreaLoader
• LigandAssemblyRequirement() : protocols::sewing::requirements::LigandAssemblyRequirement
• LigandAssemblyScorer() : protocols::sewing::scoring::LigandAssemblyScorer
• LigandBaseProtocol() : protocols::ligand_docking::LigandBaseProtocol
• LigandBindingAssemblyMover() : protocols::sewing::movers::LigandBindingAssemblyMover
• LigandBindingResPlacer() : protocols::sewing::hashing::LigandBindingResPlacer
• ligandchi_downstream_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligandchis_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• LigandClashRequirement() : protocols::sewing::requirements::LigandClashRequirement
• LigandClashRequirementCreator() : protocols::sewing::requirements::LigandClashRequirementCreator
• LigandConformer() : protocols::ligand_docking::ga_ligand_dock::LigandConformer , protocols::toolbox::match_enzdes_util::LigandConformer
• LigandConformerBuilder() : protocols::match::downstream::LigandConformerBuilder
• LigandContact() : protocols::sewing::data_storage::LigandContact
• LigandDescription() : protocols::sewing::data_storage::LigandDescription
• LigandDesign() : protocols::ligand_docking::LigandDesign
• LigandDockMain() : protocols::ligand_docking::LigandDockMain
• LigandDockProtocol() : protocols::ligand_docking::LigandDockProtocol
• liganding_atom_from_restype() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• LigandMetalContactSelector() : protocols::residue_selectors::LigandMetalContactSelector
• LigandMinusProteinPlus : protocols::ligand_docking::rdf::RDFBase
• LigandMotifSearch() : protocols::motifs::LigandMotifSearch
• ligandname : protocols::ligand_docking::ga_ligand_dock::StructInfo
• ligandnus_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• LigandPlusProteinMinus : protocols::ligand_docking::rdf::RDFBase
• LigandPropertyScore() : protocols::qsar::scoring_grid::LigandPropertyScore
• LigandResidue() : protocols::sewing::data_storage::LigandResidue
• ligands_ : protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover
• ligands_subtag_ct_namer() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• ligandscore : protocols::ligand_docking::ga_ligand_dock::StructInfo
• LigandScorer() : protocols::sewing::scoring::LigandScorer
• LigandSegment() : protocols::sewing::data_storage::LigandSegment
• ligandtaus_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligandxyz_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligandxyz_synced_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• LigBurialFilter() : protocols::enzdes::LigBurialFilter
• ligchimutWidth_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• ligchis : protocols::ligand_docking::ga_ligand_dock::ChiInfo
• LigDSasaFilter() : protocols::enzdes::LigDSasaFilter
• light_chain_ : protocols::antibody::design::AntibodyDesignMover
• light_chain_type_ : protocols::antibody::AntibodyInfo
• light_chain_type_enum_to_string() : protocols::antibody::AntibodyEnumManager
• light_chain_type_is_present() : protocols::antibody::AntibodyEnumManager
• light_chain_type_string_to_enum() : protocols::antibody::AntibodyEnumManager
• light_chain_type_to_enum_ : protocols::antibody::AntibodyEnumManager
• light_chain_type_to_string_ : protocols::antibody::AntibodyEnumManager
• LightHeavy_t_name_ : protocols::antibody::Ab_TemplateInfo
• ligid_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GridScorer , protocols::ligand_docking::ga_ligand_dock::LigandConformer
• LigInterfaceEnergyFilter() : protocols::enzdes::LigInterfaceEnergyFilter
• ligres_ : protocols::match::MatcherMover
• limit() : core::scoring::func::TopOutFunc , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo , protocols::symmetry::SetupNCSMover , protocols::wum::SilentStructStore
• limit_ : core::scoring::func::TopOutFunc , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::symmetry::SetupNCSMover
• limit_aroma_chi2() : protocols::relax::RelaxProtocolBase
• limit_aroma_chi2_ : protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::relax::RelaxProtocolBase
• limit_chi_angles_ : protocols::rotamer_recovery::RRComparerChiDiff
• limit_cluster_size : protocols::toolbox::ClusterOptions
• limit_clusters_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• limit_dlig_mem_usage_ : protocols::pack_daemon::DaemonSet
• limit_groups() : protocols::cluster::ClusterBase
• limit_groupsize() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• limit_ig_setup_threads() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• limit_library() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• limit_only_to_length_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation
• limit_per_rotamer_combo_ : protocols::match::output::LimitHitsPerRotamerFilter
• limit_primary_distance : protocols::indexed_structure_store::search::StructurePairQuery
• limit_reporting_to_these_options_ : core::simple_metrics::composite_metrics::ProtocolSettingsMetric
• limit_structures_per_cluster_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• limit_to_positions() : protocols::task_operations::ConservativeDesignOperation
• limit_total_structures() : protocols::cluster::ClusterBase
• limit_x_ : protocols::pockets::PocketGrid
• limit_y_ : protocols::pockets::PocketGrid
• limit_z_ : protocols::pockets::PocketGrid
• LimitAromaChi2_RotamerSetOperation() : protocols::task_operations::LimitAromaChi2_RotamerSetOperation
• LimitAromaChi2Operation() : protocols::task_operations::LimitAromaChi2Operation
• limitExemplars_ : protocols::pockets::PocketGrid
• LimitHitsPerRotamerFilter() : protocols::match::output::LimitHitsPerRotamerFilter
• lin_isc : protocols::peptide_deriver::DerivedPeptideEntry
• lin_mem_ : protocols::task_operations::SetIGTypeOperation
• lin_pose : protocols::peptide_deriver::DerivedPeptideEntry
• Line() : core::sequence::Line
• line_color_ : protocols::match::Bool3DGridKinemageWriter
• line_header_ : core::chemical::sdf::MolWriter
• line_starts_with_other() : core::io::silent::SilentFileData
• line_starts_with_other_header_string() : core::io::silent::SilentFileData
• line_starts_with_remark() : core::io::silent::SilentFileData
• line_starts_with_score() : core::io::silent::SilentFileData
• line_starts_with_sequence() : core::io::silent::SilentFileData
• line_to_design() : protocols::pose_creation::MakeJunctionsMover
• linear_bonded_potential_ : core::scoring::methods::CartesianBondedEnergy , protocols::features::ProteinBondGeometryFeatures
• linear_chainbreak_weight() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• linear_chainbreak_weight_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• linear_fract_out_of_bounds_func() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• linear_out_of_bounds_func() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• linear_switch_point : core::scoring::mm::MMLJEnergyTable
• linear_vector_of_results() : protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• linear_weights_ : core::scoring::ProQPotential
• linear_weights_proq2_ : core::scoring::ProQPotential
• LinearBranchEnergy() : core::scoring::methods::LinearBranchEnergy
• 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::func::LinearPenaltyFunction
• LineBuffer : protocols::jd2::SingleFileBuffer
• linecount_offset_ : protocols::loops::JSONFormattedLoopsFileReader , protocols::loops::PoseNumberedLoopFileReader
• LineMinimizationAlgorithm() : core::optimization::LineMinimizationAlgorithm
• linenum() : core::pose::RID_FileSource
• linenum_ : core::pose::RID_FileSource
• LineObject() : protocols::forge::remodel::LineObject
• lines_ : core::sequence::ABEGO
• lines_from_header_line_collection() : core::io::silent::SilentFileData
• Link : core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::forge::build::BuildInstruction
• link_ : protocols::moves::PyMOLMover
• link_all_cys_with_tbmb_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• link_map() : core::io::StructFileRep
• link_map_ : core::io::StructFileRep
• link_to() : protocols::sewing::data_storage::SmartSegment
• 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
• linkage_conformers_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• linkage_conformers_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• linkage_mover_ : protocols::carbohydrates::GlycanSampler
• linkage_notation() : core::chemical::carbohydrates::CarbohydrateInfo
• linkage_notation_ : core::chemical::carbohydrates::CarbohydrateInfo
• linkage_position_ : core::conformation::carbohydrates::GlycanNode
• linkage_type : core::scoring::carbohydrates::CHIDihedralSamplingData
• LinkageConformerMover() : protocols::carbohydrates::LinkageConformerMover
• linkages_from_pair() : core::chemical::carbohydrates::CarbohydrateInfoManager
• linked_ : core::kinematics::FoldTree
• linker_ : protocols::cyclic_peptide::CrosslinkerMover
• linker_end_ : protocols::abinitio::DomainAssembly
• linker_name() : protocols::cyclic_peptide::CrosslinkerMover
• linker_start_ : protocols::abinitio::DomainAssembly
• LinkerScore() : protocols::sic_dock::LinkerScore
• linkExemplarsThroughSolvent() : protocols::pockets::PocketGrid
• LinkResidues() : protocols::task_operations::LinkResidues
• links_ : core::pack::rotamer_set::RotamerLinks
• linmem_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• linmem_ig_ : core::pack::task::PackerTask_
• linmem_ig_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• linmem_ig_history_size_ : core::pack::task::PackerTask_
• linmem_ig_history_size_at_default_ : core::pack::task::PackerTask_
• linmin() : core::optimization::Minimizer
• linmin_deriv_cutoff() : core::optimization::MinimizerOptions
• linmin_deriv_cutoff_ : core::optimization::MinimizerOptions
• linmin_iterated() : core::optimization::Minimizer
• linmin_only_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• lipid_composition_ : protocols::membrane::AddMembraneMover
• lipid_composition_name() : core::conformation::membrane::ImplicitLipidInfo
• lipid_composition_name_ : core::conformation::membrane::ImplicitLipidInfo
• lipid_composition_name_long() : core::conformation::membrane::ImplicitLipidInfo
• lipid_composition_name_long_ : core::conformation::membrane::ImplicitLipidInfo
• LipidBurial() : core::scoring::MembraneTopology
• LipidBurial_ : core::scoring::MembraneTopology
• LipidExposure() : core::scoring::MembraneTopology
• LipidExposure_ : core::scoring::MembraneTopology
• LipoDefined() : core::scoring::MembraneTopology
• LipoDefined_ : core::scoring::MembraneTopology
• list() : core::scoring::Hairpins
• list2id() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• list_ : core::fragment::VectorCacheUnit< T > , protocols::abinitio::abscript::ResidueChunkSelection , protocols::peptide_deriver::PeptideDeriverOutputterContainer
• list_allowable_mutations() : protocols::constel::SingResCnlCrea
• list_allowed_residue_types() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• list_attributes() : core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions
• list_file_names_ : core::io::sequence_comparation::DesignContrast
• list_filters() : protocols::rosetta_scripts::XmlObjects
• list_interface_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• list_mode_ : protocols::cluster::calibur::AdjacentList
• list_movers() : protocols::rosetta_scripts::XmlObjects
• list_options_read() : core::import_pose::ImportPoseOptions , core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , core::import_pose::RNA_DeNovoSetup , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , core::pack::task::operation::ReadResfile , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask , core::scoring::DockingScoreFunction , core::scoring::etable::EtableOptions , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions , core::scoring::MinScoreScoreFunction , core::scoring::ScoreFunction , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterCreator , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator , protocols::jd3::full_model_inputters::FullModelInputterCreator , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputterCreator , protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator , protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PDBPoseInputterCreator , protocols::jd3::pose_inputters::PoseInputterCreator , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_inputters::SilentFilePoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputterCreator , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator , protocols::jd3::pose_outputters::mmTFPoseOutputter , protocols::jd3::pose_outputters::mmTFPoseOutputterCreator , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputterCreator , protocols::jd3::pose_outputters::PoseOutputterCreator , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::ScoreFileOutputterCreator , protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator , protocols::jd3::pose_outputters::SilentFilePoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator , protocols::minimization_packing::PackRotamersMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rosetta_scripts::RosettaScriptsParser , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions
• list_outputter_options_read() : protocols::jd3::pose_outputters::PoseOutputterFactory
• list_pools() : protocols::frag_picker::quota::QuotaCollector
• list_read_options() : core::io::silent::SilentFileOptions , core::scoring::ScoreFunctionFactory
• list_residue_selectors() : protocols::rosetta_scripts::XmlObjects
• list_sasa_method_hp_modes() : core::scoring::sasa::SasaMethod
• list_score_functions() : protocols::rosetta_scripts::XmlObjects
• list_secondary_outputter_options_read() : protocols::jd3::pose_outputters::PoseOutputterFactory
• list_simple_metrics() : protocols::rosetta_scripts::XmlObjects
• list_task_operations() : protocols::rosetta_scripts::XmlObjects
• listAdjacentLists() : protocols::cluster::calibur::Clustering
• listen_for_rank() : protocols::canonical_sampling::AsyncMPITemperingBase
• live() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• live_ : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• lj_cutoff() : protocols::match::output::MatchCollisionFilter
• lj_cutoff_ : protocols::match::output::MatchCollisionFilter
• lj_hbond_dis_ : core::scoring::etable::Etable
• lj_hbond_hdis : core::init::pre_talaris_2013_behavior_settings , core::scoring::etable::EtableOptions
• lj_hbond_hdis_ : core::scoring::etable::Etable
• lj_hbond_OH_donor_dis : core::init::pre_talaris_2013_behavior_settings , core::scoring::etable::EtableOptions
• lj_hbond_OH_donor_dis_ : core::scoring::etable::Etable
• lj_minimum : core::scoring::etable::EtableParamsOnePair
• lj_n_ : core::simple_metrics::per_residue_metrics::PerResidueClashMetric
• lj_r12_coeff : core::scoring::etable::EtableParamsOnePair
• lj_r12_coeff_ : core::scoring::etable::Etable
• lj_r6_coeff : core::scoring::etable::EtableParamsOnePair
• lj_r6_coeff_ : core::scoring::etable::Etable
• lj_radius() : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lj_radius_ : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lj_radius_sq() : core::chemical::MMAtomType
• lj_radius_sq_ : core::chemical::MMAtomType
• lj_radius_to_zero_e_radius() : core::simple_metrics::per_residue_metrics::PerResidueClashMetric
• lj_ramp_cycles : protocols::relax::ClassicRelax
• lj_ramp_inner_cycles : protocols::relax::ClassicRelax
• lj_sigma_ : core::scoring::etable::Etable
• lj_slope_intercept() : core::scoring::etable::Etable
• lj_slope_intercept_ : core::scoring::etable::Etable
• lj_spline_ : protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::VdwGrid
• lj_switch_dis2sigma() : core::scoring::etable::Etable , core::scoring::etable::EtableOptions
• lj_switch_dis2sigma_ : core::scoring::etable::Etable
• lj_switch_intercept : core::scoring::etable::EtableParamsOnePair
• lj_switch_intercept_ : core::scoring::etable::Etable
• lj_switch_sigma2dis_ : core::scoring::etable::Etable
• lj_switch_slope : core::scoring::etable::EtableParamsOnePair
• lj_switch_slope_ : core::scoring::etable::Etable
• lj_switch_slope_sigma2wdepth_ : core::scoring::etable::Etable
• lj_switch_value2wdepth_ : core::scoring::etable::Etable
• lj_three_bond_radius() : core::chemical::MMAtomType
• lj_three_bond_radius_ : core::chemical::MMAtomType
• lj_three_bond_radius_sq() : core::chemical::MMAtomType
• lj_three_bond_radius_sq_ : core::chemical::MMAtomType
• lj_three_bond_wdepth() : core::chemical::MMAtomType
• lj_three_bond_wdepth_ : core::chemical::MMAtomType
• lj_use_hbond_radii() : core::scoring::etable::Etable
• lj_use_hbond_radii_ : core::scoring::etable::Etable
• lj_use_lj_deriv_slope() : core::scoring::etable::Etable
• lj_use_lj_deriv_slope_ : core::scoring::etable::Etable
• lj_use_water_radii() : core::scoring::etable::Etable
• lj_use_water_radii_ : core::scoring::etable::Etable
• lj_val_at_minimum : core::scoring::etable::EtableParamsOnePair
• lj_water_dis() : core::scoring::etable::Etable
• lj_water_dis_ : core::scoring::etable::Etable
• lj_water_hdis() : core::scoring::etable::Etable
• lj_water_hdis_ : core::scoring::etable::Etable
• lj_wdepth() : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable
• lj_wdepth_ : core::chemical::AtomType , core::chemical::MMAtomType , core::scoring::etable::Etable
• ljatr() : core::scoring::etable::Etable
• ljatr_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• ljatr_cubic_poly_parameters : core::scoring::etable::EtableParamsOnePair
• ljatr_cubic_poly_xhi : core::scoring::etable::EtableParamsOnePair
• ljatr_cubic_poly_xlo : core::scoring::etable::EtableParamsOnePair
• ljatr_final_weight : core::scoring::etable::EtableParamsOnePair
• ljcorrection_factor_ : protocols::simple_moves::PeriodicBoxMover
• ljrep() : core::scoring::etable::Etable
• ljrep_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• ljrep_extra_repulsion : core::scoring::etable::EtableParamsOnePair
• ljrep_from_negcrossing : core::scoring::etable::EtableParamsOnePair
• ljrep_linear_ramp_d2_cutoff : core::scoring::etable::EtableParamsOnePair
• lk_ball() : core::scoring::lkball::LK_BallInvoker
• lk_ball_ : core::scoring::lkball::LK_BallInvoker
• LK_Ball_BB_BB_E_Invoker() : core::scoring::lkball::LK_Ball_BB_BB_E_Invoker
• LK_Ball_BB_SC_E_Invoker() : core::scoring::lkball::LK_Ball_BB_SC_E_Invoker
• LK_BALL_POSE_INFO : core::pose::datacache::CacheableDataType
• lk_ball_prefactor_ : core::scoring::lkball::LK_BallEnergy
• LK_Ball_RPE_Invoker() : core::scoring::lkball::LK_Ball_RPE_Invoker
• LK_Ball_SC_SC_E_Invoker() : core::scoring::lkball::LK_Ball_SC_SC_E_Invoker
• lk_ball_wtd_ : protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy
• LK_BallEnergy() : core::scoring::lkball::LK_BallEnergy
• LK_BallInvoker() : core::scoring::lkball::LK_BallInvoker
• lk_coeff1 : core::scoring::etable::EtableParamsOnePair
• lk_coeff2 : core::scoring::etable::EtableParamsOnePair
• lk_coeff_ : core::scoring::etable::Etable
• lk_dgfree() : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lk_dgfree_ : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lk_dgrefce() : core::scoring::etable::MembEtable
• lk_dgrefce_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy
• LK_fade_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• LK_hack() : core::scoring::methods::LK_hack
• lk_hack_weight_ : core::scoring::methods::LK_hack
• lk_inv_lambda2() : core::scoring::etable::Etable , core::scoring::magnesium::MgEnergy
• lk_inv_lambda2_ : core::scoring::etable::Etable
• lk_lambda() : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lk_lambda_ : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lk_min_dis2sigma() : core::scoring::etable::Etable
• lk_min_dis2sigma_ : core::scoring::etable::Etable
• lk_min_dis2sigma_value : core::scoring::etable::EtableParamsOnePair
• lk_min_dis2sigma_value_ : core::scoring::etable::Etable
• LK_PolarNonPolarEnergy() : core::scoring::methods::LK_PolarNonPolarEnergy
• lk_safe_max_dis2_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• LK_SigmoidalFunc() : core::scoring::methods::LK_SigmoidalFunc
• lk_solv_energy_and_deriv() : core::scoring::etable::Etable
• lk_volume() : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lk_volume_ : core::chemical::AtomType , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• lkb_ : core::scoring::lkball::lkbtrie::LKBTrieEvaluator
• lkb_clust_rad_ : protocols::simple_moves::ExplicitWaterMover
• lkb_max_dis() : core::scoring::lkball::LK_BallEnergy
• lkb_max_dis2() : core::scoring::lkball::LK_BallEnergy
• lkb_max_dis2_ : core::scoring::lkball::LK_BallEnergy
• lkb_max_dis_ : core::scoring::lkball::LK_BallEnergy
• lkb_overlap_dist_ : protocols::simple_moves::ExplicitWaterMover
• LKB_ResidueInfo() : core::scoring::lkball::LKB_ResidueInfo
• LKB_ResiduesInfo() : core::scoring::lkball::LKB_ResiduesInfo
• LKB_ResPairMinData() : core::scoring::lkball::LKB_ResPairMinData
• lkb_rotset_radius_ : protocols::simple_moves::ExplicitWaterMover
• LKBallDatabase() : core::scoring::lkball::LKBallDatabase
• LKBAtom() : core::scoring::lkball::lkbtrie::LKBAtom
• LKBe_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• lkbr_score : core::scoring::lkball::ScoredBridgingWater
• lkbr_uncpl_score : core::scoring::lkball::ScoredBridgingWater
• lkbridge_angle_widthscale_ : core::scoring::lkball::LK_BallEnergy
• lkbrinfo : protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer
• LKBTrieEvaluator() : core::scoring::lkball::lkbtrie::LKBTrieEvaluator
• LKHBondInfo() : core::scoring::hbonds::graph::LKHBondInfo
• ll : protocols::sic_dock::XfoxmScore
• lmax : core::scoring::fiber_diffraction::FiberDiffraction
• LMMinPCSDataRef() : protocols::nmr::pcs::PCSLigandTransformMover::LMMinPCSDataRef
• LnExpression() : protocols::pack_daemon::LnExpression
• Lnorm_ : protocols::hybridization::TMalign
• load() : protocols::antibody::CDRSetOptions , protocols::make_rot_lib::RotData
• load_ : protocols::antibody::CDRSetOptions
• load_APBS_potential() : core::scoring::PoissonBoltzmannPotential
• load_bin_params() : core::scoring::bin_transitions::BinTransitionCalculator , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• load_bin_params_from_file_contents() : core::scoring::bin_transitions::BinTransitionCalculator
• load_binary() : protocols::cluster::APCluster
• load_cdr_design_data() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_design_data_for_cdrs() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_pose() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_poses() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_sequences() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_sequences_for_cdr() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_sequences_for_cdr_cluster() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_sequences_for_cdr_length() : protocols::antibody::AntibodyDatabaseManager
• load_center_data() : protocols::antibody::clusters::CDRClusterMatcher
• load_chain_endings() : protocols::features::PoseConformationFeatures
• load_checkpoint_file() : protocols::monte_carlo::GenericSimulatedAnnealer
• load_conformation() : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• load_constraints() : protocols::abinitio::abscript::ConstraintPreparer
• LOAD_CSV : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• load_csv() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• load_custom_electrons() : core::scoring::epr_deer::EPRSpinLabel
• load_custom_rama_table() : core::scoring::Ramachandran
• load_data() : protocols::antibody::design::MutateFrameworkForCluster , protocols::ligand_docking::InterfaceBuilderLoader , protocols::ligand_docking::LigandAreaLoader , protocols::ligand_docking::MoveMapBuilderLoader , protocols::loops::loops_definers::LoopsDefinerLoader , protocols::parser::ConstraintGeneratorLoader , protocols::parser::DatabaseSessionLoader , protocols::parser::DataLoader , protocols::parser::FragSetLoader , protocols::parser::JumpSelectorLoader , protocols::parser::MonteCarloLoader , protocols::parser::MoveMapFactoryLoader , protocols::parser::PackerPaletteLoader , protocols::parser::ResidueSelectorLoader , protocols::parser::ResLvlTaskOperationLoader , protocols::parser::ScoreFunctionLoader , protocols::parser::SimpleMetricLoader , protocols::parser::TaskOperationLoader , protocols::qsar::scoring_grid::ScoringGridLoader
• load_data_from_db() : protocols::task_operations::ConservativeDesignOperation
• load_database() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• LOAD_DATABASE : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• load_database_table() : protocols::noesy_assign::MethylNameLibrary
• load_db() : protocols::loophash::LoopHashLibrary
• load_decoys() : protocols::jd2::archive::ArchiveBase
• load_density() : protocols::loop_grower::DensSkeleton
• load_dist_table() : protocols::noesy_assign::CovalentCompliance
• load_dotscore_bins() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• load_edge_file() : protocols::sewing::hashing::EdgeMapGenerator
• load_ensemble() : protocols::docking::DockingEnsemble
• load_exclude_pdb_component_ids() : core::chemical::GlobalResidueTypeSet
• load_ff() : core::scoring::saxs::FormFactorManager
• load_ff_from_db() : core::scoring::saxs::FormFactorManager
• load_filter_bin_params() : protocols::generalized_kinematic_closure::GeneralizedKIC
• load_fold_tree() : protocols::features::PoseConformationFeatures
• load_fragment_lookup() : protocols::indexed_structure_store::FragmentStoreManager
• load_fragment_store() : protocols::indexed_structure_store::FragmentStoreManager
• load_from_checkpoint() : protocols::splice::Splice , protocols::splice::SpliceIn
• load_grouped_fragment_store() : protocols::indexed_structure_store::FragmentStoreManager
• load_H1_ : protocols::antibody::Ab_TemplateInfo
• load_H2_ : protocols::antibody::Ab_TemplateInfo
• load_H3_ : protocols::antibody::Ab_TemplateInfo
• load_initial_conformers() : protocols::sewing::data_storage::SmartAssembly
• load_initial_pool() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• 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_job_definition_file() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• load_json_file() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• load_jumps() : protocols::features::PoseConformationFeatures
• load_kbp_data() : protocols::qsar::scoring_grid::ShapeGrid
• load_L1_ : protocols::antibody::Ab_TemplateInfo
• load_L2_ : protocols::antibody::Ab_TemplateInfo
• load_L3_ : protocols::antibody::Ab_TemplateInfo
• load_larmord_neighbor_atoms() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• load_larmord_parameters() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• load_larmord_reference_shifts() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• load_larmord_weights() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• load_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• load_matrix() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• load_menv_info() : core::scoring::membrane::MembraneData
• load_mergeddb() : protocols::loophash::LoopHashLibrary
• load_models() : protocols::ss_prediction::SS_predictor
• load_native() : protocols::rosetta_scripts::RosettaScriptsParser
• load_native_pose_from_disk() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• load_new_batch() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• load_new_set_of_user_flags() : protocols::rpc::JSON_RPC
• load_new_set_of_virtual_files() : protocols::rpc::JSON_RPC
• load_options_from_option_system() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• load_pdb_component() : core::chemical::GlobalResidueTypeSet
• load_pdb_id_from_file() : protocols::frag_picker::PdbIdChunkFilter
• load_pdb_segments_from_pose_comments() : protocols::splice::Splice , protocols::splice::SpliceOut
• load_penalty_table_from_file() : core::scoring::aa_repeat_energy::AARepeatEnergy
• load_perturber_bin_params() : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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 , protocols::simple_moves::AddChainMover
• load_pose_allocate_memory() : protocols::hybridization::TMalign
• load_pose_into_job() : protocols::jd2::JobInputter
• load_pssm() : protocols::analysis::simple_metrics::SequenceRecoveryMetric
• load_pssm_data() : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• load_reference_pool() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• load_residue_pdb_confidence() : protocols::features::PdbDataFeatures
• load_residue_pdb_identification() : protocols::features::PdbDataFeatures
• load_residue_types_from_sql_database() : core::chemical::GlobalResidueTypeSet
• load_sample_weight() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• load_score_tables() : core::scoring::dna::DNA_BasePotential , core::scoring::dna::DNA_EnvPairPotential
• load_sequence() : protocols::features::PoseConformationFeatures
• load_sheetlist_from_file() : protocols::denovo_design::components::SheetDB
• load_silent_file() : protocols::toolbox::KClusterData
• load_silent_files() : protocols::toolbox::KClusterData
• load_starting_poses_only_once_ : protocols::jd3::standard::StandardJobQueen
• load_state() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• load_store() : protocols::indexed_structure_store::DirStructureStoreBackend , protocols::indexed_structure_store::JSONStructureStoreBackend , protocols::indexed_structure_store::SilentStructureStoreBackend , protocols::indexed_structure_store::StructureStoreProvider
• load_string_data() : protocols::features::JobDataFeatures
• load_string_real_data() : protocols::features::JobDataFeatures
• load_string_string_data() : protocols::features::JobDataFeatures
• load_structure_loading_info() : protocols::antibody::AntibodyDatabaseManager
• load_structure_store() : protocols::indexed_structure_store::StructureStoreManager
• load_structures_from_cmdline_into_library() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• load_tag() : protocols::features::StructureFeatures
• load_templates_from_pdbs() : protocols::antibody::Ab_TemplateInfo
• load_trial_number_from_checkpoint() : protocols::monte_carlo::GenericMonteCarloMover
• load_user_flag_file() : protocols::rpc::JSON_RPC
• load_weights_file() : core::scoring::ScoreFunctionFactory
• loadable_structure_tags_ : protocols::antibody::AntibodyDatabaseManager
• LoadDensityMapMover() : protocols::cryst::LoadDensityMapMover
• loaded_ : protocols::fldsgn::potentials::SetAACompositionPotential
• loader_map() : protocols::parser::DataLoaderFactory
• loader_name() : protocols::ligand_docking::InterfaceBuilderLoader , protocols::ligand_docking::LigandAreaLoader , protocols::ligand_docking::MoveMapBuilderLoader , protocols::loops::loops_definers::LoopsDefinerLoader , protocols::parser::ConstraintGeneratorLoader , protocols::parser::DatabaseSessionLoader , protocols::parser::FragSetLoader , protocols::parser::JumpSelectorLoader , protocols::parser::MonteCarloLoader , protocols::parser::MoveMapFactoryLoader , protocols::parser::PackerPaletteLoader , protocols::parser::ResidueSelectorLoader , protocols::parser::ResLvlTaskOperationLoader , protocols::parser::ScoreFunctionLoader , protocols::parser::SimpleMetricLoader , protocols::parser::TaskOperationLoader , protocols::qsar::scoring_grid::ScoringGridLoader
• loader_type() : core::conformation::symmetry::SymmDataLoaderCreator , core::fragment::FragmentSetLoaderCreator , core::import_pose::PoseResourceLoaderCreator , protocols::loophash::LoopHashLibraryLoaderCreator , protocols::loops::LoopsFileLoaderCreator , protocols::surface_docking::SurfaceVectorLoaderCreator
• LoaderMap : protocols::parser::DataLoaderFactory
• loadFiberDiffractionData() : core::scoring::fiber_diffraction::FiberDiffraction
• loadGDB() : protocols::sparta::GDB
• loadPDB() : protocols::sparta::PDB
• loadPDB_Entry() : protocols::sparta::PDB
• loadPDBFromList() : protocols::cluster::calibur::PreloadedPDB
• LoadPDBMover() : protocols::simple_moves::LoadPDBMover
• loadSilentFile() : protocols::cluster::calibur::PreloadedPDB
• LoadUnboundRotMover() : protocols::simple_moves::LoadUnboundRotMover
• LoadVarSolDistSasaCalculatorMover() : protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover
• loadWeightBias3() : protocols::sparta::ANN
• loadWeights() : protocols::sparta::ANN
• local2global() : core::kinematics::Stub
• local_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• local_atom_id() : core::scoring::hbonds::graph::AtomInfo
• local_atom_id_ : core::scoring::hbonds::graph::AtomInfo
• local_atom_id_A() : core::scoring::hbonds::graph::HBondInfo
• local_atom_id_A_ : core::scoring::hbonds::graph::HBondInfo
• local_atom_id_D() : core::scoring::hbonds::graph::HBondInfo
• local_atom_id_D_ : core::scoring::hbonds::graph::HBondInfo
• local_atom_id_H() : core::scoring::hbonds::graph::HBondInfo
• local_atom_id_H_ : core::scoring::hbonds::graph::HBondInfo
• local_coord_matrix() : core::scoring::MultipoleElecResidueInfo
• local_coord_matrix_ : core::scoring::MultipoleElecResidueInfo
• local_coords : protocols::sewing::hashing::LigandCoordInfo
• local_distviol_cutoff_ : protocols::noesy_assign::PeakAssignmentParameters
• local_distviol_cutoff_buffer_ : protocols::noesy_assign::PeakAssignmentParameters
• local_distviol_global_buffer_ : protocols::noesy_assign::PeakAssignmentParameters
• local_distviol_global_factor_ : protocols::noesy_assign::PeakAssignmentParameters
• local_distviol_range_ : protocols::noesy_assign::PeakAssignmentParameters
• local_disulf_data_ : protocols::topology_broker::DisulfJumpClaimer
• local_ligands_ : protocols::sewing::data_storage::SmartAssembly
• local_options_ : protocols::rosetta_scripts::RosettaScriptsParser
• local_perturb() : protocols::hybridization::BackboneTorsionSampler
• local_pos1() : protocols::topology_broker::claims::JumpClaim
• local_pos1_ : protocols::topology_broker::claims::JumpClaim
• local_pos2() : protocols::topology_broker::claims::JumpClaim
• local_pos2_ : protocols::topology_broker::claims::JumpClaim
• local_pos_ : protocols::topology_broker::claims::BBClaim
• local_position() : protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::LegacyRootClaim
• local_position_ : protocols::topology_broker::claims::LegacyRootClaim
• local_positions() : protocols::environment::claims::EnvLabelSelector
• local_redock_only() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• local_redock_only_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• local_refine_ : protocols::symmetric_docking::SymDockProtocol
• local_result_id : protocols::jd3::dag_node_managers::ResultElements
• local_rotamer_id() : core::scoring::hbonds::graph::HBondNode
• local_rotation() : protocols::nmr::pcs::PCSLigandTransformMover
• 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_segments() : protocols::sewing::data_storage::SmartAssembly
• local_segments_ : protocols::sewing::data_storage::SmartAssembly
• local_to_pose() : protocols::denovo_design::components::Segment
• local_to_segment() : protocols::denovo_design::components::Segment
• local_variable() : protocols::pack_daemon::IterativeVectorExpression
• local_variable_map_ : protocols::pack_daemon::IterativeVectorExpression
• local_variables_ : protocols::pack_daemon::IterativeVectorExpression
• LocalBackboneMover() : protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• LocalCoordinateConstraint() : core::scoring::constraints::LocalCoordinateConstraint
• LocalCoordinateConstraintCreator() : core::scoring::constraints::LocalCoordinateConstraintCreator
• LocalInserter() : protocols::loophash::LocalInserter
• LocalInserter_SimpleMin() : protocols::loophash::LocalInserter_SimpleMin
• LocalPosition() : core::environment::LocalPosition , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvLabelSelector , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::rigid::UniformRigidBodyCM
• LocalPositions : protocols::environment::claims::EnvLabelSelector , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• LocalRelax() : protocols::relax::LocalRelax
• localstrandpair_penalty_ : core::scoring::SecondaryStructureWeights
• 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
• location_in_parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• lock_file : protocols::rna::setup::RNA_CSA_JobDistributor
• locked_ : protocols::simple_moves::RingConformationMover
• locked_res() : protocols::splice::Splice
• locked_res_ : protocols::splice::Splice
• locked_res_id() : protocols::splice::Splice
• locked_res_id_ : protocols::splice::Splice
• log() : protocols::frag_picker::QuotaDebug
• log_200_ : protocols::frag_picker::FragmentPicker
• log_25_ : protocols::frag_picker::FragmentPicker
• log_angles() : protocols::kinematic_closure::perturbers::LogFilePerturber
• log_conc_ : core::scoring::methods::IntermolEnergy
• log_lengths() : protocols::kinematic_closure::perturbers::LogFilePerturber
• log_odds : protocols::indexed_structure_store::SegmentSequenceProfileResult
• log_torsions() : protocols::kinematic_closure::perturbers::LogFilePerturber
• logarithm() : protocols::calc_taskop_filters::Operator
• logarithm_ : protocols::calc_taskop_filters::Operator
• LogFilePerturber() : protocols::kinematic_closure::perturbers::LogFilePerturber
• LoggedFragmentMover() : protocols::simple_moves::LoggedFragmentMover
• logger_ : protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopProtocol
• logic_ : core::select::residue_selector::ResiduePropertySelector
• LogicalSelector() : protocols::pose_selectors::LogicalSelector
• logs_ : protocols::simple_moves::LoggedFragmentMover
• LonePairElectronAffinity : core::chemical::gasteiger::GasteigerAtomTypeData
• LonePairElectronegativityMulliken : core::chemical::gasteiger::GasteigerAtomTypeData
• LonePairIonizationPotential : core::chemical::gasteiger::GasteigerAtomTypeData
• long_mutate_strategy() : protocols::rna::movers::RNAThreadAndMinimizeMover
• long_range_container() : core::scoring::Energies
• long_range_damping_length() : core::scoring::etable::Etable
• long_range_damping_length_ : core::scoring::etable::Etable
• long_range_energies_begin() : core::scoring::ScoreFunction
• long_range_energies_end() : core::scoring::ScoreFunction
• long_range_energy_containers_ : core::scoring::Energies
• long_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• long_range_interactions_exist_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• long_range_type() : core::energy_methods::DEEREnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , 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::methods::AspartimidePenaltyEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SASAEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::rna::RNA_StubCoordinateEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::TNA_SuiteEnergy , core::scoring::sym_e::symEnergy
• long_strategy_ : protocols::rna::movers::RNAThreadAndMinimizeMover
• long_string_rep() : protocols::contact_map::Contact
• long_strings_ : protocols::jd2::Job
• LongAxisRotationFreePeptideMover() : protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover
• LongestContinuousApolarSegmentFilter() : protocols::simple_filters::LongestContinuousApolarSegmentFilter
• LongestContinuousPolarSegmentFilter() : protocols::simple_filters::LongestContinuousPolarSegmentFilter
• longestSide() : core::grid::CartGrid< T >
• longRange_ : protocols::match::downstream::ScoringSecMatchRPE
• LongRangeTwoBodyEnergy() : core::scoring::methods::LongRangeTwoBodyEnergy , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::minimization_packing::GreenPacker
• look_for_cycles_recursively() : core::scoring::loop_graph::LoopGraph
• look_for_precompute_move() : protocols::stepwise::modeler::StepWiseModeler
• lookback() : protocols::indexed_structure_store::SSHashedFragmentStore
• lookback_account_for_dssp_inaccuracy() : protocols::indexed_structure_store::SSHashedFragmentStore
• lookback_stub() : protocols::indexed_structure_store::SSHashedFragmentStore
• lookback_uncached_stub() : protocols::indexed_structure_store::SSHashedFragmentStore
• lookup() : core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::metrics::StructureDependentCalculator , core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMLJLibrary , core::scoring::mm::MMTorsionLibrary , protocols::denovo_design::calculators::CavityCalculator , protocols::fldsgn::NcontactsCalculator , protocols::loophash::LoopHashMap , protocols::mean_field::EnergiesByTaskCalculator , protocols::pose_metric_calculators::CatPiCalculator , protocols::pose_metric_calculators::ChargeCalculator , protocols::pose_metric_calculators::ClashCountCalculator , protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::pose_metric_calculators::FragQualCalculator , protocols::pose_metric_calculators::HPatchCalculator , protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::pose_metric_calculators::NonlocalContactsCalculator , protocols::pose_metric_calculators::PackstatCalculator , protocols::pose_metric_calculators::PiPiCalculator , protocols::pose_metric_calculators::ResidueDecompositionCalculator , protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::pose_metric_calculators::SaltBridgeCalculator , protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator , protocols::pose_metric_calculators::SurfaceCalculator , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::simple_pose_metric_calculators::NumberHBondsCalculator , protocols::vardist_solaccess::VarSolDistSasaCalculator
• lookup_ : protocols::indexed_structure_store::FragmentLookup
• lookup_angle() : core::scoring::methods::IdealParametersDatabase
• lookup_angle_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_angle_params() : core::scoring::GenericBondedPotential
• lookup_bond_params() : core::scoring::GenericBondedPotential
• lookup_bondangle_buildideal() : core::scoring::methods::IdealParametersDatabase
• lookup_bondlength_buildideal() : core::scoring::methods::IdealParametersDatabase
• lookup_close_fragments() : protocols::indexed_structure_store::FragmentLookup
• lookup_close_fragments_v() : protocols::indexed_structure_store::FragmentLookup
• lookup_closest_fragment() : protocols::indexed_structure_store::FragmentLookup
• lookup_closest_fragment_subset() : protocols::indexed_structure_store::FragmentLookup
• lookup_closest_fragment_subset_v() : protocols::indexed_structure_store::FragmentLookup
• lookup_closest_fragment_v() : protocols::indexed_structure_store::FragmentLookup
• lookup_closest_pose_fragments() : protocols::indexed_structure_store::FragmentLookup
• lookup_config() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• lookup_config_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• lookup_context_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• lookup_fragment() : protocols::indexed_structure_store::FragmentLookup
• lookup_fragment_v() : protocols::indexed_structure_store::FragmentLookup
• lookup_improper() : core::scoring::methods::IdealParametersDatabase
• lookup_improper_params() : core::scoring::GenericBondedPotential
• lookup_length() : core::scoring::methods::IdealParametersDatabase
• lookup_length_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_mode_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• lookup_pose_fragments() : protocols::indexed_structure_store::FragmentLookup
• lookup_radius_ : protocols::sic_dock::LinkerScore
• lookup_result() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• lookup_result_index_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• lookup_results_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• lookup_stored_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• lookup_table_ : core::scoring::interface_::DDPlookup , core::scoring::interface_::DDPscore , core::scoring::nv::NVlookup , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore
• lookup_three_bond() : core::scoring::mm::MMLJLibrary
• lookup_tors_params() : core::scoring::GenericBondedPotential
• lookup_torsion_legacy() : core::scoring::methods::IdealParametersDatabase
• lookup_withkey() : protocols::loophash::LoopHashMap
• loop() : core::optimization::GA_Minimizer
• Loop() : core::scoring::loop_graph::Loop
• loop() : core::scoring::loop_graph::LoopCycle , protocols::anchored_design::AnchorMoversData
• LOOP : protocols::denovo_design::components::SegmentCounts
• Loop() : protocols::fldsgn::topology::Loop
• loop() : protocols::fldsgn::topology::SS_Info2
• Loop : protocols::forge::remodel::RemodelLoopMover , protocols::loops::Loop
• loop() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure
• loop_ : protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::kinematic_closure::BalancedKicMover , protocols::loop_grower::LoopGrower , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• loop_ang() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• loop_ang_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• loop_angle_conf_ : protocols::struct_fragment::StructFragmentMover
• loop_bb_min_allowed_dev_ : protocols::enzdes::EnzdesBaseProtocol
• loop_begin() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• loop_begin_ : protocols::antibody::H3RefineCCD , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::protein_interface_design::movers::PlaceOnLoop
• loop_centroid_relax() : protocols::antibody_legacy::CDRH3Modeler
• loop_close_six_d_potential_ : core::scoring::ScoringManager
• loop_close_use_6D_potential() : core::scoring::methods::EnergyMethodOptions
• loop_close_use_6D_potential_ : core::scoring::methods::EnergyMethodOptions
• loop_closer_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• loop_closure_energy() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• loop_closure_energy_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• loop_closure_movemap() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• loop_cluster_radius_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• loop_combine_rate_ : protocols::loops::loop_mover::IndependentLoopMover
• loop_cut() : protocols::protein_interface_design::movers::LoopLengthChange
• loop_cut_ : protocols::protein_interface_design::movers::LoopLengthChange
• loop_cutpoint_mode_ : protocols::relax::RepeatProteinRelax
• loop_cycles() : core::scoring::loop_graph::LoopGraph
• loop_cycles_ : core::scoring::loop_graph::LoopGraph
• loop_dbase_file_name() : protocols::splice::Splice
• loop_dbase_file_name_ : protocols::splice::Splice
• loop_def_ : protocols::cluster::ClusterPhilStyle_Loop
• loop_def_loader_ct_namer() : protocols::loops::loops_definers::LoopsDefinerLoader
• loop_definer_ : protocols::loops::FoldTreeFromLoops
• loop_definer_xml_schema_group_name() : protocols::loops::loops_definers::LoopsDefinerFactory
• loop_dih() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• loop_dih_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• loop_end() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::protein_interface_design::movers::LoopLengthChange
• loop_end_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody::H3RefineCCD , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::LoopRlxMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_end_pdb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_end_pdb_chain_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_ensemble_size_ : protocols::enzdes::EnzdesFlexBBProtocol
• loop_extension_ : protocols::jumping::JumpSelector
• loop_fa_relax() : protocols::antibody_legacy::CDRH3Modeler
• loop_file_ : protocols::anchored_design::AnchorMoversData
• loop_file_name() : protocols::loops::Loops
• loop_file_name_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• loop_filename_ : protocols::loops::Loops
• loop_fixed_cost() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• loop_fixed_cost_ : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator , core::scoring::loop_graph::LoopGraph
• loop_fixed_cost_total_ : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc
• loop_fraction() : core::fragment::SecondaryStructure
• loop_fraction_ : core::fragment::SecondaryStructure
• loop_frags() : protocols::topology_broker::LoopFragmentClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• loop_graph_ : core::scoring::loop_graph::LoopCloseEnergy
• loop_hash_library_ : protocols::sic_dock::LinkerScore
• loop_id() : protocols::fldsgn::topology::SS_Info2
• loop_id_ : protocols::fldsgn::topology::SS_Info2
• loop_index_of_residue() : protocols::loops::Loops
• loop_info() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• loop_info_from_subset() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• loop_length() : protocols::indel::IndelOptimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop
• loop_length_ : protocols::fldsgn::topology::HelixPairing , protocols::indel::IndelOptimizationMover
• loop_line_begin_token_ : protocols::loops::PoseNumberedLoopFileReader
• loop_list_ : protocols::loops::loops_definers::LoopsExplicitDefiner
• loop_melt_ : protocols::rbsegment_relax::AutoRBMover
• loop_min_mover_ : protocols::antibody::H3RefineCCD
• Loop_mm_tuple : protocols::anchored_design::AnchorMoversData
• Loop_mm_tuples : protocols::anchored_design::AnchorMoversData
• loop_model() : protocols::LoopRebuild
• loop_modeling() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• loop_mover() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• loop_mover_ : protocols::fldsgn::BluePrintBDR
• loop_mover_fold_tree_constant() : protocols::forge::components::VarLengthBuild
• loop_mover_fold_tree_constant_ : protocols::forge::components::VarLengthBuild
• loop_mover_instance() : protocols::forge::components::VarLengthBuild
• loop_mover_name_ : protocols::domain_assembly::AssembleLinkerMover
• loop_mover_str() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• loop_mover_str_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild
• loop_mover_that_owns_me_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• loop_name_ : protocols::antibody::H3RefineCCD
• loop_of_residue() : protocols::loops::Loops
• loop_pdb_source() : protocols::splice::Splice
• loop_pdb_source_ : protocols::splice::Splice
• loop_protocol_attlist() : protocols::loop_modeling::LoopProtocol
• loop_rebuild_filter : protocols::comparative_modeling::LoopRelaxThreadingMover
• loop_refine_inner_cycle_name_to_string_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• loop_relax_mover_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::loop_build::LoopBuildMover
• loop_repack_ : protocols::antibody::H3RefineCCD
• loop_residues() : protocols::recces::options::RECCES_Options
• loop_residues_ : protocols::recces::options::RECCES_Options , protocols::simple_task_operations::RestrictToInterface
• loop_rmsd : protocols::stepwise::modeler::rna::output_data_struct
• loop_rmsd_wrt_correct_minimized : protocols::stepwise::modeler::rna::output_data_struct
• loop_rmsd_wrt_minimized : protocols::stepwise::modeler::rna::output_data_struct
• loop_rsd_ : protocols::recces::scratch::ThermalSamplingMover
• loop_score_evaluator() : core::scoring::loop_graph::LoopGraph
• loop_scorefxn_centroid_ : protocols::antibody::AntibodyModelerProtocol
• loop_scorefxn_highres_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin
• loop_segments_ : protocols::relax::AtomCoordinateCstMover
• loop_seqid_threshold() : protocols::evolution::AlignmentAAFinder
• loop_seqid_threshold_ : protocols::evolution::AlignmentAAFinder
• loop_seqid_thresholds() : protocols::evolution::AlignmentGapInserter
• loop_seqid_thresholds_ : protocols::evolution::AlignmentGapInserter
• loop_size() : protocols::loops::Loops
• loop_size_ : protocols::antibody::H3RefineCCD , protocols::coupled_moves::CoupledMovesProtocol , protocols::loophash::LoopHashMap , protocols::simple_moves::CoupledMover
• loop_sizes() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• loop_sizes_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• loop_spec_ : protocols::loops::loops_definers::LoopsStringDefiner
• loop_start() : protocols::protein_interface_design::movers::LoopLengthChange
• loop_start_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::LoopRlxMover , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_start_pdb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_start_pdb_chain_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• loop_stop_ : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• loop_suites() : core::scoring::loop_graph::LoopGraph
• loop_visited_ : core::scoring::loop_graph::LoopGraph
• LoopAnalyzerFilter() : protocols::loops::filters::LoopAnalyzerFilter
• LoopAnalyzerMover() : protocols::analysis::LoopAnalyzerMover
• LoopAnchorFeatures() : protocols::features::LoopAnchorFeatures
• LoopBuilder() : protocols::loop_modeling::LoopBuilder
• LoopBuildMover() : protocols::loop_build::LoopBuildMover
• LoopCloseEnergy() : core::scoring::loop_graph::LoopCloseEnergy
• LoopClosePotentialEvaluator() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• LoopClosure() : protocols::loops::loop_closure::ccd::LoopClosure
• loopclosure_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• LoopCM() : protocols::loops::loop_mover::LoopCM
• LoopComparator() : protocols::loop_grower::LoopComparator
• LoopCycle() : core::scoring::loop_graph::LoopCycle
• loopdb_ : protocols::loophash::LoopHashMap
• loopdb_range() : protocols::loophash::LoopHashLibrary
• loopdb_range_ : protocols::loophash::LoopHashLibrary
• LoopFilter() : protocols::loop_modeling::utilities::LoopFilter
• LoopFinder() : protocols::protein_interface_design::movers::LoopFinder
• LoopFragmentClaimer() : protocols::topology_broker::LoopFragmentClaimer
• LoopFromFileData() : protocols::loops::LoopFromFileData
• loopgen_trials_ : protocols::enzdes::EnzdesFlexBBProtocol
• LoopGraph() : core::scoring::loop_graph::LoopGraph
• LoopGrower() : protocols::loop_grower::LoopGrower
• loophash_cycles() : protocols::forge::remodel::RemodelLoopMover
• loophash_cycles_ : protocols::forge::remodel::RemodelLoopMover
• loophash_scan_type_ : protocols::mpi_refinement::MPI_Refine_Master
• loophash_split_size_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• loophash_stage() : protocols::forge::remodel::RemodelLoopMover
• LoopHashDiversifier() : protocols::loophash::LoopHashDiversifier
• LoopHashLibrary() : protocols::loophash::LoopHashLibrary
• LoopHashLibraryLoader() : protocols::loophash::LoopHashLibraryLoader
• LoopHashMap() : protocols::loophash::LoopHashMap
• LoopHashMoverWrapper() : protocols::loophash::LoopHashMoverWrapper
• LoopHashPerturber() : protocols::loop_modeler::perturbers::LoopHashPerturber
• LoopHashRelaxProtocol() : protocols::loophash::LoopHashRelaxProtocol
• LoopHashSampler() : protocols::loophash::LoopHashSampler
• LoopJumpFoldCst() : protocols::abinitio::LoopJumpFoldCst
• loopLength_ : protocols::pose_length_moves::PossibleLoop
• LoopLengthChange() : protocols::protein_interface_design::movers::LoopLengthChange
• loopLengthRangeHigh_ : protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• loopLengthRangeLow_ : protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• LoopList : protocols::loops::Loops
• LoopModeler() : protocols::loop_modeler::LoopModeler
• LoopMover() : protocols::loop_modeling::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_QuickCCD() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• LoopMover_Perturb_QuickCCD_Moves() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
• 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_SlidingWindow() : protocols::loop_build::LoopMover_SlidingWindow
• LoopMoverFactory() : protocols::loops::LoopMoverFactory
• LoopMoverFromCommandLine() : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• LoopMoverGroup() : protocols::loop_modeling::utilities::LoopMoverGroup
• loopnumber_ : protocols::loop_grower::LoopGrower
• looporder_ : protocols::loop_grower::FragmentExtension
• LoopOver() : protocols::protein_interface_design::movers::LoopOver
• LoopPartialSolution() : protocols::loop_grower::LoopPartialSolution
• LoopPartialSolutionStore() : protocols::loop_grower::LoopPartialSolutionStore
• LoopProtocol() : protocols::loop_modeling::LoopProtocol
• LoopRebuild() : protocols::LoopRebuild
• LoopRefine() : protocols::LoopRefine
• LoopRefineInnerCycle() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• LoopRefineInnerCycleContainer() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• 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_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• loopres_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base2_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base2_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base2_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• loopres_base_atoms_ : protocols::forge::remodel::ResidueVicinityInfo
• loopresidues_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• LoopRlxMover() : protocols::antibody_legacy::LoopRlxMover
• LoopRmsdEvaluator() : protocols::simple_filters::LoopRmsdEvaluator
• loops() : core::scoring::loop_graph::LoopCycle , protocols::anchored_design::AnchorMoversData , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::ThreadingJob
• Loops : protocols::dna::DesignProteinBackboneAroundDNA
• loops() : protocols::fldsgn::topology::SS_Info2
• Loops : protocols::forge::components::VarLengthBuild
• loops() : protocols::forge::remodel::RemodelLoopMover
• Loops : protocols::forge::remodel::RemodelLoopMover
• loops : protocols::forge::remodel::RemodelWorkingSet
• LOOPS : protocols::loop_modeling::ToolboxKeys
• loops() : protocols::loops::FoldTreeFromLoops , protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_mover::LoopMover , protocols::loops::Loops
• Loops() : protocols::loops::Loops
• loops() : protocols::simple_task_operations::RestrictToLoops
• loops_ : core::scoring::loop_graph::LoopCycle , core::scoring::loop_graph::LoopGraph , protocols::abinitio::LoopJumpFoldCst , protocols::analysis::LoopAnalyzerMover , protocols::anchored_design::AnchorMoversData , protocols::denovo_design::movers::FoldTreeFromFoldGraphMover , protocols::fldsgn::topology::SS_Info2 , protocols::forge::remodel::RemodelLoopMover , protocols::grafting::AnchoredGraftMover , protocols::hybridization::CartesianSampler , protocols::loop_grower::LoopComparator , protocols::loop_modeling::utilities::TrajectoryLogger , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::FoldTreeFromLoops , protocols::loops::GuardedLoopsFromFile , protocols::loops::Loops , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_task_operations::RestrictToLoops
• loops_and_cen_mms_ : protocols::anchored_design::AnchorMoversData
• loops_and_fa_mms_ : protocols::anchored_design::AnchorMoversData
• loops_buns_polar_calc_name() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• loops_definer() : protocols::loops::GuardedLoopsFromFile
• loops_definer_ : protocols::loops::GuardedLoopsFromFile
• loops_file_data() : protocols::comparative_modeling::LoopRelaxMover , protocols::loops::GuardedLoopsFromFile
• loops_file_data_ : protocols::loops::GuardedLoopsFromFile , protocols::loops::LoopsFileData
• loops_flag_ : protocols::antibody_legacy::CDRH3Modeler
• loops_from_domain_ : core::scoring::loop_graph::LoopGraph
• loops_from_observer_cache_ : protocols::loops::loop_mover::LoopMover
• loops_in_ : protocols::abinitio::AbrelaxApplication
• Loops_in_ : protocols::LoopRebuild , protocols::LoopRefine
• loops_input_ : protocols::rbsegment_relax::RBSegmentRelax
• loops_operation_ : protocols::antibody::design::GeneralAntibodyModeler
• loops_to_build : protocols::forge::remodel::RemodelData
• LoopsDatabaseDefiner() : protocols::loops::loops_definers::LoopsDatabaseDefiner
• LoopsDatabaseDefinerCreator() : protocols::loops::loops_definers::LoopsDatabaseDefinerCreator
• LoopsDefinerCreator() : protocols::loops::loops_definers::LoopsDefinerCreator
• LoopsDefinerCreatorMap : protocols::loops::loops_definers::LoopsDefinerFactory
• 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
• LoopsFileIO() : protocols::loops::LoopsFileIO
• LoopsFileLoader() : protocols::loops::LoopsFileLoader
• loopsizes_ : protocols::sic_dock::LinkerScore
• loopsop_having_allcdrs_ : protocols::antibody::AntibodyInfo
• LoopsStringDefiner() : protocols::loops::loops_definers::LoopsStringDefiner
• LoopsStringDefinerCreator() : protocols::loops::loops_definers::LoopsStringDefinerCreator
• loopy_interface_ : protocols::simple_task_operations::RestrictToInterface
• loose_rep_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• lores() : protocols::stepwise::options::StepWiseBasicOptions
• lores_ : protocols::stepwise::options::StepWiseBasicOptions
• lores_monte_carlo() : protocols::rna::denovo::movers::RNA_Relaxer
• lores_pose() : protocols::jd3::chunk_library::ChunkLibraryJobResult , protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_pose_ : protocols::jd3::chunk_library::ChunkLibraryJobResult , protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_score_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• lores_score_early() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_score_early_ : protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_score_final() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_score_final_ : protocols::rna::denovo::RNA_FragmentMonteCarlo
• lores_scorefxn() : core::import_pose::options::RNA_DeNovoProtocolOptions
• lores_scorefxn_ : core::import_pose::options::RNA_DeNovoProtocolOptions , protocols::protein_interface_design::movers::PlaceOnLoop
• lores_silent_file_ : protocols::rna::denovo::RNA_DeNovoProtocol
• low : protocols::cryst::CheshireCell , protocols::make_rot_lib::TorsionRange
• low_ : core::scoring::func::SmoothStepFunc
• low_color_ : protocols::qsar::RenderGridsToKinemage
• low_EMap_ : core::scoring::constraints::AmbiguousConstraint
• low_energy : protocols::boinc::BoincSharedMemory
• low_energy_conformers_are_known() : core::chemical::rings::RingConformerSet
• low_energy_pose_buf : protocols::boinc::BoincSharedMemory
• low_energy_pose_exists : protocols::boinc::BoincSharedMemory
• low_energy_update_cnt : protocols::boinc::BoincSharedMemory
• low_memory_mode() : protocols::generalized_kinematic_closure::GeneralizedKIC
• low_memory_mode_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• low_poly_ : core::scoring::etable::coulomb::Coulomb
• low_poly_end2_ : core::scoring::etable::coulomb::Coulomb
• low_poly_end_ : core::scoring::etable::coulomb::Coulomb
• low_poly_start2_ : core::scoring::etable::coulomb::Coulomb
• low_poly_start_ : core::scoring::etable::coulomb::Coulomb
• low_res() : protocols::floppy_tail::FloppyTailMover
• low_res_kink_constraint() : protocols::antibody::snugdock::SnugDockProtocol
• low_res_kink_constraint_ : protocols::antibody::snugdock::SnugDockProtocol
• low_res_protocol_only_ : protocols::docking::DockingProtocol , protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• low_res_refine_cdr_h2_ : protocols::antibody::snugdock::SnugDockProtocol
• low_res_refine_cdr_h3_ : protocols::antibody::snugdock::SnugDockProtocol
• low_ring_conformers() : core::chemical::MutableResidueType , core::chemical::ResidueType
• low_ring_conformers_ : core::chemical::MutableResidueType , core::chemical::ResidueType
• low_temp() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• low_temp_ : core::pack::task::PackerTask_ , protocols::task_operations::ModifyAnnealer
• low_temp_annealing_ : core::pack::annealer::SimAnnealerBase
• lowAddRes_ : protocols::pose_length_moves::InsertResMover
• lower : core::chemical::sdf::BondData , protocols::denovo_design::components::Segment , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter , protocols::task_operations::SelectByDeltaScoreOperation
• lower_ : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter , protocols::task_operations::SelectByDeltaScoreOperation
• lower_anchor() : protocols::denovo_design::components::StructureData
• lower_anchor_connID_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• lower_angle_ : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• lower_bound() : core::scoring::epr_deer::DEERDistanceDistribution , core::scoring::PoissonBoltzmannPotential , protocols::qsar::ColorGradient , protocols::simple_filters::DisulfideEntropyFilter
• lower_bound_ : core::scoring::epr_deer::DEERDistanceDistribution , core::scoring::nv::NVscore , core::scoring::PoissonBoltzmannPotential , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::RangeFilter
• lower_bound_dy_ : core::scoring::func::SplineFunc
• lower_bound_squared_ : core::scoring::nv::NVscore
• lower_bound_x_ : core::scoring::func::SplineFunc
• lower_bound_y_ : core::scoring::func::SplineFunc
• lower_chain() : protocols::task_operations::RestrictToInterfaceVectorOperation
• lower_chains_ : protocols::task_operations::RestrictToInterfaceVectorOperation
• lower_connect() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• lower_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• lower_connect_angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• lower_connect_atom() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• lower_connect_id() : core::chemical::MutableResidueType , core::chemical::ResidueType
• lower_connect_id_ : core::chemical::MutableResidueType , core::chemical::ResidueType
• lower_dihedrals() : protocols::denovo_design::components::Segment
• lower_dihedrals_ : protocols::denovo_design::components::Segment
• lower_fasta_ : protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• lower_left_coords_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• lower_local() : protocols::denovo_design::components::Segment
• lower_neighbor_id() : 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
• lower_numbered_node_symmetry_copy_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• lower_numbered_node_symmetry_copy_index_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• lower_padding() : protocols::denovo_design::components::Segment
• lower_phi() : protocols::denovo_design::components::ResidueDihedrals
• lower_phi_ : protocols::denovo_design::components::ResidueDihedrals
• lower_pose_ : protocols::loop_grower::LoopPartialSolutionStore
• lower_quartile_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• lower_range_dof_jumps1_ : core::conformation::symmetry::SymDof
• lower_range_dof_jumps2_ : core::conformation::symmetry::SymDof
• lower_residue() : protocols::denovo_design::components::Segment
• lower_residue_ : protocols::denovo_design::components::Segment
• lower_residues_ : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• lower_segment() : protocols::denovo_design::components::Segment
• lower_segment_ : protocols::denovo_design::components::Segment
• lower_terminus_is_occupied_according_to_link_map() : core::io::pose_from_sfr::PoseFromSFRBuilder
• lower_threshold() : protocols::matdes::InterfacePackingFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter
• lower_threshold_ : core::select::residue_selector::ScoreTermValueBasedSelector , protocols::enzdes::LigDSasaFilter , protocols::matdes::InterfacePackingFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• lower_trim_ : protocols::filters::ReplicateFilter
• lowers1_ : protocols::sic_dock::LinkerScore
• lowers2_ : protocols::sic_dock::LinkerScore
• lowest_acceptable_value_ : protocols::frag_picker::scores::FragmentScoringMethod
• lowest_ranked_native_ : protocols::loop_grower::LoopGrower
• lowest_ring_conformer() : core::chemical::MutableResidueType
• lowest_ring_conformer_ : core::chemical::MutableResidueType , core::chemical::ResidueType
• lowest_ring_conformers() : core::chemical::ResidueType
• lowest_score() : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo
• lowest_score_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo , protocols::sewing::movers::AssemblyMover
• lowest_score_pose() : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::rational_mc::RationalMonteCarlo
• lowest_score_pose_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo
• lowest_scores() : protocols::monte_carlo::GenericMonteCarloMover
• lowest_scores_ : protocols::monte_carlo::GenericMonteCarloMover
• lowest_scoring_assembly_ : protocols::sewing::movers::AssemblyMover
• lowres_ : protocols::docking::membrane::MPDockingMover
• lowres_abinitio : protocols::flexpep_docking::FlexPepDockingFlags
• lowres_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• lowres_filter_ : protocols::docking::ConformerSwitchMover , protocols::docking::DockingProtocol
• lowres_inner_cycle() : protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble
• lowres_inner_cycles_ : protocols::docking::DockingProtocol
• lowres_outer_cycles_ : protocols::docking::DockingProtocol
• lowres_preoptimize : protocols::flexpep_docking::FlexPepDockingFlags
• lowres_reference_energies_ : protocols::docking::DockingEnsemble
• lowres_reference_energy() : protocols::docking::DockingEnsemble
• lowres_scorefxn_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler , protocols::docking::membrane::MPDockingMover , protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer , protocols::ub_e2c::ubi_e2c_modeler
• lowstrand_ : protocols::fldsgn::potentials::sspot::SSPairPotential
• lowtemp : core::pack::annealer::SimAnnealerBase
• lowtemp_ : core::pack::annealer::SimAnnealerBase
• lowval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• lowval_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• lr() : core::conformation::PseudoBond
• LR_2B_MethodIterator : core::scoring::ScoreFunction
• LR_2B_Methods : core::scoring::ScoreFunction
• lr_2b_methods_ : core::scoring::ScoreFunction
• lr_As_ : core::scoring::CenHBPotential
• LR_AtomData() : core::scoring::packstat::LR_AtomData
• lr_conn_ : core::conformation::PseudoBond
• lr_conn_id() : core::conformation::PseudoBond
• lr_dist_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• lr_energies_exist_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• LR_MP_AtomData() : core::scoring::packstat::LR_MP_AtomData
• lr_mus_ : core::scoring::CenHBPotential
• lr_prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• lr_resconnid() : core::conformation::PseudoBond
• lr_sigmas_ : core::scoring::CenHBPotential
• lr_stack_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• LRmsdFilter() : protocols::protein_interface_design::filters::LRmsdFilter
• LSMSearchPattern() : protocols::hotspot_hashing::LSMSearchPattern
• lsmspec_ : protocols::hotspot_hashing::LSMSearchPattern
• lstart() : protocols::forge::remodel::ResidueVicinityRCG
• lstart_ : protocols::forge::remodel::ResidueVicinityRCG
• lstop() : protocols::forge::remodel::ResidueVicinityRCG
• lstop_ : protocols::forge::remodel::ResidueVicinityRCG
• lt_dih() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• lt_dih_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• LW_orientation() : core::pose::rna::BasePair
• LW_orientation_ : core::pose::rna::BasePair
• lX_ : core::grid::CartGrid< T >
• lY_ : core::grid::CartGrid< T >
• lZ_ : core::grid::CartGrid< T >