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

- l -

• L1_t_name_ : protocols::antibody::Ab_TemplateInfo
• L1_t_pose_ : protocols::antibody::Ab_TemplateInfo
• 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_chain_ : protocols::antibody::AntibodyInfo
• L_mult_ : protocols::frag_picker::scores::TalosSSSimilarity
• label() : protocols::abinitio::abscript::StructPerturberCM , protocols::environment::claims::JumpClaim , protocols::environment::claims::JumpElement , protocols::environment::claims::ResidueElement , 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_ : protocols::abinitio::abscript::StructPerturberCM , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::JumpClaim , 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::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_resonance() : protocols::noesy_assign::PeakAssignment
• label_resonance_id() : protocols::noesy_assign::PeakAssignment
• label_tolerance() : protocols::noesy_assign::CrossPeakInfo
• label_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• LabelResonance() : protocols::noesy_assign::LabelResonance
• LAMBEGO_IO() : protocols::frag_picker::LAMBEGO_IO
• LAMBEGO_Similarity() : protocols::frag_picker::scores::LAMBEGO_Similarity
• large_cluster_pose_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• large_cutoff_square_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• LargeFragWeight() : protocols::topology_broker::weights::LargeFragWeight
• 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
• 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_pose() : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• last_accepted_pose_ : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• last_accepted_pose_buf : protocols::boinc::BoincSharedMemory
• last_accepted_pose_exists : protocols::boinc::BoincSharedMemory
• last_accepted_score() : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• last_accepted_score_ : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• last_accepted_scores() : protocols::simple_moves::GenericMonteCarloMover
• last_accepted_scores_ : protocols::simple_moves::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_batch_id() : protocols::jd2::archive::BaseArchiveManager
• LAST_CENTROID_START : protocols::abinitio::IterativeBase
• 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_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_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_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_inner_score_delta_over_temperature() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• last_input_pose_ : protocols::forge::remodel::RemodelMover
• last_input_tag_ : protocols::jd2::JD2ResourceManagerJobInputter
• last_inserted_frag_begin() : protocols::frags::TorsionFragmentMover
• last_inserted_frag_begin_ : protocols::frags::TorsionFragmentMover
• last_key() : protocols::noesy_assign::ResonanceList
• 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_nchi() : protocols::simple_moves::sidechain_moves::SidechainMover
• last_nchi_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• 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() : protocols::kinematic_closure::ClosureProblem , protocols::topology_broker::claims::DofClaim
• last_residue_index_ : protocols::frag_picker::PhiPsiTalosIO
• last_run_successful() : protocols::generalized_kinematic_closure::GeneralizedKIC
• last_run_successful_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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
• 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_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_tag_ : protocols::qsar::scoring_grid::GridManager
• last_temp_ : protocols::antibody::H3RefineCCD
• last_tested_scores() : protocols::simple_moves::GenericMonteCarloMover
• last_tested_scores_ : protocols::simple_moves::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
• lastRes : protocols::sparta::Sparta::SpartaLib
• late_factory_ : protocols::anchored_design::AnchorMoversData
• launch_atom() : protocols::match::downstream::ClassicMatchAlgorithm
• launch_points_ : protocols::match::downstream::ClassicMatchAlgorithm
• Layer : protocols::flxbb::LayerDesignOperation
• layer() : protocols::toolbox::SelectResiduesByLayer
• layer_mode_ : protocols::flxbb::FlxbbDesign
• layer_nc_residues_ : protocols::flxbb::LayerDesignOperation
• layer_operation_ : protocols::flxbb::LayerDesignOperation
• layer_residues_ : protocols::flxbb::LayerDesignOperation
• layer_specification_ : protocols::flxbb::LayerDesignOperation
• LayerDefinition : protocols::flxbb::LayerDesignOperation
• LayerDefinitions : protocols::flxbb::LayerDesignOperation
• LayerDesignOperation() : protocols::flxbb::LayerDesignOperation
• LayerNCDefinitions : protocols::flxbb::LayerDesignOperation
• LayerNCResidues : protocols::flxbb::LayerDesignOperation
• LayerOperationType : protocols::flxbb::LayerDesignOperation
• LayerResidues : protocols::flxbb::LayerDesignOperation
• LayerSpecificationType : protocols::flxbb::LayerDesignOperation
• lazy_ : protocols::toolbox::task_operations::SetIGTypeOperation
• LazySilentFileJobInputter() : protocols::jd2::LazySilentFileJobInputter
• LazySortedVector1() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• lbuf : protocols::sparta::Sparta::SpartaLib
• LeastNativeLike9merFilter() : protocols::simple_filters::LeastNativeLike9merFilter
• leave_as_is() : protocols::toolbox::task_operations::DatabaseThread
• leave_as_is_ : protocols::toolbox::task_operations::DatabaseThread
• leave_coord_csts_after_placement_ : protocols::protein_interface_design::movers::PlaceStubMover
• left : protocols::forge::build::Interval
• 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_skip : protocols::forge::build::CountFromLeft
• left_stub_atoms() : protocols::forge::build::ConnectRight
• left_stub_atoms_ : protocols::forge::build::ConnectRight
• legacy_dof_allow_move_ : protocols::simple_moves::ConstrainToIdealMover
• legacy_mode_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• LegacyKicSampler() : protocols::loop_modeling::samplers::LegacyKicSampler
• LegacyRootClaim() : protocols::topology_broker::claims::LegacyRootClaim
• len_ : protocols::frag_picker::scores::JCoupling
• length : protocols::antibody::clusters::ClusterData , protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , 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_ : protocols::antibody::clusters::CDRCluster , protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol , protocols::viewer::ConformationViewer
• length_event_link_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• length_normalized_distance() : protocols::antibody::clusters::CDRCluster
• length_obs_link() : protocols::forge::build::BuildInstruction
• length_obs_link_ : protocols::forge::build::BuildInstruction
• length_type() : protocols::antibody::CDRSetOptions
• length_types_ : protocols::antibody::CDRSetOptions
• 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
• 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_ : 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_radii_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• level_radius() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• level_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• lfr_ : protocols::antibody_legacy::Antibody
• Lfr_t_name_ : protocols::antibody::Ab_TemplateInfo
• LH_dock_jump_ : protocols::antibody::RefineBetaBarrel
• 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
• library() : protocols::frags::FragLib , protocols::motifs::MotifLibrary
• library_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , 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_map_ : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• 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_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_packer_weight_ : protocols::enzdes::ProteinLigandInterfaceUpweighter
• 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_superposition_file_read_ : protocols::enzdes::EnzdesBaseProtocol
• LIGAND : protocols::pockets::ComparisonGrid
• ligand_ : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid , protocols::topology_broker::MetalloClaimer
• ligand_areas_ : protocols::ligand_docking::InterfaceBuilder
• ligand_atom : protocols::ligand_docking::rdf::AtomPairData
• 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_name_ : protocols::metal_interface::MetalSiteResidue
• 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
• ligand_crystal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_discrim_data_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_indices_ : protocols::comparative_modeling::StealLigandMover
• Ligand_info() : protocols::ligand_docking::Ligand_info
• ligand_jump_id_ : protocols::simple_moves::CoupledMover
• ligand_native_decoy_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• ligand_natoms_elstscalc_ : protocols::pockets::DarcParticleSwarmMinimizer
• ligand_natoms_shapecalc_ : protocols::pockets::DarcParticleSwarmMinimizer
• 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_resno() : protocols::enzdes::EnzdesConstraintReporter
• ligand_resnum_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• ligand_restype_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ligand_seqpos_ : protocols::enzdes::EnzdesConstraintReporter , protocols::membrane::AddMPLigandMover
• ligand_shear_moves_ : protocols::ligand_docking::LigandDockProtocol
• 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_weight_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• LigandArea() : protocols::ligand_docking::LigandArea
• LigandAreaLoader() : protocols::ligand_docking::LigandAreaLoader
• LigandBaseProtocol() : protocols::ligand_docking::LigandBaseProtocol
• LigandConformer() : protocols::toolbox::match_enzdes_util::LigandConformer
• LigandConformerBuilder() : protocols::match::downstream::LigandConformerBuilder
• LigandDesign() : protocols::ligand_docking::LigandDesign
• LigandDockMain() : protocols::ligand_docking::LigandDockMain
• LigandDockProtocol() : protocols::ligand_docking::LigandDockProtocol
• LigandMinusProteinPlus : protocols::ligand_docking::rdf::RDFBase
• LigandMotifSearch() : protocols::motifs::LigandMotifSearch
• LigandPlusProteinMinus : protocols::ligand_docking::rdf::RDFBase
• LigandPropertyScore() : protocols::qsar::scoring_grid::LigandPropertyScore
• LigBurialFilter() : protocols::enzdes::LigBurialFilter
• LigDSasaFilter() : protocols::enzdes::LigDSasaFilter
• 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
• LigInterfaceEnergyFilter() : protocols::enzdes::LigInterfaceEnergyFilter
• ligres_ : protocols::match::MatcherMover
• limit() : protocols::simple_moves::symmetry::SetupNCSMover , protocols::wum::SilentStructStore
• limit_ : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::simple_moves::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_dlig_mem_usage_ : protocols::pack_daemon::DaemonSet
• limit_groups() : protocols::cluster::ClusterBase
• limit_groupsize() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• limit_library() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• limit_per_rotamer_combo_ : protocols::match::output::LimitHitsPerRotamerFilter
• limit_to_positions() : protocols::antibody::design::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::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• LimitAromaChi2Operation() : protocols::toolbox::task_operations::LimitAromaChi2Operation
• LimitHitsPerRotamerFilter() : protocols::match::output::LimitHitsPerRotamerFilter
• lin_mem_ : protocols::toolbox::task_operations::SetIGTypeOperation
• line_color_ : protocols::match::Bool3DGridKinemageWriter
• linear_bonded_potential_ : protocols::features::ProteinBondGeometryFeatures
• linear_chainbreak_weight_ : protocols::farna::RNA_DeNovoProtocol
• LineBuffer : protocols::jd2::SingleFileBuffer
• linecount_offset_ : protocols::loops::JSONFormattedLoopsFileReader , protocols::loops::PoseNumberedLoopFileReader
• linenum() : protocols::loops::ResidueIndexDescriptionFromFile
• linenum_ : protocols::loops::ResidueIndexDescriptionFromFile
• Link : protocols::forge::build::BuildInstruction
• link_ : protocols::moves::PyMolMover
• link_cache() : protocols::wum2::WorkUnit
• linker_end_ : protocols::abinitio::DomainAssembly
• linker_start_ : protocols::abinitio::DomainAssembly
• LinkerScore() : protocols::sic_dock::LinkerScore
• linkExemplarsThroughSolvent() : protocols::pockets::PocketGrid
• LinkResidues() : protocols::toolbox::task_operations::LinkResidues
• linmin_only_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• LipoFileLoader() : protocols::membrane::io::LipoFileLoader
• LipoFileOptions() : protocols::membrane::io::LipoFileOptions
• lipsfile() : protocols::membrane::AddMembraneMover
• lipsfile_ : protocols::membrane::AddMembraneMover
• list2id() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• list_ : protocols::abinitio::abscript::ResidueChunkSelection , protocols::analysis::PeptideDeriverOutputterContainer
• list_pools() : protocols::frag_picker::quota::QuotaCollector
• listen_for_rank() : protocols::canonical_sampling::AsyncMPITemperingBase
• listen_wu_sendrecv() : protocols::wum2::EndPoint
• lj_cutoff() : protocols::match::output::MatchCollisionFilter
• lj_cutoff_ : protocols::match::output::MatchCollisionFilter
• lj_ramp_cycles : protocols::relax::ClassicRelax
• lj_ramp_inner_cycles : protocols::relax::ClassicRelax
• lj_spline_ : protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::VdwGrid
• ll : protocols::sic_dock::XfoxmScore
• LnExpression() : protocols::pack_daemon::LnExpression
• Lnorm : protocols::hybridization::TMalign
• load() : protocols::antibody::CDRSetOptions , protocols::make_rot_lib::RotData
• load_ : protocols::antibody::CDRSetOptions
• load_bin_params() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• load_binary() : protocols::cluster::APCluster
• load_cdr_design_data() : protocols::antibody::AntibodyDatabaseManager
• load_cdr_poses() : protocols::antibody::AntibodyDatabaseManager
• load_center_data() : protocols::antibody::clusters::CDRClusterMatcher
• load_chain_endings() : protocols::features::PoseConformationFeatures
• load_conformation() : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• load_constraints() : protocols::abinitio::abscript::ConstraintPreparer
• load_data() : protocols::jd2::parser::DataLoader , protocols::jd2::parser::FragSetLoader , protocols::jd2::parser::MonteCarloLoader , protocols::jd2::parser::ResidueSelectorLoader , protocols::jd2::parser::ScoreFunctionLoader , protocols::jd2::parser::TaskOperationLoader , protocols::ligand_docking::InterfaceBuilderLoader , protocols::ligand_docking::LigandAreaLoader , protocols::ligand_docking::MoveMapBuilderLoader , protocols::loops::loops_definers::LoopsDefinerLoader , protocols::qsar::scoring_grid::ScoringGridLoader
• load_data_from_db() : protocols::antibody::design::ConservativeDesignOperation
• load_data_from_file() : protocols::antibody::design::ConservativeDesignOperation
• load_database_table() : protocols::noesy_assign::MethylNameLibrary
• load_db() : protocols::loophash::LoopHashLibrary
• load_decoys() : protocols::jd2::archive::ArchiveBase
• load_dist_table() : protocols::noesy_assign::CovalentCompliance
• load_dotscore_bins() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• load_ensemble() : protocols::docking::DockingEnsemble
• load_filter_bin_params() : protocols::generalized_kinematic_closure::GeneralizedKIC
• load_fold_tree() : protocols::features::PoseConformationFeatures
• load_H1_ : protocols::antibody::Ab_TemplateInfo
• load_H2_ : protocols::antibody::Ab_TemplateInfo
• load_H3_ : protocols::antibody::Ab_TemplateInfo
• load_into_pose() : protocols::features::FeaturesReporter , protocols::features::JobDataFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures , protocols::features::StructureFeatures
• load_jumps() : protocols::features::PoseConformationFeatures
• load_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_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• load_mergeddb() : protocols::loophash::LoopHashLibrary
• load_models() : protocols::ss_prediction::SS_predictor
• 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_id_from_file() : protocols::frag_picker::PdbIdChunkFilter
• load_perturber_bin_params() : protocols::generalized_kinematic_closure::GeneralizedKIC
• load_phi_theta_bins() : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• load_pool() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• load_pose() : protocols::features::ProteinSilentReport , protocols::optimize_weights::IterativeOptEDriver
• load_pose_allocate_memory() : protocols::hybridization::TMalign
• load_pose_into_job() : protocols::jd2::JobInputter
• load_pssm_data() : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• load_residue_pdb_confidence() : protocols::features::PdbDataFeatures
• load_residue_pdb_identification() : protocols::features::PdbDataFeatures
• load_sample_weight() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• load_sequence() : protocols::features::PoseConformationFeatures
• load_silent_file() : protocols::toolbox::KClusterData
• load_silent_files() : protocols::toolbox::KClusterData
• load_state() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• load_string_data() : protocols::features::JobDataFeatures
• load_string_real_data() : protocols::features::JobDataFeatures
• load_string_string_data() : protocols::features::JobDataFeatures
• load_structures_from_cmdline_into_library() : protocols::loophash::MPI_LoopHashRefine , 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::simple_moves::GenericMonteCarloMover
• load_user_flag_file() : protocols::rpc::JSON_RPC
• LoadDensityMapMover() : protocols::cryst::LoadDensityMapMover
• loaded_ : protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies
• loader_type() : protocols::loophash::LoopHashLibraryLoaderCreator , protocols::loops::LoopsFileLoaderCreator , protocols::membrane::io::LipoFileLoaderCreator , protocols::membrane::io::SpanFileLoaderCreator , protocols::surface_docking::SurfaceVectorLoaderCreator
• LoaderMap : protocols::jd2::parser::DataLoaderFactory
• loadGDB() : protocols::sparta::GDB
• loadPDB() : protocols::sparta::PDB
• loadPDB_Entry() : protocols::sparta::PDB
• LoadPDBMover() : protocols::simple_moves::LoadPDBMover
• LoadUnboundRotMover() : protocols::simple_moves::LoadUnboundRotMover
• loadWeightBias3() : protocols::sparta::ANN
• loadWeights() : protocols::sparta::ANN
• local_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• 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_minimize_at_chainbreaks() : protocols::farna::RNA_LoopCloser
• 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_rna_low_resolution_potential_ : protocols::farna::RNA_DeNovoProtocol
• local_rotid_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_rotid_for_rotamer_on_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_rotid_start_for_moltenres_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• local_variable() : protocols::pack_daemon::IterativeVectorExpression
• local_variable_map_ : protocols::pack_daemon::IterativeVectorExpression
• local_variables_ : protocols::pack_daemon::IterativeVectorExpression
• LocalInserter() : protocols::loophash::LocalInserter
• LocalInserter_SimpleMin() : protocols::loophash::LocalInserter_SimpleMin
• 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
• locate_anchor_loop() : protocols::anchored_design::AnchorMoversData
• location_in_parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• location_in_parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• lock_file : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• locked_ : protocols::simple_moves::RingConformationMover
• 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_lengths() : protocols::kinematic_closure::perturbers::LogFilePerturber
• log_torsions() : protocols::kinematic_closure::perturbers::LogFilePerturber
• logarithm() : protocols::simple_filters::Operator
• logarithm_ : protocols::simple_filters::Operator
• LogFilePerturber() : protocols::kinematic_closure::perturbers::LogFilePerturber
• LoggedFragmentMover() : protocols::simple_moves::LoggedFragmentMover
• LogicalSelector() : protocols::pose_selectors::LogicalSelector
• logs_ : protocols::simple_moves::LoggedFragmentMover
• long_string_rep() : protocols::contact_map::Contact
• long_strings_ : protocols::jd2::Job
• longRange_ : protocols::match::downstream::ScoringSecMatchRPE
• LongRangeTwoBodyEnergy : protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::simple_moves::GreenPacker
• look_for_precompute_move() : protocols::stepwise::modeler::StepWiseModeler
• lookbackMaxRmsd() : protocols::simple_moves::VallLookbackFragMover
• lookup() : protocols::fldsgn::NcontactsCalculator , protocols::loophash::LoopHashMap , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• lookup_mode_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• lookup_radius_ : protocols::sic_dock::LinkerScore
• lookup_result() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• lookup_stored_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• lookup_withkey() : protocols::loophash::LoopHashMap
• loop() : protocols::anchored_design::AnchorMoversData
• 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::kinematic_closure::BalancedKicMover , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , 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_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::RefineOneCDRLoopCentroid , protocols::antibody_legacy::CDRH3Modeler
• loop_closer_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• 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_def_ : protocols::cluster::ClusterPhilStyle_Loop
• 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_file_reader_ : protocols::loops::Loops
• loop_filename_ : protocols::loops::Loops
• loop_frags() : protocols::topology_broker::LoopFragmentClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• 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_length() : protocols::protein_interface_design::movers::PlaceOnLoop
• loop_length_ : protocols::fldsgn::topology::HelixPairing
• loop_line_begin_token_ : protocols::loops::PoseNumberedLoopFileReader
• loop_list_ : protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner
• 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_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_rebuild_filter : protocols::comparative_modeling::LoopRelaxThreadingMover
• loop_refine_inner_cycle_name_to_string_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• loop_refinement_method_ : protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol
• 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::toolbox::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_scorefxn_centroid_ : protocols::antibody::AntibodyModelerProtocol
• loop_scorefxn_highres_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin
• loop_segments_ : protocols::relax::AtomCoordinateCstMover
• loop_size() : protocols::loops::Loops
• loop_size_ : protocols::antibody::H3RefineCCD , protocols::loophash::LoopHashMap
• loop_sizes() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibraryOptions , protocols::loophash::LoopHashMoverWrapper
• loop_sizes_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibraryOptions , protocols::loophash::LoopHashMoverWrapper
• 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_str() : protocols::loops::FoldTreeFromLoops
• loop_str_ : protocols::loops::FoldTreeFromLoops
• LoopAnalyzerMover() : protocols::analysis::LoopAnalyzerMover
• LoopAnchorFeatures() : protocols::features::LoopAnchorFeatures
• LoopAnchorFeaturesCreator() : protocols::features::LoopAnchorFeaturesCreator
• LoopBuilder() : protocols::loop_modeling::LoopBuilder
• LoopBuildMover() : protocols::loop_build::LoopBuildMover
• LoopClosure() : protocols::loops::loop_closure::ccd::LoopClosure
• loopclosure_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• LoopCM() : protocols::loops::loop_mover::LoopCM
• 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
• 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
• LoopHashLibraryOptions() : protocols::loophash::LoopHashLibraryOptions
• LoopHashLibraryOptionsCreator() : protocols::loophash::LoopHashLibraryOptionsCreator
• LoopHashMap() : protocols::loophash::LoopHashMap
• LoopHashMoverWrapper() : protocols::loophash::LoopHashMoverWrapper
• LoopHashRelaxProtocol() : protocols::loophash::LoopHashRelaxProtocol
• LoopHashSampler() : protocols::loophash::LoopHashSampler
• LoopJumpFoldCst() : protocols::abinitio::LoopJumpFoldCst
• LoopLengthChange() : protocols::protein_interface_design::movers::LoopLengthChange
• LoopList : protocols::loops::Loops
• LoopModeler() : protocols::loop_modeling::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_KICCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator
• LoopMover_Perturb_QuickCCD() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• LoopMover_Perturb_QuickCCD_Moves() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
• LoopMover_Perturb_QuickCCD_MovesCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator
• LoopMover_Perturb_QuickCCDCreator() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator
• LoopMover_Refine_Backrub() : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub
• LoopMover_Refine_CCD() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• LoopMover_Refine_KIC() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• LoopMover_Refine_KICCreator() : protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator
• LoopMover_SlidingWindow() : protocols::loop_build::LoopMover_SlidingWindow
• LoopMover_SlidingWindowCreator() : protocols::loop_build::LoopMover_SlidingWindowCreator
• LoopMoverFactory() : protocols::loops::LoopMoverFactory
• LoopMoverFromCommandLine() : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• LoopMoverGroup() : protocols::loop_modeling::utilities::LoopMoverGroup
• LoopOver() : protocols::protein_interface_design::movers::LoopOver
• 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
• LoopRefineInnerCycleContainerCreator() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator
• LoopRefineInnerCycleFactory() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• LoopRelaxMover() : protocols::comparative_modeling::LoopRelaxMover
• LoopRelaxThreadingMover() : protocols::comparative_modeling::LoopRelaxThreadingMover
• LoopRemodel() : protocols::protein_interface_design::movers::LoopRemodel
• loopres_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• loopres_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() : 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 , protocols::forge::remodel::RemodelLoopMover
• loops() : protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelWorkingSet
• LOOPS : protocols::loop_modeling::ToolboxKeys
• loops() : protocols::loops::FoldTreeFromLoops , protocols::loops::GuardedLoopsFromFile , protocols::loops::loop_mover::LoopMover
• Loops() : protocols::loops::Loops
• loops() : protocols::loops::Loops
• Loops() : protocols::loops::Loops
• loops() : protocols::toolbox::task_operations::RestrictToLoops
• loops_ : protocols::abinitio::LoopJumpFoldCst , protocols::analysis::LoopAnalyzerMover , protocols::anchored_design::AnchorMoversData , protocols::fldsgn::topology::SS_Info2 , protocols::forge::remodel::RemodelLoopMover , protocols::grafting::AnchoredGraftMover , protocols::hybridization::CartesianSampler , 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::toolbox::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_file_data() : protocols::comparative_modeling::LoopRelaxMover , protocols::loops::GuardedLoopsFromFile
• loops_file_data_ : protocols::loops::GuardedLoopsFromFile , protocols::loops::LoopsFileData
• loops_flag_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• 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::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• 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
• LoopsFileFallbackConfiguration() : protocols::loops::LoopsFileFallbackConfiguration
• LoopsFileIO() : protocols::loops::LoopsFileIO
• LoopsFileLoader() : protocols::loops::LoopsFileLoader
• LoopsFileOptions() : protocols::loops::LoopsFileOptions
• loopsizes_ : protocols::sic_dock::LinkerScore
• loopsop_having_allcdrs_ : protocols::antibody::AntibodyInfo
• loopy_interface_ : protocols::toolbox::task_operations::RestrictToInterface
• loose_rep_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• lores_monte_carlo() : protocols::farna::RNA_Relaxer
• lores_score_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• lores_score_early_ : protocols::farna::RNA_DeNovoProtocol
• lores_score_final_ : protocols::farna::RNA_DeNovoProtocol
• lores_scorefxn_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::protein_interface_design::movers::PlaceOnLoop
• lores_silent_file_ : protocols::farna::RNA_DeNovoProtocol
• low : protocols::make_rot_lib::TorsionRange
• low_color_ : protocols::qsar::RenderGridsToKinemage
• low_energy : protocols::boinc::BoincSharedMemory
• low_energy_pose_buf : protocols::boinc::BoincSharedMemory
• low_energy_pose_exists : protocols::boinc::BoincSharedMemory
• low_energy_update_cnt : protocols::boinc::BoincSharedMemory
• low_res_protocol_only_ : protocols::docking::DockingProtocol , protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• low_res_refine_cdr_h2_ : protocols::antibody::SnugDockProtocol
• low_res_refine_cdr_h3_ : protocols::antibody::SnugDockProtocol
• low_temp_ : protocols::toolbox::task_operations::ModifyAnnealer
• lower() : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• lower_ : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• lower_anchor_connID_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• lower_angle_ : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• lower_bound : protocols::qsar::ColorGradient , protocols::simple_filters::DisulfideEntropyFilter
• lower_bound_ : protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::RangeFilter
• lower_chain() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• lower_chains_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• lower_quartile_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• lower_threshold() : protocols::matdes::InterfacePackingFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter
• lower_threshold_ : 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
• lower_value() : protocols::helical_bundle::PerturbBundleOptions
• lower_value_ : protocols::helical_bundle::PerturbBundleOptions
• lowers1_ : protocols::sic_dock::LinkerScore
• lowers2_ : protocols::sic_dock::LinkerScore
• lowest_acceptable_value_ : protocols::frag_picker::scores::FragmentScoringMethod
• lowest_score() : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• lowest_score_ : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• lowest_score_pose() : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• lowest_score_pose_ : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• lowest_scores() : protocols::simple_moves::GenericMonteCarloMover
• lowest_scores_ : protocols::simple_moves::GenericMonteCarloMover
• 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_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::ModelCDRH3 , protocols::antibody::RefineOneCDRLoopCentroid , 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
• lowval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• lowval_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• lr_energies_exist_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• 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