- l -

• l : basic::options::OptionKeys::in::file
• l1 : test::G201_Module_Structure
• l1_template : basic::options::OptionKeys::antibody
• l2_template : basic::options::OptionKeys::antibody
• l3_template : basic::options::OptionKeys::antibody
• L_alpha_comp_file : basic::options::OptionKeys::cyclic_peptide
• L_beta_comp_file : basic::options::OptionKeys::cyclic_peptide
• large_frag_mover_stage1_weight : basic::options::OptionKeys::broker
• last_accepted_pose_dir : basic::options::OptionKeys::ddg
• last_pose : test::Workshop4test
• last_score : test::Workshop4test
• layer : basic::options::OptionKeys::flxbb::layer
• layer_lines : basic::options::OptionKeys::score::fiber_diffraction
• layered_sasa : basic::options::OptionKeys::bunsat_calc2
• lazy_ig : basic::options::OptionKeys::packing
• lazy_silent : basic::options::OptionKeys::in::file
• lazy_silent_file_reader : basic::options::OptionKeys::jd2
• lbfgs_M : basic::options::OptionKeys::optimization
• ldsrbb_high_scale : basic::options::OptionKeys::score
• ldsrbb_low_scale : basic::options::OptionKeys::score
• ldsrbb_maxlength : basic::options::OptionKeys::score
• ldsrbb_minlength : basic::options::OptionKeys::score
• leave_antiparallel_way_H_bonded_models_by_terminal_strands : basic::options::OptionKeys::sewing
• leave_certain_model_ids : basic::options::OptionKeys::sewing
• leave_models_by_ss_num : basic::options::OptionKeys::sewing
• leave_models_with_E_terminal_ss : basic::options::OptionKeys::sewing
• leave_models_with_H_terminal_ss : basic::options::OptionKeys::sewing
• leave_other_waters : basic::options::OptionKeys::magnesium
• leave_parallel_way_H_bonded_models_by_terminal_strands : basic::options::OptionKeys::sewing
• leave_these_model_ids : basic::options::OptionKeys::sewing
• left : basic::options::OptionKeys::ufv
• legacy_fastdens_score : basic::options::OptionKeys::edensity
• legacy_kic : basic::options::OptionKeys::loops
• legal_minimization_types : options_rosetta
• len_score : test::Workshop9test
• length : basic::options::OptionKeys::hotspot , make_symmdef_file_denovo
• length_dep_srbb : basic::options::OptionKeys::score
• level : basic::options::OptionKeys::out , basic::options::OptionKeys::packing::ex1 , basic::options::OptionKeys::packing::ex1aro , basic::options::OptionKeys::packing::ex1aro_exposed , basic::options::OptionKeys::packing::ex2 , basic::options::OptionKeys::packing::ex2aro , basic::options::OptionKeys::packing::ex2aro_exposed , basic::options::OptionKeys::packing::ex3 , basic::options::OptionKeys::packing::ex4 , basic::options::OptionKeys::packing::exdna , BuildPackagedBindings
• levels : basic::options::OptionKeys::out
• lh : basic::options::OptionKeys::lh
• lh_cbreak_selection : basic::options::OptionKeys::remodel
• lh_closure_filter : basic::options::OptionKeys::remodel
• lh_ex_limit : basic::options::OptionKeys::remodel
• lh_filter_string : basic::options::OptionKeys::remodel
• library_expiry_time : basic::options::OptionKeys::lh
• license : app::pyrosetta_toolkit::modules::prettytable::setup
• lig : basic::options::OptionKeys::mh::filter
• lig_name : basic::options::OptionKeys::match
• lig_packer_weight : basic::options::OptionKeys::enzdes
• ligand : basic::options::OptionKeys::docking::ligand
• ligand_motif_sphere : basic::options::OptionKeys::motifs
• ligand_p : test::T880_Other
• ligand_params : demo::D120_Ligand_interface
• ligand_res : basic::options::OptionKeys::magnesium
• ligand_rotamer_index : basic::options::OptionKeys::match
• ligandFlag : calccontacts
• light_chain : basic::options::OptionKeys::antibody
• light_heavy_template : basic::options::OptionKeys::antibody
• limit_aroma_chi2 : basic::options::OptionKeys::relax
• limit_bad_scores : basic::options::OptionKeys::optE
• limit_cluster_size : basic::options::OptionKeys::cluster
• limit_cluster_size_percent : basic::options::OptionKeys::cluster
• limit_clusters : basic::options::OptionKeys::cluster
• limit_dist_matrix : basic::options::OptionKeys::cluster
• limit_per_pair : basic::options::OptionKeys::mh::dump
• limit_total_structures : basic::options::OptionKeys::cluster
• line : clean_pdb_keep_ligand
• line_edit : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• linear_bonded_potential : basic::options::OptionKeys::score
• linear_chainbreak_weight : basic::options::OptionKeys::relax
• lines : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , setup_pyrosetta , toolbox::make_rna_rosetta_ready
• linkage_conformer_data_file : basic::options::OptionKeys::carbohydrates
• linker_cst : basic::options::OptionKeys::smhybrid
• linmem_ig : basic::options::OptionKeys::packing
• linmin : score_app
• linmin_mover : loops_kic , test::T650_LoopsKIC
• linmin_only : basic::options::OptionKeys::cm::hybridize
• lipid_acc : basic::options::OptionKeys::mp::lipid_acc
• lipofile : basic::options::OptionKeys::in::file
• lipsfile : basic::options::OptionKeys::mp::setup
• list : basic::options::OptionKeys::in::file
• list_dnaconformers : basic::options::OptionKeys::motifs
• list_motifs : basic::options::OptionKeys::motifs
• lite : basic::options::OptionKeys::cluster
• lj_hbond_hdis : basic::options::OptionKeys::corrections::score
• lj_hbond_OH_donor_dis : basic::options::OptionKeys::corrections::score
• lk_ball_for_bb : basic::options::OptionKeys::dna::specificity
• lk_ball_ramp_width_A2 : basic::options::OptionKeys::dna::specificity
• lk_ball_water_fade : basic::options::OptionKeys::dna::specificity
• lk_ball_wtd_prefactors : basic::options::OptionKeys::dna::specificity
• lk_ball_wtd_tag : basic::options::OptionKeys::dna::specificity
• load_from_silent : basic::options::OptionKeys::optE
• load_PDB_components : basic::options::OptionKeys::in::file
• local_opt_only : basic::options::OptionKeys::ddg
• local_pdb_database : clean_pdb_keep_ligand
• local_redock_only : basic::options::OptionKeys::stepwise::monte_carlo
• local_relax : basic::options::OptionKeys::cp
• localbb : basic::options::OptionKeys::canonical_sampling::probabilities
• lock_rings : basic::options::OptionKeys::rings
• log_accepted_moves : basic::options::OptionKeys::rigid
• log_config : BuildPackagedBindings
• log_frags : basic::options::OptionKeys::abinitio
• log_scores_in_MC : basic::options::OptionKeys::mc
• logger : pyrosetta , src
• long_frag_filename : demo::D060_Folding
• long_frag_length : demo::D060_Folding
• long_inserts : demo::D060_Folding
• longer_names : amino_acids , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• LongLong : fmt
• longname : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• loodo : basic::options::OptionKeys::loodo
• loop : test::G200_Module_Region , test::T660_LoopBuilding
• loop1 : test::Workshop8test
• loop2 : basic::options::OptionKeys::chunk , test::Workshop8test
• loop_bb_min_allowed_dev : basic::options::OptionKeys::enzdes
• loop_begin : demo::D080_Loop_modeling , loops , loops_kic , test::T650_LoopsKIC
• loop_close_level : basic::options::OptionKeys::cm
• loop_combine_rate : basic::options::OptionKeys::loops
• loop_cut : loops_kic , test::T650_LoopsKIC
• loop_cutpoint : demo::D080_Loop_modeling
• loop_definition_from_file : basic::options::OptionKeys::jumps
• loop_end : demo::D080_Loop_modeling , loops , loops_kic , test::T650_LoopsKIC
• loop_file : basic::options::OptionKeys::loops
• loop_fixed_cost : basic::options::OptionKeys::score
• loop_generator_trials : basic::options::OptionKeys::enzdes
• loop_model : basic::options::OptionKeys::loops
• loop_mov_cterm : basic::options::OptionKeys::fold_from_loops
• loop_mov_nterm : basic::options::OptionKeys::fold_from_loops
• loop_mover : basic::options::OptionKeys::cm
• loop_p : test::T660_LoopBuilding
• loop_rebuild_filter : basic::options::OptionKeys::cm
• loop_refine : loops , loops_kic , test::T650_LoopsKIC , test::T660_LoopBuilding , test::Workshop8test
• loop_string : basic::options::OptionKeys::lh , test::G101_Functions_Output , test::G102_Functions_General , test::G103_Functions_Analysis
• loopfcst : basic::options::OptionKeys::loopfcst
• loophash_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• loophash_filter_acceptance_rate : basic::options::OptionKeys::abinitio
• LoopModel : basic::options::OptionKeys::LoopModel
• loopresdef : basic::options::OptionKeys::lh
• looprlx_cycle_ratio : basic::options::OptionKeys::loops
• loops : basic::options::OptionKeys::cluster , basic::options::OptionKeys::loops , test::G200_Module_Region , test::T660_LoopBuilding , test::Workshop8test
• loops_as_strings : test::G101_Functions_Output , test::G102_Functions_General , test::G103_Functions_Analysis
• loops_subset : basic::options::OptionKeys::loops
• loopscores : basic::options::OptionKeys::loops
• loopsizes : basic::options::OptionKeys::lh
• lores : basic::options::OptionKeys::stepwise
• lores_scan : basic::options::OptionKeys::magnesium
• lores_scorefxn : basic::options::OptionKeys::rna::farna
• loud : basic::options::OptionKeys::loodo
• low_patch : basic::options::OptionKeys::docking
• low_pose : test::Workshop4test
• low_res_protocol_only : basic::options::OptionKeys::docking
• low_score : test::Workshop4test
• lowest_x_decoys : basic::options::OptionKeys::ddg
• lowres : basic::options::OptionKeys::mp::dock
• lowres_abinitio : basic::options::OptionKeys::flexPepDocking
• lowres_preoptimize : basic::options::OptionKeys::flexPepDocking
• Lrms : loops
• lrms : test::Workshop8test
• Lrmsd : basic::options::OptionKeys::evaluation