- l -

• l : basic::options::OptionKeys::in::file , extract_by_sidechain_sasa_score
• L : pyrosetta.distributed.cluster.logging_handlers , pyrosetta.distributed.cluster.logging_support , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• 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
• label : autocorrelation , compute_difference , correlation_time , plot , predPRE , torsion_vs_time
• label_chain : predPRE
• label_resnum : predPRE
• labeledres : PREcst
• labeledx : predPRE
• labeledy : predPRE
• labeledz : predPRE
• LacNAc : test.C001_Carbohydrates_Demo01
• lactose : test.C001_Carbohydrates_Demo01
• lambda_i : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• lambda_mat : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• language : conf
• lanthionine_positions : basic::options::OptionKeys::cyclic_peptide
• large_frag_mover_stage1_weight : basic::options::OptionKeys::broker
• lariat_sample_cis : basic::options::OptionKeys::cyclic_peptide
• lariat_sidechain_index : basic::options::OptionKeys::cyclic_peptide
• larmor : PREcst , predPRE
• last_accepted_pose_dir : basic::options::OptionKeys::ddg
• last_flags : drrafter_rna
• last_ligand_res : metapatch
• last_of_first_chain : create_a3b_hbs
• last_pose : test.Workshop4test
• last_round : drrafter_rna
• last_score : test.Workshop4test
• latex_documents : conf
• latex_elements : conf
• layer : basic::options::OptionKeys::flxbb::layer
• layer_lines : basic::options::OptionKeys::score::fiber_diffraction
• layered_sasa : basic::options::OptionKeys::bunsat_calc2 , bur_nodon_tyr
• 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::legacy_sewing
• leave_certain_model_ids : basic::options::OptionKeys::legacy_sewing
• leave_models_by_ss_num : basic::options::OptionKeys::legacy_sewing
• leave_models_with_E_terminal_ss : basic::options::OptionKeys::legacy_sewing
• leave_models_with_H_terminal_ss : basic::options::OptionKeys::legacy_sewing
• leave_other_waters : basic::options::OptionKeys::magnesium
• leave_parallel_way_H_bonded_models_by_terminal_strands : basic::options::OptionKeys::legacy_sewing
• leave_these_model_ids : basic::options::OptionKeys::legacy_sewing
• left : basic::options::OptionKeys::ufv
• legacy : basic::options::OptionKeys::ddg
• legacy_fastdens_score : basic::options::OptionKeys::edensity
• legacy_kic : basic::options::OptionKeys::loops
• legacy_sewing : basic::options::OptionKeys::legacy_sewing
• legal : options_will
• legal_minimization_types : options_rosetta
• len_score : test.Workshop9test
• length : basic::options::OptionKeys::hotspot , make_symmdef_file_denovo , oop_conformations
• length_dep_srbb : basic::options::OptionKeys::score
• length_error : make_comparison
• length_key : subloop_histogram
• length_to_derive : peptide_deriver
• lengths : internal_coordinates , subloop_histogram
• leu : evaluate_beta_mutants
• leu_min : evaluate_beta_mutants
• leu_mm : evaluate_beta_mutants
• leu_pos : evaluate_beta_mutants
• 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 , pyrosetta.tests.distributed.test_dask
• levels : basic::options::OptionKeys::out
• Lex : test.C001_Carbohydrates_Demo01
• 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
• libraries : pilot_app_settings
• library_expiry_time : basic::options::OptionKeys::lh
• library_path : pilot_app_settings
• library_project_template : update_ui_project
• lig : basic::options::OptionKeys::mh::filter
• lig_min_atom_sep : hbscan
• lig_name : basic::options::OptionKeys::match
• lig_packer_weight : basic::options::OptionKeys::enzdes
• lig_seqpos : hbscan
• ligand : basic::options::OptionKeys::docking::ligand
• ligand_1_letter_code : basic::options::OptionKeys::motifs
• ligand_3_letter_code : basic::options::OptionKeys::motifs , local
• ligand_chain : basic::options::OptionKeys::ligand_evolution
• ligand_cst_atoms : local
• ligand_ensemble : basic::options::OptionKeys::docking::ligand
• ligand_evolution : basic::options::OptionKeys::ligand_evolution
• ligand_full_name : basic::options::OptionKeys::motifs
• ligand_mode : basic::options::OptionKeys::coupled_moves
• ligand_motif_output_directory_name : basic::options::OptionKeys::motifs
• ligand_motif_output_file_name : basic::options::OptionKeys::motifs
• ligand_motif_sphere : basic::options::OptionKeys::motifs
• ligand_p : test.T880_Other
• ligand_params : demo.D120_Ligand_interface
• ligand_prob : basic::options::OptionKeys::coupled_moves
• ligand_res : basic::options::OptionKeys::magnesium
• ligand_rotamer_index : basic::options::OptionKeys::match
• ligand_weight : basic::options::OptionKeys::coupled_moves
• ligand_wts_fxn_cutoff : basic::options::OptionKeys::motifs
• 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::energy_based_clustering , basic::options::OptionKeys::cluster
• limit_dist_matrix : basic::options::OptionKeys::cluster
• limit_per_pair : basic::options::OptionKeys::mh::dump
• limit_structures_per_cluster : basic::options::OptionKeys::cluster::energy_based_clustering
• limit_to__all__ : pyrosetta.distributed.cluster , pyrosetta.distributed.viewer
• limit_total_structures : basic::options::OptionKeys::cluster
• limited_data : add_xyz_to_pose
• line : clean_pdb_keep_ligand , closure_error , extract_by_sidechain_sasa_score , make_static_database
• line_edit : clean_pdb_keep_ligand
• line_split : erraser_analysis
• linear_bonded_potential : basic::options::OptionKeys::score
• linear_chainbreak_weight : basic::options::OptionKeys::relax
• lines : build_restypes , cal_NBR_radius , clean_pdb_keep_ligand , erraser_analysis , hist2d , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , solution_counts , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• linestyle : score_vs_rmsd , subloop_histogram
• linewidth : PREcst , predPRE , subloop_histogram
• link_all_cys_with_paraBBMB : basic::options::OptionKeys::cyclic_peptide
• link_all_cys_with_TBMB : basic::options::OptionKeys::cyclic_peptide
• 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
• lipids : basic::options::OptionKeys::mp::lipids
• 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
• list_pose_range : align
• list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t : pyrosetta
• 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_bridge_angle_widthscale : basic::options::OptionKeys::dna::specificity
• lk_ball_for_bb : basic::options::OptionKeys::dna::specificity
• lk_ball_overlap_gap : basic::options::OptionKeys::dna::specificity
• lk_ball_overlap_width_A2 : 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_waters_donor : basic::options::OptionKeys::dna::specificity
• lk_ball_waters_ring : basic::options::OptionKeys::dna::specificity
• lk_ball_waters_sp2 : basic::options::OptionKeys::dna::specificity
• lk_ball_waters_sp3 : basic::options::OptionKeys::dna::specificity
• lk_ball_wtd_prefactors : basic::options::OptionKeys::dna::specificity
• lk_ball_wtd_tag : basic::options::OptionKeys::dna::specificity
• lk_dome_ball_overlap_width_A2 : basic::options::OptionKeys::dna::specificity
• lk_dome_h2o_radius : basic::options::OptionKeys::dna::specificity
• lk_dome_max_angle : basic::options::OptionKeys::dna::specificity
• lk_dome_min_angle : basic::options::OptionKeys::dna::specificity
• lk_dome_occlusion_max : basic::options::OptionKeys::dna::specificity
• lk_dome_occlusion_min : basic::options::OptionKeys::dna::specificity
• lk_dome_overlap_width_A2 : basic::options::OptionKeys::dna::specificity
• lk_dome_ramp_width_A2 : basic::options::OptionKeys::dna::specificity
• lk_dome_water_adjust : basic::options::OptionKeys::dna::specificity
• lk_dome_water_dist : basic::options::OptionKeys::dna::specificity
• lk_polar_without_proline_N : basic::options::OptionKeys::score
• lkb_cluster_radius : basic::options::OptionKeys::corrections::water
• lkb_overlap_distance : basic::options::OptionKeys::corrections::water
• lkb_rotset_radius : basic::options::OptionKeys::corrections::water
• load_from_silent : basic::options::OptionKeys::optE
• load_input_poses_only_once : basic::options::OptionKeys::jd3
• load_PDB_components : basic::options::OptionKeys::in::file
• loc : correlation_time , plot
• local_mysql_url : job_manager
• 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_frags : basic::options::OptionKeys::abinitio
• log_g : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• log_path : average_rmsds
• log_rho : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• log_scores_in_MC : basic::options::OptionKeys::mc
• logger : pyrosetta.distributed.utility.pickle , pyrosetta
• long_frag_filename : demo.D060_Folding
• long_frag_length : demo.D060_Folding
• long_inserts : demo.D060_Folding
• longer_names : amino_acids , DRRAFTER_util
• longname : clean_pdb_keep_ligand
• loodo : basic::options::OptionKeys::loodo
• lookback_csts : unalignedEvaluate
• loop : internal_coordinates , kic_runner , make_comparison , test.G200_Module_Region , test.T660_LoopBuilding
• loop1 : test.Workshop8test
• loop2 : basic::options::OptionKeys::chunk , test.Workshop8test
• loop_3mer_cycles : basic::options::OptionKeys::remodel::staged_sampling
• loop_3mer_score_file : basic::options::OptionKeys::remodel::staged_sampling
• loop_9mer_cycles : basic::options::OptionKeys::remodel::staged_sampling
• loop_9mer_score_file : basic::options::OptionKeys::remodel::staged_sampling
• loop_bb_min_allowed_dev : basic::options::OptionKeys::enzdes
• loop_begin : demo.D080_Loop_modeling , loops , loops_kic , test.T650_LoopsKIC
• loop_btw_parametric_components : basic::options::OptionKeys::remodel::staged_sampling
• loop_close : basic::options::OptionKeys::score::loop_close
• 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 , pivot_selection , test.T650_LoopsKIC
• loop_file : basic::options::OptionKeys::loops , kic_runner
• loop_fixed_cost : basic::options::OptionKeys::score::loop_close
• loop_generator_trials : basic::options::OptionKeys::enzdes
• loop_length : indel
• 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_path : kic_runner
• loop_rebuild_filter : basic::options::OptionKeys::cm
• loop_refine : loops , loops_kic , test.T650_LoopsKIC , test.T660_LoopBuilding , test.Workshop8test
• loop_residues : basic::options::OptionKeys::recces::thermal_sampling
• loop_start : pivot_selection
• 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_only : chrisk
• 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::denovo
• loud : basic::options::OptionKeys::loodo
• low_patch : basic::options::OptionKeys::docking
• low_pose : test.Workshop4test
• low_res : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• low_res_inner_cycles : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• low_res_outer_cycles : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• low_res_protocol_only : basic::options::OptionKeys::docking
• low_score : test.Workshop4test
• lower : options_will , test_terpenes
• lower_chains : basic::options::OptionKeys::msd
• lowest_energy : oop_conformations
• 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
• lowres_weights : basic::options::OptionKeys::score
• Lrms : loops
• lrms : test.Workshop8test
• Lrmsd : basic::options::OptionKeys::evaluation
• lsmdef : basic::options::OptionKeys
• lys_id : lactamize
• lys_one : azide_link_creator
• lys_one_pdb : azide_link_creator
• lys_two : azide_link_creator
• lys_two_pdb : azide_link_creator