- l -

• l : basic::options::OptionKeys::in::file
• l1_template : basic::options::OptionKeys::antibody
• l2_template : basic::options::OptionKeys::antibody
• l3_template : basic::options::OptionKeys::antibody
• last_accepted_pose_dir : basic::options::OptionKeys::ddg
• layer : basic::options::OptionKeys::flxbb::layer
• 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
• left : basic::options::OptionKeys::ufv
• left_tail : basic::options::OptionKeys::krassk
• legacy_fastdens_score : basic::options::OptionKeys::edensity
• legacy_kic : basic::options::OptionKeys::loops
• length : basic::options::OptionKeys::hotspot
• 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
• 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
• 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_pdb : basic::options::OptionKeys::cm
• ligand_rotamer_index : basic::options::OptionKeys::match
• 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_total_structures : basic::options::OptionKeys::cluster
• linear_bonded_potential : basic::options::OptionKeys::score
• linear_chainbreak_weight : basic::options::OptionKeys::relax
• linker_cst : basic::options::OptionKeys::smhybrid
• linkers_pdb1 : basic::options::OptionKeys::assembly
• linkers_pdb2 : basic::options::OptionKeys::assembly
• linmem_ig : basic::options::OptionKeys::packing
• linmin_only : basic::options::OptionKeys::cm::hybridize
• lipid_acc_files : basic::options::OptionKeys::membrane
• lipofile : basic::options::OptionKeys::in::file
• 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
• load_from_silent : basic::options::OptionKeys::optE
• local_opt_only : basic::options::OptionKeys::ddg
• 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::carbohydrates
• log_accepted_moves : basic::options::OptionKeys::rigid
• log_frags : basic::options::OptionKeys::abinitio
• loop2 : basic::options::OptionKeys::chunk
• loop_bb_min_allowed_dev : basic::options::OptionKeys::enzdes
• loop_close_level : basic::options::OptionKeys::cm
• loop_closure : basic::options::OptionKeys::loops::loop_closure
• loop_combine_rate : basic::options::OptionKeys::loops
• loop_definition_from_file : basic::options::OptionKeys::jumps
• loop_farlx : basic::options::OptionKeys::loops
• loop_file : basic::options::OptionKeys::LoopModel , basic::options::OptionKeys::loops
• loop_fixed_cost : basic::options::OptionKeys::score
• loop_generator_trials : basic::options::OptionKeys::enzdes
• loop_insert : basic::options::OptionKeys::loops::loop_closure
• loop_insert_rclrc : basic::options::OptionKeys::loops::loop_closure
• 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_rebuild_filter : basic::options::OptionKeys::cm
• loopfcst : basic::options::OptionKeys::loopfcst
• loophash_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• LoopModel : basic::options::OptionKeys::LoopModel
• looprlx_cycle_ratio : basic::options::OptionKeys::loops
• loops : basic::options::OptionKeys::cluster , basic::options::OptionKeys::loops
• loops_subset : basic::options::OptionKeys::loops
• loopscores : basic::options::OptionKeys::loops
• loopsizes : basic::options::OptionKeys::lh
• low_patch : basic::options::OptionKeys::docking
• low_res_protocol_only : basic::options::OptionKeys::docking
• lowest_x_decoys : basic::options::OptionKeys::ddg
• lowres_abinitio : basic::options::OptionKeys::flexPepDocking
• lowres_preoptimize : basic::options::OptionKeys::flexPepDocking
• Lrmsd : basic::options::OptionKeys::evaluation
• lys_dun_th : basic::options::OptionKeys::willmatch