- n -

• n_anchor_dock_std_devs : basic::options::OptionKeys::pepspec
• n_append : basic::options::OptionKeys::pepspec
• n_build_loop : basic::options::OptionKeys::pepspec
• N_CA_vector : test::Workshop2test
• n_candidates : basic::options::OptionKeys::frags
• n_cgrelax_loop : basic::options::OptionKeys::pepspec
• n_cycles : basic::options::OptionKeys::run
• n_design_cycles : basic::options::OptionKeys::optE
• n_designs : basic::options::OptionKeys::james
• n_dock_loop : basic::options::OptionKeys::pepspec
• n_frags : basic::options::OptionKeys::frags
• N_in_2 : test::Workshop9test
• n_inner : basic::options::OptionKeys::dna::specificity
• n_kbins : basic::options::OptionKeys::edensity
• n_masters : basic::options::OptionKeys::wum
• n_moves : test::T400_Refinement , test::Workshop5test
• n_multi_templates : basic::options::OptionKeys::antibody
• n_outer : basic::options::OptionKeys::dna::specificity
• n_peptides : basic::options::OptionKeys::pepspec
• n_prepend : basic::options::OptionKeys::pepspec
• n_replica : basic::options::OptionKeys::run
• n_res : app::delta_score_per_mutation
• n_sample : basic::options::OptionKeys::stepwise::protein
• n_slaves_per_master : basic::options::OptionKeys::wum
• n_tail_res : basic::options::OptionKeys::chemically_conjugated_docking
• n_top_natives_to_optimize : basic::options::OptionKeys::optE
• N_xyz : test::Workshop2test
• name : app::pyrosetta_toolkit::modules::prettytable::setup , tools::CppParser
• name3_property_codes : basic::options::OptionKeys::in
• named : basic::options::OptionKeys::constraints
• Nargs : contacts
• native : basic::options::OptionKeys::in::file , ContactMap
• native1 : basic::options::OptionKeys::willmatch
• native2 : basic::options::OptionKeys::willmatch
• native_align : basic::options::OptionKeys::pepspec
• native_alignment_res : basic::options::OptionKeys::stepwise::rna
• native_ca_cst : basic::options::OptionKeys::fold_from_loops
• native_contacts : basic::options::OptionKeys::in::file
• native_edensity_score_cutoff : basic::options::OptionKeys::stepwise::rna
• native_exclude_res : basic::options::OptionKeys::in::file
• native_pdb_list : sequence_recovery
• native_pep_anchor : basic::options::OptionKeys::pepspec
• native_pep_chain : basic::options::OptionKeys::pepspec
• native_pose : test::Workshop7test
• native_sequence : usec
• native_virtual_res : basic::options::OptionKeys::stepwise::rna
• nblist_autoupdate : basic::options::OptionKeys::run
• nblist_autoupdate_narrow : basic::options::OptionKeys::run
• nblist_autoupdate_wide : basic::options::OptionKeys::run
• ncycle : basic::options::OptionKeys::flxbb
• ncycles : basic::options::OptionKeys::cp
• ndruns : basic::options::OptionKeys::packing
• nds_prob : basic::options::OptionKeys::blivens::disulfide_scorer
• neg_r : basic::options::OptionKeys::matdes::dock
• neighbor_by_distance_cutoff : basic::options::OptionKeys::pose_metrics
• neighbor_cutoff : basic::options::OptionKeys::sewing
• neighbor_dis : basic::options::OptionKeys::antibody::design
• neighbor_dist : basic::options::OptionKeys::loops
• neighbors : basic::options::OptionKeys::frags::contacts
• netpdbname : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• new_chain_order : basic::options::OptionKeys::in::file
• new_model_file_name : basic::options::OptionKeys::sewing
• new_move_selector : basic::options::OptionKeys::stepwise
• new_mover : test::T850_SubClassing
• new_score : test::Workshop4test
• new_structures : basic::options::OptionKeys::canonical_sampling::out
• newdna : basic::options::OptionKeys::corrections
• newnum : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• newpath : app::surface_docking::surface_docking
• NFunctions : make_templates
• njumps : basic::options::OptionKeys::jumps
• nloop : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::phil
• nloop_scmove : basic::options::OptionKeys::rot_anl
• nlsrepeat : basic::options::OptionKeys::rdc
• NMdist : basic::options::OptionKeys::lh
• nmer_pssm : basic::options::OptionKeys::score
• nmer_pssm_list : basic::options::OptionKeys::score
• nmer_pssm_scorecut : basic::options::OptionKeys::score
• nmer_ref_energies : basic::options::OptionKeys::score
• nmer_ref_energies_list : basic::options::OptionKeys::score
• nmer_ref_seq_length : basic::options::OptionKeys::score
• nmer_svm : basic::options::OptionKeys::score
• nmer_svm_aa_matrix : basic::options::OptionKeys::score
• nmer_svm_list : basic::options::OptionKeys::score
• nmer_svm_pssm_feat : basic::options::OptionKeys::score
• nmer_svm_scorecut : basic::options::OptionKeys::score
• nmer_svm_term_length : basic::options::OptionKeys::score
• nmoves : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range
• nn : basic::options::OptionKeys::cm
• no_bb_movement : basic::options::OptionKeys::ddg
• no_binary_dunlib : basic::options::OptionKeys::in::file
• no_catres_min_in_loopgen : basic::options::OptionKeys::enzdes
• no_cen : basic::options::OptionKeys::pepspec
• no_cen_rottrials : basic::options::OptionKeys::pepspec
• no_chainbreak_in_relax : basic::options::OptionKeys::jumps
• no_chainend_ter : basic::options::OptionKeys::out::file
• no_combine_if_fail : basic::options::OptionKeys::loops
• no_constraints : basic::options::OptionKeys::ddg
• no_cst_in_relax : basic::options::OptionKeys::constraints
• no_culling : basic::options::OptionKeys::templates
• no_design : basic::options::OptionKeys::optE , basic::options::OptionKeys::pepspec , basic::options::OptionKeys::remodel::design
• no_design_pdb_output : basic::options::OptionKeys::optE
• no_detailed_balance : basic::options::OptionKeys::canonical_sampling::sampling
• no_ecalc : basic::options::OptionKeys::patterson
• no_extra_sdf_data : basic::options::OptionKeys::out::file
• no_filters : basic::options::OptionKeys::docking
• no_frags : basic::options::OptionKeys::AnchoredDesign
• no_global_frame : basic::options::OptionKeys::cm::hybridize
• no_hb_bb : basic::options::OptionKeys::mh::filter
• no_hb_env_dependence : basic::options::OptionKeys::optE
• no_hb_env_dependence_DNA : basic::options::OptionKeys::optE
• no_hbonds_to_ether_oxygens : basic::options::OptionKeys::chemical
• no_his_DE_pairE : basic::options::OptionKeys::corrections::score
• no_his_his_pairE : basic::options::OptionKeys::corrections::score
• no_interpolate_Mpair : basic::options::OptionKeys::membrane , basic::options::OptionKeys::mp
• no_jd2_output : basic::options::OptionKeys::canonical_sampling::probabilities
• no_jumps : basic::options::OptionKeys::remodel
• no_linearize_bounded : basic::options::OptionKeys::constraints
• no_lk_polar_desolvation : basic::options::OptionKeys::score
• no_looprebuild : basic::options::OptionKeys::loops
• no_minimize : basic::options::OptionKeys::fold_cst
• no_neighborhood_design : basic::options::OptionKeys::ufv
• no_nstruct_label : basic::options::OptionKeys::out
• NO_OCCUPANCY : clean_pdb_keep_ligand
• no_optH : basic::options::OptionKeys::packing
• no_output : basic::options::OptionKeys::jd2
• no_output_cen : basic::options::OptionKeys::out::file
• no_packstat_calculation : basic::options::OptionKeys::enzdes
• no_pick_fragments : basic::options::OptionKeys::templates
• no_prepack_prot : basic::options::OptionKeys::pepspec
• no_pro_close_ring_closure : basic::options::OptionKeys::score
• no_prof_info_in_silentout : basic::options::OptionKeys::run
• no_randomize_loop : basic::options::OptionKeys::loops
• no_recover_low_at_constraint_switch : basic::options::OptionKeys::fold_cst
• no_rotamer_bump : basic::options::OptionKeys::motifs
• no_sample_ss_jumps : basic::options::OptionKeys::jumps
• no_scorefile : basic::options::OptionKeys::run
• no_scores_in_pdb : basic::options::OptionKeys::out::file
• no_shear : basic::options::OptionKeys::jumps
• no_smooth_etables : basic::options::OptionKeys::score
• no_unconstrained_repack : basic::options::OptionKeys::enzdes
• no_wobble : basic::options::OptionKeys::jumps
• no_write_failures : basic::options::OptionKeys::abinitio
• nodelay : basic::options::OptionKeys::run
• nodisulf : basic::options::OptionKeys::mh::filter
• nohelix : basic::options::OptionKeys::mh::score
• noloops : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::score
• non_helix : basic::options::OptionKeys::mp
• non_ideal_loop_closing : basic::options::OptionKeys::loops
• NONE : app::pyrosetta_toolkit::modules::prettytable::prettytable
• nonideal : basic::options::OptionKeys::optimization
• nonlocal : basic::options::OptionKeys::frags::nonlocal , basic::options::OptionKeys::nonlocal
• nonlocal_pairs : basic::options::OptionKeys::frags
• nonpivot_torsion_sampling : basic::options::OptionKeys::loops
• nooutput : basic::options::OptionKeys::out
• nopdb : basic::options::OptionKeys::dna::design
• nopdbout : clean_pdb_keep_ligand
• norepack1 : basic::options::OptionKeys::docking
• norepack2 : basic::options::OptionKeys::docking
• normal : basic::options::OptionKeys::mp::setup
• normal_angle_delta : basic::options::OptionKeys::mp
• normal_angle_start : basic::options::OptionKeys::mp
• normal_cycles : basic::options::OptionKeys::membrane
• normal_delta_angle : basic::options::OptionKeys::membrane
• normal_mag : basic::options::OptionKeys::membrane
• normal_max_angle : basic::options::OptionKeys::membrane
• normal_search : basic::options::OptionKeys::membrane
• normal_search_cycles : basic::options::OptionKeys::mp
• normal_start : basic::options::OptionKeys::mp
• normal_start_angle : basic::options::OptionKeys::membrane
• normalization_id : basic::options::OptionKeys::PCS , basic::options::OptionKeys::PCSTS1 , basic::options::OptionKeys::PCSTS2 , basic::options::OptionKeys::PCSTS3 , basic::options::OptionKeys::PCSTS4
• normalize : basic::options::OptionKeys::ProQ
• normalize_decoy_score_spread : basic::options::OptionKeys::optE
• normalize_mixture_func : basic::options::OptionKeys::constraints
• normalize_score_ncontact : basic::options::OptionKeys::mh
• normalize_to_thk : basic::options::OptionKeys::mp::output
• nosheets : basic::options::OptionKeys::mh::score
• noshmem : basic::options::OptionKeys::boinc
• nosmallshear_ref : app::surface_docking::surface_docking
• not_restype : basic::options::OptionKeys::mh::filter
• not_restype_one : basic::options::OptionKeys::mh::filter
• nproc : basic::options::OptionKeys::run
• nr_large_copies : basic::options::OptionKeys::frags , basic::options::OptionKeys::templates
• nr_scored_fragments : basic::options::OptionKeys::fast_loops
• nr_scored_sampling_passes : basic::options::OptionKeys::fast_loops
• nr_small_copies : basic::options::OptionKeys::templates
• nrbmoves : basic::options::OptionKeys::RBSegmentRelax
• nrboutercycles : basic::options::OptionKeys::RBSegmentRelax
• nres : basic::options::OptionKeys::threadsc , clean_pdb_keep_ligand
• nres_mono : basic::options::OptionKeys::smhybrid
• nshells : basic::options::OptionKeys::patterson
• nstep_water : basic::options::OptionKeys::dna::specificity
• nstruct : basic::options::OptionKeys::out , local
• nstruct_centroid : basic::options::OptionKeys::stepwise::protein
• nsub : make_symmdef_file_denovo
• Ntermini : basic::options::OptionKeys::in
• ntrials : basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::sampling , basic::options::OptionKeys::jd2
• nucleic_letters : pyrosetta::toolbox::mutants , toolbox::mutants
• num_clusters : basic::options::OptionKeys::cmiles::kcluster
• num_desired_loops : basic::options::OptionKeys::loops
• num_edges_to_follow : basic::options::OptionKeys::sewing
• num_fragments : basic::options::OptionKeys::cm::sanitize
• num_frags : basic::options::OptionKeys::loodo
• num_interfaces : make_symmdef_file_denovo
• num_iterations : basic::options::OptionKeys::casp
• num_min_rebuild : basic::options::OptionKeys::cyclization
• num_model : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• num_models_to_dump : basic::options::OptionKeys::sewing
• num_packs : basic::options::OptionKeys::ms
• num_partitions : basic::options::OptionKeys::lh
• num_pdb : ContactMap
• num_points : basic::options::OptionKeys::mp::viewer
• num_pose_minimize : basic::options::OptionKeys::stepwise
• num_procs : basic::options::OptionKeys::sewing
• num_random_samples : basic::options::OptionKeys::stepwise
• num_repacks : basic::options::OptionKeys::motifs
• num_repeats : basic::options::OptionKeys::sewing
• num_segments_to_match : basic::options::OptionKeys::sewing
• num_subs_building_block : basic::options::OptionKeys::matdes
• num_subs_total : basic::options::OptionKeys::matdes
• num_trajectory : basic::options::OptionKeys::remodel
• number_3mer_frags : basic::options::OptionKeys::abinitio
• number_9mer_frags : basic::options::OptionKeys::abinitio
• number_of_swarm_cycles : basic::options::OptionKeys::optE
• number_of_swarm_particles : basic::options::OptionKeys::optE
• numbering_scheme : basic::options::OptionKeys::antibody
• numeric_classes : src::numeric
• numresults : basic::options::OptionKeys::ms
• NV_lbound : basic::options::OptionKeys::score
• NV_table : basic::options::OptionKeys::score
• NV_ubound : basic::options::OptionKeys::score