- n -

• n_anchor_dock_std_devs() : pepspec
• n_append() : pepspec
• n_build_loop() : pepspec
• n_candidates() : basic::options::OptionKeys::frags , frags
• n_cgrelax_loop() : pepspec
• n_clusters() : basic::options::OptionKeys::james , james
• n_cycles() : run
• n_design_cycles() : basic::options::OptionKeys::optE , optE
• n_designs() : basic::options::OptionKeys::james , james
• n_dock_loop() : pepspec
• n_frags() : basic::options::OptionKeys::frags , frags
• n_inner() : basic::options::OptionKeys::dna::specificity , dna::specificity
• n_kbins() : basic::options::OptionKeys::edensity , edensity
• n_masters() : wum
• n_outer() : basic::options::OptionKeys::dna::specificity , dna::specificity
• n_peptides() : pepspec
• n_prepend() : pepspec
• n_rebuild_tries() : basic::options::OptionKeys::loops , loops
• n_replica() : run
• n_sample() : stepwise::protein
• n_slaves_per_master() : wum
• n_tail_res() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• n_top_natives_to_optimize() : basic::options::OptionKeys::optE , optE
• name_from_database_mode() : utility::sql_database
• name_from_transaction_mode() : utility::sql_database
• name_to_listener_tag() : basic::message_listening
• named() : basic::options::OptionKeys::constraints , constraints
• nat_ro_file() : sewing
• native() : basic::options::OptionKeys::in::file , in::file
• native1() : willmatch
• native2() : willmatch
• native_align() : pepspec
• native_alignment_res() : stepwise::rna
• native_ca_cst() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• native_contacts() : basic::options::OptionKeys::in::file , in::file
• native_edensity_score_cutoff() : stepwise::rna
• native_exclude_res() : basic::options::OptionKeys::in::file , in::file
• native_pep_anchor() : pepspec
• native_pep_chain() : pepspec
• native_virtual_res() : stepwise::rna
• nblist_autoupdate() : run
• nblist_autoupdate_narrow() : run
• nblist_autoupdate_wide() : run
• ncycle() : basic::options::OptionKeys::flxbb , flxbb
• ncycles() : basic::options::OptionKeys::cp , cp
• ndruns() : packing
• nds_prob() : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer
• nearest() : numeric
• nearest_angle() : numeric
• nearest_angle_degrees() : numeric
• nearest_angle_radians() : numeric
• nearest_int() : numeric
• nearest_neighbor() : numeric::kdtree
• nearest_neighbors() : numeric::kdtree
• nearest_periodic_value() : numeric::interpolation::periodic_range::periodic_value::full , numeric::interpolation::periodic_range::periodic_value::half
• nearest_size() : numeric
• nearest_ssize() : numeric
• neg_r() : basic::options::OptionKeys::matdes::dock , matdes::dock
• neighbor_by_distance_cutoff() : pose_metrics
• neighbor_dis() : antibody::design , basic::options::OptionKeys::antibody::design
• neighbor_dist() : basic::options::OptionKeys::loops , loops
• neighbors() : basic::options::OptionKeys::frags::contacts , frags::contacts
• new_chain_order() : basic::options::OptionKeys::in::file , in::file
• new_structures() : basic::options::OptionKeys::canonical_sampling::out , canonical_sampling::out
• nint() : numeric
• njumps() : basic::options::OptionKeys::jumps , jumps
• nloop() : basic::options::OptionKeys::dna::specificity , dna::specificity , phil
• nloop_scmove() : rot_anl
• nlsrepeat() : rdc
• nmer_pssm() : score
• nmer_pssm_list() : score
• nmer_pssm_scorecut() : score
• nmer_ref_energies() : score
• nmer_ref_energies_list() : score
• nmer_ref_seq_length() : score
• nmer_svm() : score
• nmer_svm_aa_matrix() : score
• nmer_svm_list() : score
• nmer_svm_pssm_feat() : score
• nmer_svm_scorecut() : score
• nmer_svm_term_length() : score
• nn() : basic::options::OptionKeys::cm , cm
• no_bb_movement() : basic::options::OptionKeys::ddg , ddg
• no_binary_dunlib() : basic::options::OptionKeys::in::file , in::file
• no_catres_min_in_loopgen() : basic::options::OptionKeys::enzdes , enzdes
• no_cen() : pepspec
• no_cen_rottrials() : pepspec
• no_chainbreak_in_relax() : basic::options::OptionKeys::jumps , jumps
• no_combine_if_fail() : basic::options::OptionKeys::loops , loops
• no_constraints() : basic::options::OptionKeys::ddg , ddg
• no_cst_in_relax() : basic::options::OptionKeys::constraints , constraints
• no_culling() : templates
• no_design() : basic::options::OptionKeys::optE , optE , pepspec , remodel::design
• no_design_pdb_output() : basic::options::OptionKeys::optE , optE
• no_detailed_balance() : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• no_ecalc() : patterson
• no_edens_in_minimizer() : basic::options::OptionKeys::edensity , edensity
• no_filters() : basic::options::OptionKeys::docking , docking
• no_frags() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• no_global_frame() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• no_hb_bb() : basic::options::OptionKeys::mh::filter , mh::filter
• no_hb_env_dependence() : basic::options::OptionKeys::optE , optE
• no_hb_env_dependence_DNA() : basic::options::OptionKeys::optE , optE
• no_his_DE_pairE() : basic::options::OptionKeys::corrections::score , corrections::score
• no_his_his_pairE() : basic::options::OptionKeys::corrections::score , corrections::score
• no_interpolate_Mpair() : basic::options::OptionKeys::membrane , membrane
• no_jd2_output() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• no_jumps() : remodel
• no_linearize_bounded() : basic::options::OptionKeys::constraints , constraints
• no_lk_polar_desolvation() : score
• no_looprebuild() : basic::options::OptionKeys::loops , loops
• no_minimize() : basic::options::OptionKeys::fold_cst , fold_cst
• no_neighborhood_design() : ufv
• no_nstruct_label() : out
• no_optH() : packing
• no_output() : basic::options::OptionKeys::jd2 , jd2
• no_output_cen() : out::file
• no_packstat_calculation() : basic::options::OptionKeys::enzdes , enzdes
• no_pick_fragments() : templates
• no_prepack_prot() : pepspec
• no_prof_info_in_silentout() : run
• no_randomize_loop() : basic::options::OptionKeys::loops , loops
• no_recover_low_at_constraint_switch() : basic::options::OptionKeys::fold_cst , fold_cst
• no_rotamer_bump() : basic::options::OptionKeys::motifs , motifs
• no_sample_ss_jumps() : basic::options::OptionKeys::jumps , jumps
• no_scorefile() : run
• no_shear() : basic::options::OptionKeys::jumps , jumps
• no_smooth_etables() : score
• no_unconstrained_repack() : basic::options::OptionKeys::enzdes , enzdes
• no_wobble() : basic::options::OptionKeys::jumps , jumps
• no_write_failures() : abinitio , basic::options::OptionKeys::abinitio
• nodelay() : run
• nodisulf() : basic::options::OptionKeys::mh::filter , mh::filter
• noloops() : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::score , mh::filter , mh::score
• non_ideal_loop_closing() : basic::options::OptionKeys::loops , loops
• non_printable_to_string() : utility::json_spirit
• nonideal() : basic::options::OptionKeys::optimization , optimization
• nonlocal() : basic::options::OptionKeys::frags::nonlocal , basic::options::OptionKeys::nonlocal , frags::nonlocal , nonlocal
• nonlocal_pairs() : basic::options::OptionKeys::frags , frags
• nonnegative_principal_angle() : numeric
• nonnegative_principal_angle_degrees() : numeric
• nonnegative_principal_angle_radians() : numeric
• nonpivot_torsion_sampling() : basic::options::OptionKeys::loops , loops
• nooutput() : out
• nopack() : basic::options::OptionKeys::dna::design , dna::design
• nopdb() : basic::options::OptionKeys::dna::design , dna::design
• norepack1() : basic::options::OptionKeys::docking , docking
• norepack2() : basic::options::OptionKeys::docking , docking
• norm() : numeric::kinematic_closure
• normal_cycles() : basic::options::OptionKeys::membrane , membrane
• normal_delta_angle() : basic::options::OptionKeys::membrane , membrane
• normal_mag() : basic::options::OptionKeys::membrane , membrane
• normal_max_angle() : basic::options::OptionKeys::membrane , membrane
• normal_search() : basic::options::OptionKeys::membrane , membrane
• normal_start_angle() : basic::options::OptionKeys::membrane , membrane
• normalization_id() : PCS , PCSTS1 , PCSTS2 , PCSTS3 , PCSTS4
• normalize() : numeric::kinematic_closure , numeric , ProQ
• normalize_decoy_score_spread() : basic::options::OptionKeys::optE , optE
• normalize_mixture_func() : basic::options::OptionKeys::constraints , constraints
• normalize_score_ncontact() : basic::options::OptionKeys::mh , mh
• noshmem() : basic::options::OptionKeys::boinc , boinc
• not_equal_length() : numeric
• not_restype() : basic::options::OptionKeys::mh::filter , mh::filter
• not_restype_one() : basic::options::OptionKeys::mh::filter , mh::filter
• nproc() : run
• nr_large_copies() : basic::options::OptionKeys::frags , frags , templates
• nr_scored_fragments() : basic::options::OptionKeys::fast_loops , fast_loops
• nr_scored_sampling_passes() : basic::options::OptionKeys::fast_loops , fast_loops
• nr_small_copies() : templates
• nrbmoves() : RBSegmentRelax
• nrboutercycles() : RBSegmentRelax
• nres() : threadsc
• nres_mono() : smhybrid
• nshells() : patterson
• nstep_water() : basic::options::OptionKeys::dna::specificity , dna::specificity
• nstruct() : out
• nstruct_centroid() : stepwise::protein
• nterm_seq() : assembly , basic::options::OptionKeys::assembly
• Ntermini() : basic::options::OptionKeys::in , in
• ntrials() : basic::options::OptionKeys::canonical_sampling::sampling , basic::options::OptionKeys::jd2 , canonical_sampling::sampling , jd2
• num_clusters() : basic::options::OptionKeys::cmiles::kcluster , cmiles::kcluster
• num_desired_loops() : basic::options::OptionKeys::loops , loops
• num_frag_moves() : remodel
• num_fragments() : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• num_iterations() : basic::options::OptionKeys::casp , casp
• num_packs() : basic::options::OptionKeys::ms , ms
• num_partitions() : basic::options::OptionKeys::lh , lh
• num_pose_minimize() : stepwise
• num_random_samples() : stepwise
• num_repacks() : basic::options::OptionKeys::motifs , motifs
• num_subs_building_block() : basic::options::OptionKeys::matdes , matdes
• num_subs_total() : basic::options::OptionKeys::matdes , matdes
• num_traj() : basic::options::OptionKeys::els , els
• num_trajectory() : remodel
• number_3mer_frags() : abinitio , basic::options::OptionKeys::abinitio
• number_9mer_frags() : abinitio , basic::options::OptionKeys::abinitio
• number_of_swarm_cycles() : basic::options::OptionKeys::optE , optE
• number_of_swarm_particles() : basic::options::OptionKeys::optE , optE
• numbering_scheme() : antibody , basic::options::OptionKeys::antibody
• numchanges() : numeric::kinematic_closure
• numresults() : basic::options::OptionKeys::ms , ms
• numroots() : numeric::kinematic_closure
• NV_lbound() : score
• NV_table() : score
• NV_ubound() : score