- a -

• a : basic::options::OptionKeys::score::fiber_diffraction , test::T850_SubClassing
• a1 : test::Workshop3test
• a2 : test::Workshop3test
• aa : basic::options::OptionKeys::mh::match
• aa1 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match
• aa2 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match
• aa_composition_setup_file : basic::options::OptionKeys::score
• aa_during_build : basic::options::OptionKeys::ufv
• aa_during_design_refine : basic::options::OptionKeys::ufv
• aa_repeat_energy_penalty_file : basic::options::OptionKeys::score
• AAs : app::delta_score_per_mutation
• ab : test::T400_Refinement
• ab_struct : test::G201_Module_Structure
• ABEGO : basic::options::OptionKeys::frags::ABEGO
• abinitio : app::surface_docking::surface_docking , basic::options::OptionKeys::abinitio
• abinitio_cycles : basic::options::OptionKeys::smhybrid
• abinitio_design : basic::options::OptionKeys::smhybrid
• abrelax : basic::options::OptionKeys::abrelax
• accept_aborted_loops : basic::options::OptionKeys::loops
• action : basic::options::OptionKeys::evolution , toolbox::adjust_library_path
• active_site_definition_by_gridlig : basic::options::OptionKeys::match
• active_site_definition_by_residue : basic::options::OptionKeys::match
• adapt_graft : basic::options::OptionKeys::antibody::design
• add_atom_at_cen : basic::options::OptionKeys::smhybrid
• add_atom_type_set_parameters : basic::options::OptionKeys::chemical
• add_backrub_pivots : basic::options::OptionKeys::antibody::design
• add_buffer_res : basic::options::OptionKeys::pepspec
• add_cavities : basic::options::OptionKeys::smhybrid
• add_constraints : basic::options::OptionKeys::cyclization
• add_cst_loop : basic::options::OptionKeys::fold_from_loops
• add_delete_frequency : basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::stepwise::monte_carlo
• add_esp : basic::options::OptionKeys::fingerprint
• add_graft_log_to_pdb : basic::options::OptionKeys::antibody::design
• add_metal_at_0 : basic::options::OptionKeys::smhybrid
• add_non_init_chunks : basic::options::OptionKeys::cm::hybridize
• add_orbitals : basic::options::OptionKeys::in
• add_proposal_density_factor : basic::options::OptionKeys::stepwise::monte_carlo
• add_relax_cycles : basic::options::OptionKeys::fold_from_loops
• add_res_after : basic::options::OptionKeys::smhybrid
• add_res_before : basic::options::OptionKeys::smhybrid
• add_ss_after : basic::options::OptionKeys::smhybrid
• add_ss_before : basic::options::OptionKeys::smhybrid
• add_virt_root : basic::options::OptionKeys::stepwise::rna
• additional_objective_functions : basic::options::OptionKeys::lh
• additional_packing_ligand_rb_confs : basic::options::OptionKeys::enzdes
• adducts : basic::options::OptionKeys::packing
• ads : extract_scores_and_constraints
• ads_cycles : app::surface_docking::surface_docking
• ads_inner_cycles : app::surface_docking::surface_docking
• ads_outer_cycles : app::surface_docking::surface_docking
• ads_pdb : extract_scores_and_constraints
• agg_with_max : basic::options::OptionKeys::mh::harvest
• AHD_cutoff : basic::options::OptionKeys::bunsat_calc2
• akash : basic::options::OptionKeys::AnchoredDesign::akash
• ala : test::T100_Basic
• ala_scan : basic::options::OptionKeys::matdes::mutalyze
• align_pdb : basic::options::OptionKeys::stepwise
• align_rmsd_column : basic::options::OptionKeys::evaluation
• align_rmsd_fns : basic::options::OptionKeys::evaluation
• align_rmsd_format : basic::options::OptionKeys::evaluation
• align_rmsd_target : basic::options::OptionKeys::evaluation
• aligner : basic::options::OptionKeys::cm
• alignment : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• alignment2 : basic::options::OptionKeys::in::file
• alignment_res : basic::options::OptionKeys::stepwise::rna
• ALL : app::pyrosetta_toolkit::modules::prettytable::prettytable
• all : basic::options::OptionKeys::out::path , utility::options::OptionKeys::options
• all_atom_mode_kink_constraint : basic::options::OptionKeys::antibody
• all_hydration_frames : basic::options::OptionKeys::magnesium
• allow_anchor_repack : basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen : basic::options::OptionKeys::stepwise::rna
• allow_bulge : basic::options::OptionKeys::rna::farna
• allow_bulge_at_chainbreak : basic::options::OptionKeys::stepwise::rna
• allow_chain_boundary_jump_partner_right_at_fixed_BP : basic::options::OptionKeys::stepwise::rna
• allow_complex_loop_graph : basic::options::OptionKeys::score
• allow_consecutive_bulges : basic::options::OptionKeys::rna::farna
• allow_fixed_res_at_moving_res : basic::options::OptionKeys::stepwise::rna
• allow_flips : basic::options::OptionKeys::mp::dock
• allow_fragment_moves_in_bps : basic::options::OptionKeys::rna::farna
• allow_gly : basic::options::OptionKeys::hotspot
• allow_internal_hinge_moves : basic::options::OptionKeys::stepwise::monte_carlo
• allow_internal_local_moves : basic::options::OptionKeys::stepwise::monte_carlo
• allow_jump_in_numbering : basic::options::OptionKeys::full_model
• allow_lig_move : basic::options::OptionKeys::loops
• allow_omega_mismatches_for_north_clusters : basic::options::OptionKeys::antibody
• allow_omega_move : basic::options::OptionKeys::loops
• allow_proline : basic::options::OptionKeys::hotspot
• allow_rare_aro_chi : basic::options::OptionKeys::remodel::design
• allow_skip_bulge : basic::options::OptionKeys::stepwise::monte_carlo
• allow_split_off : basic::options::OptionKeys::stepwise::monte_carlo
• allow_submotif_split : basic::options::OptionKeys::stepwise::monte_carlo
• allow_takeoff_torsion_move : basic::options::OptionKeys::loops
• allow_variable_bond_geometry : basic::options::OptionKeys::stepwise::monte_carlo
• allow_virtual_o2prime_hydrogens : basic::options::OptionKeys::stepwise::rna
• allow_virtual_side_chains : basic::options::OptionKeys::stepwise::protein
• allowed_bulge_res : basic::options::OptionKeys::rna::farna
• allowed_closure_attempts : basic::options::OptionKeys::remodel::RemodelLoopMover
• allowed_pdb : basic::options::OptionKeys::frags
• allowed_residues_by_position : basic::options::OptionKeys::cyclic_peptide
• aln_format : basic::options::OptionKeys::cm
• aln_length_filter : basic::options::OptionKeys::cm
• aln_length_filter_quantile : basic::options::OptionKeys::cm
• alpha_increment : basic::options::OptionKeys::sample_around
• alter_spec_disruption_mode : protocols::pmut_scan
• alternate_3_letter_codes : basic::options::OptionKeys::in
• alternative_closure_protocol : basic::options::OptionKeys::loops
• altpos : clean_pdb_keep_ligand
• always_remodel_full_loop : basic::options::OptionKeys::loops
• ambig_talos_cs_A : basic::options::OptionKeys::in::file
• ambig_talos_cs_B : basic::options::OptionKeys::in::file
• amino_acids : amino_acids
• analytic_etable_evaluation : basic::options::OptionKeys::score
• analyzer : app::pyrosetta_toolkit::modules::ScoreAnalysis
• anchor : basic::options::OptionKeys::AnchoredDesign
• anchor_noise_constraints_mode : basic::options::OptionKeys::AnchoredDesign::testing
• anchor_offset : basic::options::OptionKeys::ms
• anchor_pdb : basic::options::OptionKeys::AnchoredPDBCreator
• anchor_type : basic::options::OptionKeys::pepspec
• anchor_via_constraints : basic::options::OptionKeys::AnchoredDesign::testing
• AnchoredDesign : basic::options::OptionKeys::AnchoredDesign
• angle : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::matdes
• angle_cutoff : basic::options::OptionKeys::mp::lipid_acc
• angle_max : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range
• angle_res : basic::options::OptionKeys::hotspot
• annealer : basic::options::OptionKeys::flexpack::annealer , basic::options::OptionKeys::rotamerdump
• annotate : basic::options::OptionKeys::frags
• ansi_colors : app::pyrosetta_toolkit::window_modules::interactive_terminal::interactive_terminal
• anti_polar_weight : basic::options::OptionKeys::mh::score
• antibody : basic::options::OptionKeys::antibody
• antibody_database : basic::options::OptionKeys::antibody::design
• apbs_debug : basic::options::OptionKeys::pb_potential
• apbs_path : basic::options::OptionKeys::pb_potential
• apc : test::T250_Constraints
• APDBC_cycles : basic::options::OptionKeys::AnchoredPDBCreator
• append_rc : setup_pyrosetta
• append_surf_ads : app::surface_docking::surface_docking
• append_surf_sol : app::surface_docking::surface_docking
• approximate_decoy_entropy : basic::options::OptionKeys::optE
• archive : basic::options::OptionKeys::archive , basic::options::OptionKeys::run
• arg_sweep_cutoff : basic::options::OptionKeys::enzdes
• arg_sweep_interface : basic::options::OptionKeys::enzdes
• arglist : contacts
• args : app::delta_score_per_mutation , app::pyrosetta_toolkit::modules::DesignBreakdown , app::surface_docking::surface_docking , loops_kic
• armijo_min_stepsize : basic::options::OptionKeys::optimization
• aromatic_motifs : basic::options::OptionKeys::motifs
• asp_hack : mrlo
• aspartimide_penalty_value : basic::options::OptionKeys::score
• assembly : basic::options::OptionKeys::assembly
• assembly_type : basic::options::OptionKeys::sewing
• assign_gasteiger_atom_types : basic::options::OptionKeys::in::file
• assign_ss : basic::options::OptionKeys::rescore
• at5C : test::T100_Basic
• at5CA : test::T100_Basic
• at5N : test::T100_Basic
• atom1 : test::T220_AtomAtomPairEnergies
• atom2 : test::T220_AtomAtomPairEnergies
• atom_mask : basic::options::OptionKeys::edensity
• atom_mask_min : basic::options::OptionKeys::edensity
• atom_names : basic::options::OptionKeys::james
• atom_pair_cst_weight : basic::options::OptionKeys::antibody::design
• atom_radius_buffer : basic::options::OptionKeys::fingerprint
• atom_radius_scale : basic::options::OptionKeys::fingerprint
• atom_scores : basic::options::OptionKeys::holes
• atom_tree_diff : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• atom_tree_diff_bb : basic::options::OptionKeys::out::file
• atom_tree_diff_bl : basic::options::OptionKeys::out::file
• atom_tree_diff_sc : basic::options::OptionKeys::out::file
• atomC : test::T100_Basic
• atomCA : test::T100_Basic
• atomic_burial_cutoff : basic::options::OptionKeys::pose_metrics
• atomN : test::T100_Basic
• ATOMS : PDBInfo
• atr_rep_screen : basic::options::OptionKeys::stepwise
• atr_rep_screen_for_docking : basic::options::OptionKeys::stepwise
• attach_as_sc : basic::options::OptionKeys::smhybrid
• attach_as_sc_sub : basic::options::OptionKeys::smhybrid
• attach_atom : basic::options::OptionKeys::smhybrid
• attach_rsd : basic::options::OptionKeys::smhybrid
• attached_pdb : basic::options::OptionKeys::ufv::insert
• attempt_pyrimidine_flip : basic::options::OptionKeys::rna::farna::erraser
• author : app::pyrosetta_toolkit::modules::prettytable::setup
• author_email : app::pyrosetta_toolkit::modules::prettytable::setup
• auto_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize
• auto_generate_kink_constraint : basic::options::OptionKeys::antibody
• auto_setup_metals : basic::options::OptionKeys::in
• auto_tune : basic::options::OptionKeys::cluster
• autofilter : basic::options::OptionKeys::rna::farna
• AvNAPSA_negative : local
• AvNAPSA_positive : local