- a -

• aa1 : basic::options::OptionKeys::mh::filter
• aa2 : basic::options::OptionKeys::mh::filter
• aa_during_build : basic::options::OptionKeys::ufv
• aa_during_design_refine : basic::options::OptionKeys::ufv
• ab_dock_chains : basic::options::OptionKeys::antibody::design
• ABEGO : basic::options::OptionKeys::frags::ABEGO
• abinitio : 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
• active_site_definition_by_gridlig : basic::options::OptionKeys::match
• active_site_definition_by_residue : basic::options::OptionKeys::match
• add_atom_at_cen : basic::options::OptionKeys::smhybrid
• add_atom_type_set_parameters : basic::options::OptionKeys::chemical
• add_buffer_res : basic::options::OptionKeys::pepspec
• add_cavities : basic::options::OptionKeys::smhybrid
• add_cst_loop : basic::options::OptionKeys::fold_from_loops
• add_delete_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• add_metal_at_0 : basic::options::OptionKeys::smhybrid
• add_non_init_chunks : basic::options::OptionKeys::cm::hybridize
• add_orbitals : basic::options::OptionKeys::in
• 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_packing_ligand_rb_confs : basic::options::OptionKeys::enzdes
• adducts : basic::options::OptionKeys::packing
• AHD_cutoff : basic::options::OptionKeys::bunsat_calc2
• akash : basic::options::OptionKeys::AnchoredDesign::akash
• ala_scan : basic::options::OptionKeys::matdes::mutalyze
• align_file : basic::options::OptionKeys::phil
• 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_from_chunk_mapping : basic::options::OptionKeys::cm::hybridize
• alignment_from_template_seqpos : basic::options::OptionKeys::cm::hybridize
• alignment_res : basic::options::OptionKeys::stepwise::rna
• all : basic::options::OptionKeys::out::path , utility::options::OptionKeys::options
• allow_anchor_repack : basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen : basic::options::OptionKeys::stepwise::rna
• allow_bulge_at_chainbreak : basic::options::OptionKeys::stepwise::rna
• allow_chain_boundary_jump_partner_right_at_fixed_BP : basic::options::OptionKeys::stepwise::rna
• allow_fixed_res_at_moving_res : basic::options::OptionKeys::stepwise::rna
• 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_lig_move : basic::options::OptionKeys::loops
• 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_takeoff_torsion_move : basic::options::OptionKeys::loops
• allow_variable_bond_geometry : basic::options::OptionKeys::stepwise::monte_carlo
• allow_virtual_side_chains : basic::options::OptionKeys::stepwise::protein
• allowed_closure_attempts : basic::options::OptionKeys::remodel::RemodelLoopMover
• allowed_pdb : basic::options::OptionKeys::frags
• aln_format : basic::options::OptionKeys::cm
• aln_length_filter : basic::options::OptionKeys::cm
• aln_length_filter_quantile : basic::options::OptionKeys::cm
• alternative_closure_protocol : basic::options::OptionKeys::loops
• 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
• analytic_etable_evaluation : basic::options::OptionKeys::score
• anchor : basic::options::OptionKeys::AnchoredDesign
• anchor_noise_constraints_mode : basic::options::OptionKeys::AnchoredDesign::testing
• anchor_offset : basic::options::OptionKeys::ms
• 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_res : basic::options::OptionKeys::hotspot
• annealer : basic::options::OptionKeys::flexpack::annealer , basic::options::OptionKeys::rotamerdump
• annotate : basic::options::OptionKeys::frags
• 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
• apply_rot_cst_to_mutation_region_only : basic::options::OptionKeys::ddg
• approximate_decoy_entropy : basic::options::OptionKeys::optE
• archive : basic::options::OptionKeys::archive , basic::options::OptionKeys::run
• arg_dun_th : basic::options::OptionKeys::willmatch
• arg_sweep_cutoff : basic::options::OptionKeys::enzdes
• arg_sweep_interface : basic::options::OptionKeys::enzdes
• armijo_min_stepsize : basic::options::OptionKeys::optimization
• aromatic_motifs : basic::options::OptionKeys::motifs
• asp_dun_th : basic::options::OptionKeys::willmatch
• assembly : basic::options::OptionKeys::assembly
• assign_ss : basic::options::OptionKeys::rescore
• atom_mask : basic::options::OptionKeys::edensity
• atom_mask_min : basic::options::OptionKeys::edensity
• atom_names : basic::options::OptionKeys::james
• 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
• atomic_burial_cutoff : basic::options::OptionKeys::pose_metrics
• 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
• auto_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize
• auto_setup_metals : basic::options::OptionKeys::in
• auto_tune : basic::options::OptionKeys::cluster
• autopilot : basic::options::OptionKeys::remodel
• avg_rot_cst_enrg : basic::options::OptionKeys::ddg
• awesome_mode : basic::options::OptionKeys::james