- a -

• aa1() : basic::options::OptionKeys::mh::filter , mh::filter
• aa2() : basic::options::OptionKeys::mh::filter , mh::filter
• aa_during_build() : ufv
• aa_during_design_refine() : ufv
• ab_dock_chains() : antibody::design , basic::options::OptionKeys::antibody::design
• ABEGO() : basic::options::OptionKeys::frags::ABEGO , frags::ABEGO
• abinitio() : abinitio , basic::options::OptionKeys::abinitio
• abinitio_cycles() : smhybrid
• abinitio_design() : smhybrid
• abrelax() : abrelax , basic::options::OptionKeys::abrelax
• abs_difference() : numeric
• accept_aborted_loops() : basic::options::OptionKeys::loops , loops
• action() : basic::options::OptionKeys::evolution , evolution
• active_site_definition_by_gridlig() : basic::options::OptionKeys::match , match
• active_site_definition_by_residue() : basic::options::OptionKeys::match , match
• add() : numeric
• add_atom_at_cen() : smhybrid
• add_atom_type_set_parameters() : basic::options::OptionKeys::chemical , chemical
• add_buffer_res() : pepspec
• add_cavities() : smhybrid
• add_cst_loop() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_delete_frequency() : stepwise::monte_carlo
• add_esc_char() : utility::json_spirit
• add_esc_chars() : utility::json_spirit
• add_exit_callback() : utility
• add_metal_at_0() : smhybrid
• add_non_init_chunks() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• add_orbitals() : basic::options::OptionKeys::in , in
• add_posn_iter_and_read_range_or_throw() : utility::json_spirit
• add_relax_cycles() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_res_after() : smhybrid
• add_res_before() : smhybrid
• add_spaces_left_align() : utility
• add_spaces_right_align() : utility
• add_ss_after() : smhybrid
• add_ss_before() : smhybrid
• add_virt_root() : stepwise::rna
• additional_packing_ligand_rb_confs() : basic::options::OptionKeys::enzdes , enzdes
• adducts() : packing
• AHD_cutoff() : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• akash() : AnchoredDesign::akash , basic::options::OptionKeys::AnchoredDesign::akash
• ala_scan() : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• align_file() : phil
• align_pdb() : stepwise
• align_rmsd_column() : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_fns() : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_format() : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_target() : basic::options::OptionKeys::evaluation , evaluation
• aligner() : basic::options::OptionKeys::cm , cm
• alignment() : basic::options::OptionKeys::in::file , in::file , out::file
• alignment2() : basic::options::OptionKeys::in::file , in::file
• alignment_from_chunk_mapping() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• alignment_from_template_seqpos() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• alignment_res() : stepwise::rna
• alignVectorSets() : numeric
• all() : out::path
• allow_anchor_repack() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen() : stepwise::rna
• allow_bulge_at_chainbreak() : stepwise::rna
• allow_chain_boundary_jump_partner_right_at_fixed_BP() : stepwise::rna
• allow_fixed_res_at_moving_res() : stepwise::rna
• allow_gly() : basic::options::OptionKeys::hotspot , hotspot
• allow_internal_hinge_moves() : stepwise::monte_carlo
• allow_internal_local_moves() : stepwise::monte_carlo
• allow_lig_move() : basic::options::OptionKeys::loops , loops
• allow_omega_move() : basic::options::OptionKeys::loops , loops
• allow_proline() : basic::options::OptionKeys::hotspot , hotspot
• allow_rare_aro_chi() : remodel::design
• allow_skip_bulge() : stepwise::monte_carlo
• allow_split_off() : stepwise::monte_carlo
• allow_takeoff_torsion_move() : basic::options::OptionKeys::loops , loops
• allow_variable_bond_geometry() : stepwise::monte_carlo
• allow_virtual_side_chains() : stepwise::protein
• allowed_closure_attempts() : remodel::RemodelLoopMover
• allowed_pdb() : basic::options::OptionKeys::frags , frags
• aln_format() : basic::options::OptionKeys::cm , cm
• aln_length_filter() : basic::options::OptionKeys::cm , cm
• aln_length_filter_quantile() : basic::options::OptionKeys::cm , cm
• alternative_closure_protocol() : basic::options::OptionKeys::loops , loops
• always_remodel_full_loop() : basic::options::OptionKeys::loops , loops
• ambig_talos_cs_A() : basic::options::OptionKeys::in::file , in::file
• ambig_talos_cs_B() : basic::options::OptionKeys::in::file , in::file
• analytic_etable_evaluation() : score
• anchor() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• anchor_noise_constraints_mode() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• anchor_offset() : basic::options::OptionKeys::ms , ms
• anchor_type() : pepspec
• anchor_via_constraints() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• AnchoredDesign() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• angle() : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::matdes , hotspot , matdes
• angle_degrees() : numeric
• angle_degrees_double() : numeric
• angle_in_range() : basic
• angle_of() : numeric
• angle_p1_deriv() : numeric::deriv
• angle_p1_p2_p3_deriv() : numeric::deriv
• angle_p2_deriv() : numeric::deriv
• angle_radians() : numeric
• angle_radians_double() : numeric
• angle_res() : basic::options::OptionKeys::hotspot , hotspot
• annealer() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer , rotamerdump
• annotate() : basic::options::OptionKeys::frags , frags
• antibody() : antibody , basic::options::OptionKeys::antibody
• antibody_database() : antibody::design , basic::options::OptionKeys::antibody::design
• apbs_debug() : pb_potential
• apbs_path() : pb_potential
• append_double() : utility::json_spirit
• append_esc_char_and_incr_iter() : utility::json_spirit
• apply_rot_cst_to_mutation_region_only() : basic::options::OptionKeys::ddg , ddg
• approximate_decoy_entropy() : basic::options::OptionKeys::optE , optE
• arccos() : numeric
• archive() : archive , basic::options::OptionKeys::archive , run
• arg_dun_th() : willmatch
• arg_greatest_several() : utility
• arg_least_several() : utility
• arg_max() : utility
• arg_min() : utility
• arg_sweep_cutoff() : basic::options::OptionKeys::enzdes , enzdes
• arg_sweep_interface() : basic::options::OptionKeys::enzdes , enzdes
• argmax() : utility
• argmin() : utility
• armijo_min_stepsize() : basic::options::OptionKeys::optimization , optimization
• aromatic_motifs() : basic::options::OptionKeys::motifs , motifs
• asp_dun_th() : willmatch
• assembly() : assembly , basic::options::OptionKeys::assembly
• assign_ss() : rescore
• atom_mask() : basic::options::OptionKeys::edensity , edensity
• atom_mask_min() : basic::options::OptionKeys::edensity , edensity
• atom_names() : basic::options::OptionKeys::james , james
• atom_radius_buffer() : basic::options::OptionKeys::fingerprint , fingerprint
• atom_radius_scale() : basic::options::OptionKeys::fingerprint , fingerprint
• atom_scores() : basic::options::OptionKeys::holes , holes
• atom_tree_diff() : basic::options::OptionKeys::in::file , in::file , out::file
• atom_tree_diff_bb() : out::file
• atom_tree_diff_bl() : out::file
• atom_tree_diff_sc() : out::file
• atomic_burial_cutoff() : pose_metrics
• attach_as_sc() : smhybrid
• attach_as_sc_sub() : smhybrid
• attach_atom() : smhybrid
• attach_rsd() : smhybrid
• attached_pdb() : ufv::insert
• auto_frag_insertion_weight() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• auto_setup_metals() : basic::options::OptionKeys::in , in
• auto_tune() : basic::options::OptionKeys::cluster , cluster
• autopilot() : remodel
• average_link_clustering() : numeric
• avg_rot_cst_enrg() : basic::options::OptionKeys::ddg , ddg
• awesome_mode() : basic::options::OptionKeys::james , james