- a -

• a : basic::options::OptionKeys::score::fiber_diffraction , compute_difference
• A : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• a : test.T110_numeric , test.T850_SubClassing
• a1 : docking , test.Workshop3test
• a2 : docking , test.Workshop3test
• a3 : docking
• A3BHbsCreatorMoverCOP : create_a3b_hbs
• A3BHbsCreatorMoverOP : create_a3b_hbs
• a_form_range : basic::options::OptionKeys::recces
• 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
• ab : test.T400_Refinement
• ab_struct : test.G201_Module_Structure
• ab_template_db_path : basic::options::OptionKeys::tcrmodel
• 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
• accept_no_op_moves : basic::options::OptionKeys::recces
• action : app_runner , auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , basic::options::OptionKeys::evolution , cache_trajectory , closure_error , correlation_time , DRRAFTER , drrafter_rna , execute , explosion_error , gaussian-sampling , general_RNP_setup_script , job_manager , kic_runner , percent_subangstrom , relax_starting_structure , run_backbone , run_sidechain , setup_for_complex_scoring_general , solution_counts , submit_jobs
• 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
• adapting : adapt_rotamers
• AdaptiveType : pyrosetta.distributed.cluster.utilities
• add_atom_at_cen : basic::options::OptionKeys::smhybrid
• add_atom_type_set_parameters : basic::options::OptionKeys::chemical
• add_atom_types : 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_ligand_constraints : local
• add_metal_at_0 : basic::options::OptionKeys::smhybrid
• add_mm_atom_type_set_parameters : basic::options::OptionKeys::chemical
• 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_decoy_info : loops , test.Workshop8test
• additional_objective_functions : basic::options::OptionKeys::lh
• additional_packing_ligand_rb_confs : basic::options::OptionKeys::enzdes
• address : basic::options::OptionKeys::run::PyMOLMover
• adducts : basic::options::OptionKeys::packing
• agg_with_max : basic::options::OptionKeys::mh::harvest
• aharm2 : vancomycin
• AHD_cutoff : basic::options::OptionKeys::bunsat_calc2
• akash : basic::options::OptionKeys::AnchoredDesign::akash
• ala : orn_macrocycle , test.T100_basic
• ala_pose : oop_conformations
• ala_scan : basic::options::OptionKeys::matdes::mutalyze
• ala_type : orn_macrocycle
• algorithm_choices : kic_runner
• align_native_seq : byres_data
• 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
• aligned : challenge
• aligner : basic::options::OptionKeys::cm
• alignment : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• alignment2 : basic::options::OptionKeys::in::file
• alignment_anchor_res : basic::options::OptionKeys::stepwise
• alignment_res : basic::options::OptionKeys::stepwise::rna
• alignment_sharpness : basic::options::OptionKeys::score
• all : basic::options::OptionKeys::out::path , utility::options::OptionKeys::options
• all_3mer_cycles : basic::options::OptionKeys::remodel::staged_sampling
• all_3mer_score_file : basic::options::OptionKeys::remodel::staged_sampling
• all_9mer_cycles : basic::options::OptionKeys::remodel::staged_sampling
• all_9mer_score_file : basic::options::OptionKeys::remodel::staged_sampling
• all_arrays_exist : cache_trajectory
• all_atom_mode_kink_constraint : basic::options::OptionKeys::antibody
• all_count_table : cal_vdw_radius_pool
• all_hydration_frames : basic::options::OptionKeys::magnesium
• all_phi : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• all_positions : basic::options::OptionKeys::ralford::dump_rotamers
• all_psi : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• allow_anchor_repack : basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen : basic::options::OptionKeys::stepwise::rna
• allow_bulge : basic::options::OptionKeys::rna::denovo
• 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::loop_close
• allow_consecutive_bulges : basic::options::OptionKeys::rna::denovo
• allow_de : local
• 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::denovo
• allow_gly : basic::options::OptionKeys::hotspot
• allow_glycan_torsion_moves : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• allow_his : local
• 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_rbmin : InterfaceMutMaker
• 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::denovo
• allowed_closure_attempts : basic::options::OptionKeys::remodel::RemodelLoopMover
• allowed_elements : local
• 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 : compute_difference
• alpha_beta_pattern : ss_finder
• alpha_cdr1_template_id : basic::options::OptionKeys::tcrmodel
• alpha_cdr1_template_pdb : basic::options::OptionKeys::tcrmodel
• alpha_cdr2_template_id : basic::options::OptionKeys::tcrmodel
• alpha_cdr2_template_pdb : basic::options::OptionKeys::tcrmodel
• alpha_cdr3_template_id : basic::options::OptionKeys::tcrmodel
• alpha_cdr3_template_pdb : basic::options::OptionKeys::tcrmodel
• alpha_framework_template_id : basic::options::OptionKeys::tcrmodel
• alpha_framework_template_pdb : basic::options::OptionKeys::tcrmodel
• alpha_germline_template_id : basic::options::OptionKeys::tcrmodel
• alpha_germline_template_pdb : basic::options::OptionKeys::tcrmodel
• alpha_increment : basic::options::OptionKeys::sample_around
• alpha_orientation_template_id : basic::options::OptionKeys::tcrmodel
• alpha_orientation_template_pdb : basic::options::OptionKeys::tcrmodel
• alphaphi : create_a3b_hbs
• alphapsi : create_a3b_hbs
• also_pack : metapatch
• alter_spec_disruption_mode : protocols::pmut_scan
• alternate_3_letter_codes : basic::options::OptionKeys::in
• alternate_fullatom_ats : basic::options::OptionKeys::corrections::chemical
• alternative_closure_protocol : basic::options::OptionKeys::loops
• alternative_score_file : basic::options::OptionKeys::cluster::energy_based_clustering
• altpos : clean_pdb_keep_ligand
• always_remodel_full_loop : basic::options::OptionKeys::loops
• ambig : beta_nonlocal
• ambig_talos_cs_A : basic::options::OptionKeys::in::file
• ambig_talos_cs_B : basic::options::OptionKeys::in::file
• amino_acids : amino_acids
• amphetamine : basic::options::OptionKeys::constel
• an : docking
• analytic_etable_evaluation : basic::options::OptionKeys::score
• analytic_membetable_evaluation : basic::options::OptionKeys::mp::scoring
• anarci_path : basic::options::OptionKeys::tcrmodel
• 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_residue : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• anchor_type : basic::options::OptionKeys::pepspec
• anchor_via_constraints : basic::options::OptionKeys::AnchoredDesign::testing
• AnchoredDesign : basic::options::OptionKeys::AnchoredDesign
• ancillary_hs : inverse_rotlib_dump
• ancillary_hs_stub_libs : scaffold_matcher
• ang : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• ang_lst : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• ang_mat : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• angle : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::matdes
• angle1 : erraser_analysis
• angle2 : erraser_analysis
• angle_cutoff : basic::options::OptionKeys::mp::lipid_acc
• angle_error : make_comparison
• angle_length_relax_rounds : basic::options::OptionKeys::cyclic_peptide
• angle_max : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range
• angle_range_bb : basic::options::OptionKeys::recces::thermal_sampling
• angle_range_chi : basic::options::OptionKeys::recces::thermal_sampling
• angle_range_free_bb : basic::options::OptionKeys::recces::thermal_sampling
• angle_range_free_chi : basic::options::OptionKeys::recces::thermal_sampling
• angle_relax_rounds : basic::options::OptionKeys::cyclic_peptide
• angle_res : basic::options::OptionKeys::hotspot
• angle_sampling : basic::options::OptionKeys
• angles : internal_coordinates , oop_conformations
• annealer : basic::options::OptionKeys::flexpack::annealer , basic::options::OptionKeys::rotamerdump
• annealing : basic::options::OptionKeys::stepwise::monte_carlo::csa
• annotate : basic::options::OptionKeys::frags
• ans : cal_vdw_radius_pool
• anti_polar_weight : basic::options::OptionKeys::mh::score
• antibody : basic::options::OptionKeys::antibody
• antibody_database : basic::options::OptionKeys::antibody::design
• anything_okay_for_orientation : oop_scan
• apbs_debug : basic::options::OptionKeys::pb_potential
• apbs_exe : PB_potential
• apbs_path : basic::options::OptionKeys::pb_potential
• apc : pna , test.T250_Constraints
• APDBC_cycles : basic::options::OptionKeys::AnchoredPDBCreator
• app : job_manager
• app_list_template : update_ui_project
• app_run_shell_script_template : update_ui_project
• append_n_residues : oop_creator
• append_nonlocal_residues : local
• apply_end_bias : basic::options::OptionKeys::abinitio
• approximate_buried_unsat_penalty_assume_const_backbone : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_burial_atomic_depth : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_burial_probe_radius : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_burial_resolution : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_hbond_bonus_cross_chain : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_hbond_energy_threshold : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_lys_ok_with_1 : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_natural_corrections1 : basic::options::OptionKeys::score
• approximate_buried_unsat_penalty_oversat_penalty : basic::options::OptionKeys::score
• approximate_decoy_entropy : basic::options::OptionKeys::optE
• arc : test.T008_Serialization
• archive : basic::options::OptionKeys::archive , basic::options::OptionKeys::run
• archive_on_disk : basic::options::OptionKeys::jd3
• arg_cation_pi_his_can_be_pi : basic::options::OptionKeys::score
• arg_sweep_cutoff : basic::options::OptionKeys::enzdes
• arg_sweep_interface : basic::options::OptionKeys::enzdes
• args : auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , combine_pdbs , demo.D010_Pose_structure , demo.D020_Pose_scoring , demo.D030_Fold_tree , demo.D040_Movemap , demo.D050_Packer_task , demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D090_Ala_scan , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface , DRRAFTER , drrafter_rna , finalize_models , find_lowest_scoring_relaxed_struct , general_RNP_setup_script , get_final_ddG_scores , get_lowest_scoring_relaxed_models , gpu_set_args , loops_kic , pyrosetta.tests.distributed.cluster.print_discovered_test_cases , pyrosetta.tests.distributed.test_dask , relax_starting_structure , setup_for_complex_scoring_general , submit_jobs
• arguments : 3d_histogram , app_runner , autocorrelation , bin_torsions , cache_trajectory , closure_error , correlation_time , delete_job , dummy-distribution , execute , explosion_error , gaussian-sampling , histogram , internal_coordinates , job_manager , kic_runner , legacy_score_vs_rmsd , make_comparison , percent_subangstrom , pivot_selection , plot , progress_bar , run_backbone , run_sidechain , score_vs_rmsd , score_vs_time , solution_counts , subloop_histogram , torsion_vs_time , wipe_cache
• argv : cal_NBR_radius
• armijo_min_stepsize : basic::options::OptionKeys::optimization
• aromatic : basic::options::OptionKeys::constel
• aromatic_motifs : basic::options::OptionKeys::motifs
• artists : subloop_histogram
• asn : vancomycin
• asn_type : vancomycin
• aspartimide_penalty_value : basic::options::OptionKeys::score
• assembly : basic::options::OptionKeys::assembly , basic::options::OptionKeys::mp::assembly
• assembly_type : basic::options::OptionKeys::legacy_sewing
• assign_by_field_names : pyrosetta.protocols.h5_importer
• assign_cdr : basic::options::OptionKeys::tcrmodel
• assign_cdr1a : basic::options::OptionKeys::tcrmodel
• assign_cdr1b : basic::options::OptionKeys::tcrmodel
• assign_cdr2a : basic::options::OptionKeys::tcrmodel
• assign_cdr2b : basic::options::OptionKeys::tcrmodel
• assign_cdr3a : basic::options::OptionKeys::tcrmodel
• assign_cdr3b : basic::options::OptionKeys::tcrmodel
• assign_gasteiger_atom_types : basic::options::OptionKeys::in::file
• assign_ss : basic::options::OptionKeys::rescore
• assume_command_line_has_pose_numbering : find_position_matches_using_inverse_rotamers
• at5C : test.T100_basic
• at5CA : test.T100_basic
• at5N : test.T100_basic
• atom : val2thr
• atom_index_1 : test.T220_AtomAtomPairEnergies
• atom_index_2 : 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_sasa_cutoff : local
• 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 : erraser_analysis
• atr : test.T220_AtomAtomPairEnergies
• atr1 : test_mm_lj
• atr2 : test_mm_lj
• atr_rep_screen : basic::options::OptionKeys::stepwise
• atr_rep_screen_for_docking : basic::options::OptionKeys::stepwise
• atr_total : test.T220_AtomAtomPairEnergies
• 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_all_polar : basic::options::OptionKeys::hydrate
• attempt_pyrimidine_flip : basic::options::OptionKeys::rna::erraser
• auth : basic::options::OptionKeys::cloud
• author : conf
• auto_detect_glycan_connections : basic::options::OptionKeys::in
• auto_download : basic::options::OptionKeys::machine_learning
• auto_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize
• auto_generate_h3_kink_constraint : basic::options::OptionKeys::antibody
• auto_generate_kink_constraint : basic::options::OptionKeys::antibody
• auto_setup_metals : basic::options::OptionKeys::in
• auto_tune : basic::options::OptionKeys::cluster
• autocorrelation : autocorrelation
• autodetect_loops : HelixAssemblyDesigner
• autofilter : basic::options::OptionKeys::rna::denovo
• AvNAPSA_negative : local
• AvNAPSA_positive : local
• ax : hist2d , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_common
• axes : subloop_histogram
• axis : build_jacobian
• axis_rot_sampling : basic::options::OptionKeys::corrections::water