- d -

• d2h_sa_reweight : basic::options::OptionKeys::in::file
• D_alpha_comp_file : basic::options::OptionKeys::cyclic_peptide
• D_beta_comp_file : basic::options::OptionKeys::cyclic_peptide
• d_max : basic::options::OptionKeys::score::saxs
• d_min : basic::options::OptionKeys::score::saxs
• d_step : basic::options::OptionKeys::score::saxs
• da_eval_pose_map : basic::options::OptionKeys::DomainAssembly
• da_linker_file : basic::options::OptionKeys::DomainAssembly
• da_linker_file_rna : basic::options::OptionKeys::DomainAssembly
• da_nruns : basic::options::OptionKeys::DomainAssembly
• da_require_buried : basic::options::OptionKeys::DomainAssembly
• da_setup : basic::options::OptionKeys::DomainAssembly
• da_setup_option_file : basic::options::OptionKeys::DomainAssembly
• da_setup_output_pdb : basic::options::OptionKeys::DomainAssembly
• da_start_pdb : basic::options::OptionKeys::DomainAssembly
• da_start_pdb_num : basic::options::OptionKeys::DomainAssembly
• dalphaball : basic::options::OptionKeys::holes
• darc_components : basic::options::OptionKeys::fingerprint
• darc_elsts_only : basic::options::OptionKeys::fingerprint
• darc_shape_only : basic::options::OptionKeys::fingerprint
• data : erraser_single_res_analysis
• data_file : basic::options::OptionKeys::motifs , basic::options::OptionKeys::rna
• data_in : basic::options::OptionKeys::optE
• data_out : basic::options::OptionKeys::optE
• database : basic::options::OptionKeys::in::path , pyrosetta::toolbox::load_ligand
• database_cache_dir : basic::options::OptionKeys::in::path
• database_filter : basic::options::OptionKeys::out
• database_name : basic::options::OptionKeys::inout::dbms
• database_partition : basic::options::OptionKeys::inout::dbms
• database_protocol_id : basic::options::OptionKeys::out
• date : version
• datefmt : pyrosetta::tests::distributed::test_dask
• db : basic::options::OptionKeys::out::path , basic::options::OptionKeys::rna::denovo::db
• db_path : basic::options::OptionKeys::lh
• dbms : basic::options::OptionKeys::in::dbms , basic::options::OptionKeys::inout::dbms
• dc : basic::options::OptionKeys::dc , basic::options::OptionKeys::in::file
• dd_parser : basic::options::OptionKeys::jd2
• ddg : basic::options::OptionKeys::ddg
• DDG_cutoff : protocols::pmut_scan
• ddg_cycles : revert_app
• ddg_predictions_file : basic::options::OptionKeys::in::file
• debug : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::edensity , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::holes , basic::options::OptionKeys::james , basic::options::OptionKeys::loodo , basic::options::OptionKeys::loops , basic::options::OptionKeys::membrane , basic::options::OptionKeys::run , basic::options::OptionKeys::smhybrid
• debug_derivatives : basic::options::OptionKeys::edensity
• debug_inaccurate_G : basic::options::OptionKeys::optimization
• debug_loop_closure : basic::options::OptionKeys::loops
• debug_output : basic::options::OptionKeys::ddg
• debug_structures : basic::options::OptionKeys::abinitio
• decoystats : basic::options::OptionKeys::run
• default : 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
• default_buffer_size : utility::io::mpi_stream , zlib_stream
• DEFAULT_DEPRECATION_MESSAGE : ez_setup
• default_max_cycles : basic::options::OptionKeys::optimization
• default_movement_params : basic::options::OptionKeys::RBSegmentRelax
• default_rama_sampling_table : basic::options::OptionKeys::cyclic_peptide
• default_repeats : basic::options::OptionKeys::relax
• DEFAULT_SAVE_DIR : ez_setup
• DEFAULT_URL : ez_setup
• DEFAULT_VERSION : ez_setup
• define_match_by_single_downstream_positioning : basic::options::OptionKeys::match
• definitely_virtualize : basic::options::OptionKeys::stepwise
• deg2rad : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• degrees_to_radians : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• delay : basic::options::OptionKeys::run
• delete_checkpoints : basic::options::OptionKeys::run
• delete_interface_native_sidechains : basic::options::OptionKeys::AnchoredDesign::testing
• delete_old_poses : basic::options::OptionKeys::jd2
• delphi_grid : basic::options::OptionKeys::fingerprint
• delta1 : erraser_analysis
• delta2 : erraser_analysis
• deltaE : test::Workshop4test
• denied_pdb : basic::options::OptionKeys::frags
• denovo : basic::options::OptionKeys::rna::denovo
• DenovoProteinDesign : basic::options::OptionKeys::DenovoProteinDesign
• density : basic::options::OptionKeys::hotspot
• depth : basic::options::OptionKeys::frags
• deriv_check : basic::options::OptionKeys::rna::denovo::minimize
• derive_torsion_string_from_native_pose : basic::options::OptionKeys::loops
• describe_fragments : basic::options::OptionKeys::frags
• description_file : basic::options::OptionKeys::boinc
• design : basic::options::OptionKeys::antibody::design , basic::options::OptionKeys::dna::design , basic::options::OptionKeys::matdes::design , basic::options::OptionKeys::remodel::design , basic::options::OptionKeys::rot_anl , basic::options::OptionKeys::smhybrid , revert_app
• design_all : basic::options::OptionKeys::remodel::design
• design_antigen : basic::options::OptionKeys::antibody::design
• design_around_ligand : basic::options::OptionKeys::remodel
• design_chains : basic::options::OptionKeys::docking
• design_contrast : basic::options::OptionKeys::out::file
• design_DNA : basic::options::OptionKeys::dna::specificity
• design_first : basic::options::OptionKeys::optE
• design_framework : basic::options::OptionKeys::antibody::design
• design_H3_stem : basic::options::OptionKeys::antibody::design
• design_hydrophobic : basic::options::OptionKeys::smhybrid
• design_interface : basic::options::OptionKeys::willmatch
• design_linker : basic::options::OptionKeys::smhybrid
• design_loop_num : hbs_design , oop_design , peptoid_design
• design_min_cycles : basic::options::OptionKeys::enzdes
• design_neighbors : basic::options::OptionKeys::remodel::design
• design_peptide : basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::flexPepDocking
• design_proline : basic::options::OptionKeys::antibody::design
• design_protocol : basic::options::OptionKeys::antibody::design
• design_res_files : basic::options::OptionKeys::smhybrid
• design_with_minpack : basic::options::OptionKeys::optE
• design_with_offrotpack : basic::options::OptionKeys::optE
• designable_second_shell : basic::options::OptionKeys::dna::design
• designing_with_noncanonicals : basic::options::OptionKeys::stepwise::monte_carlo
• desn_mc_temp : dddm
• detect_bonds : basic::options::OptionKeys::symmetry
• detect_design_interface : basic::options::OptionKeys::enzdes
• detect_disulf : basic::options::OptionKeys::in
• detect_disulf_tolerance : basic::options::OptionKeys::in
• detect_disulfide_before_relax : basic::options::OptionKeys::abinitio
• detect_oops : basic::options::OptionKeys::in
• device : basic::options::OptionKeys::gpu
• diff : erraser_analysis
• dihedral_cst_weight : basic::options::OptionKeys::antibody::design
• disable_all_filters : basic::options::OptionKeys::filters
• disable_co_filter : basic::options::OptionKeys::filters
• disable_orientation_dependent_rna_ch_o_bonds : basic::options::OptionKeys::score::rna
• disable_rg_filter : basic::options::OptionKeys::filters
• disable_sampling_of_loop_takeoff : basic::options::OptionKeys::stepwise::protein
• disable_sheet_filter : basic::options::OptionKeys::filters
• disallow_aa : basic::options::OptionKeys::antibody::design
• disallow_bps_at_extra_min_res : basic::options::OptionKeys::rna::denovo
• disallow_pack_polar_hydrogens : basic::options::OptionKeys::stepwise::polar_hydrogens
• disallow_vary_geometry_proton_chi : basic::options::OptionKeys::stepwise::polar_hydrogens
• display_water_hb_network : basic::options::OptionKeys::hydrate
• disregard_num_segment_matches : basic::options::OptionKeys::legacy_sewing
• dist_cut_off : basic::options::OptionKeys::fingerprint
• dist_cutoff : basic::options::OptionKeys::bunsat_calc2 , basic::options::OptionKeys::mp::lipid_acc
• dist_cutoffs : basic::options::OptionKeys::frags::contacts
• dist_thresholds : basic::options::OptionKeys::james
• distance_cutoff : basic::options::OptionKeys::contactMap
• distance_matrix : basic::options::OptionKeys::contactMap
• distance_tolerance : basic::options::OptionKeys::loodo
• distinguish_pucker : basic::options::OptionKeys::stepwise::rna
• disulf_cutoff_postrelax : basic::options::OptionKeys::cyclic_peptide
• disulf_cutoff_prerelax : basic::options::OptionKeys::cyclic_peptide
• disulf_landing_range : basic::options::OptionKeys::remodel
• disulf_matching_probe : basic::options::OptionKeys::score
• disulfide_file : basic::options::OptionKeys::stepwise::protein
• disulfide_positions : basic::options::OptionKeys::cluster::energy_based_clustering
• disulfide_res : basic::options::OptionKeys::full_model
• disulfide_scorer : basic::options::OptionKeys::blivens::disulfide_scorer
• DisulfideInsertion : basic::options::OptionKeys::DisulfideInsertion
• diversify_lvl : basic::options::OptionKeys::pepspec
• diversify_pep_seqs : basic::options::OptionKeys::pepspec
• DMS_careful_base_pair_classifier : basic::options::OptionKeys::score::rna
• DMS_separate_features : basic::options::OptionKeys::score::rna
• dna : basic::options::OptionKeys::dna
• dna_backbone_torsion_sdevs : basic::options::OptionKeys::dna::specificity
• dna_chi_torsion_sdev : basic::options::OptionKeys::dna::specificity
• dna_defs : basic::options::OptionKeys::dna::design
• dna_defs_file : basic::options::OptionKeys::dna::design
• dna_move : basic::options::OptionKeys::relax
• dna_p : test::T880_Other
• dna_sugar_torsion_sdev : basic::options::OptionKeys::dna::specificity
• do_dock : basic::options::OptionKeys::antibody::design
• do_final_repack : basic::options::OptionKeys::relax::centroid
• do_minimization : basic::options::OptionKeys::make_mainchain_potential
• do_minimize : basic::options::OptionKeys::peptide_deriver
• do_not_archive_on_node0 : basic::options::OptionKeys::jd3
• do_not_autoassign_SS : basic::options::OptionKeys::out::file
• do_not_count_adjacent_res_hbonds : basic::options::OptionKeys::cyclic_peptide
• do_not_remove_connection_inconsistencies : basic::options::OptionKeys::legacy_sewing
• do_not_sample_multiple_virtual_sugar : basic::options::OptionKeys::stepwise::rna
• dock : basic::options::OptionKeys::matdes::dock , basic::options::OptionKeys::mp::dock
• dock_cycle_rounds : basic::options::OptionKeys::antibody::design
• dock_each_chunk : basic::options::OptionKeys::rna::denovo
• dock_each_chunk_per_chain : basic::options::OptionKeys::rna::denovo
• dock_hires : test::Workshop7test
• dock_into_density : basic::options::OptionKeys::rna::denovo
• dock_into_density_legacy : basic::options::OptionKeys::rna::denovo
• dock_jump : docking , test::T600_Docking
• dock_lowres : test::Workshop7test
• dock_lowres_filter : basic::options::OptionKeys::docking
• dock_mcm_first_cycles : basic::options::OptionKeys::docking
• dock_mcm_rot_magnitude : basic::options::OptionKeys::docking
• dock_mcm_second_cycles : basic::options::OptionKeys::docking
• dock_mcm_trans_magnitude : basic::options::OptionKeys::docking
• dock_min : basic::options::OptionKeys::docking
• dock_p : test::T600_Docking
• dock_pert : basic::options::OptionKeys::docking , docking , test::T600_Docking
• dock_ppk : basic::options::OptionKeys::docking
• dock_prot : docking
• dock_rtmin : basic::options::OptionKeys::docking
• dock_trials : basic::options::OptionKeys::enzdes
• docking : basic::options::OptionKeys::docking
• docking_centroid_inner_cycles : basic::options::OptionKeys::docking
• docking_centroid_outer_cycles : basic::options::OptionKeys::docking
• docking_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• docking_highres : docking
• docking_interface_score : basic::options::OptionKeys::score
• docking_local_refine : basic::options::OptionKeys::docking
• docking_low_res_score : basic::options::OptionKeys::docking
• docking_lowres : docking , test::T600_Docking
• docking_move_size : basic::options::OptionKeys::rna::denovo
• docklowres_rot_magnitude : basic::options::OptionKeys::docking
• docklowres_trans_magnitude : basic::options::OptionKeys::docking
• DockMetrics : basic::options::OptionKeys::evaluation
• DomainAssembly : basic::options::OptionKeys::DomainAssembly
• domainFusion : basic::options::OptionKeys::remodel::domainFusion
• dont_hydrate_hb_engaged_bb_O : basic::options::OptionKeys::hydrate
• dont_minimize_omega : basic::options::OptionKeys::chemically_conjugated_docking
• dont_mutate_correct_charge : local
• dont_mutate_glyprocys : local
• dont_mutate_hbonded_sidechains : local
• dont_rewrite_dunbrack_database : basic::options::OptionKeys::out::file
• dont_use_reference_energies : basic::options::OptionKeys::optE
• dont_use_symm_in_pcalc : basic::options::OptionKeys::patterson
• double_lazy_ig : basic::options::OptionKeys::packing
• double_mutant_scan : protocols::pmut_scan
• dr_cycles : basic::options::OptionKeys::remodel , basic::options::OptionKeys::ufv
• dry_run : basic::options::OptionKeys::out , basic::options::OptionKeys::run
• dscore_cutoff : basic::options::OptionKeys::dna::design::reversion
• dspec_cutoff : basic::options::OptionKeys::dna::design::reversion
• dssp : basic::options::OptionKeys::in::file
• dssp1 : basic::options::OptionKeys::mh::filter
• dssp2 : basic::options::OptionKeys::mh::filter
• dtest : basic::options::OptionKeys::motifs
• dualspace : basic::options::OptionKeys::relax
• dump : basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::mh::dump , basic::options::OptionKeys::mh::harvest , basic::options::OptionKeys::rna::denovo::out , basic::options::OptionKeys::stepwise
• dump_all_As : basic::options::OptionKeys::loodo
• dump_all_Bs : basic::options::OptionKeys::loodo
• dump_cg_bb : basic::options::OptionKeys::pepspec
• dump_chainA_only : basic::options::OptionKeys::matdes::dock
• dump_connollySurface : basic::options::OptionKeys::pocket_grid
• dump_coord_cst_weight_array : basic::options::OptionKeys::loopfcst
• dump_cst_set : basic::options::OptionKeys::constraints
• dump_cyclic_poses : basic::options::OptionKeys::peptide_deriver
• dump_espGrid : basic::options::OptionKeys::pocket_grid
• dump_every_model : basic::options::OptionKeys::legacy_sewing
• dump_final_repack_without_ligand_pdb : basic::options::OptionKeys::enzdes
• dump_frags : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::jumps
• dump_freq : basic::options::OptionKeys::recces
• dump_Grid : basic::options::OptionKeys::pocket_grid
• dump_input_pdb : basic::options::OptionKeys::mh
• dump_inverse_rotamers : basic::options::OptionKeys::enzdes
• dump_loop_samples : basic::options::OptionKeys::enzdes
• dump_loops_only : basic::options::OptionKeys::canonical_sampling::sampling
• dump_matching_motifs : basic::options::OptionKeys::mh
• dump_motif_pdbs : basic::options::OptionKeys::mh
• dump_motifs : basic::options::OptionKeys::motifs
• dump_pdb : basic::options::OptionKeys::matdes::dock , basic::options::OptionKeys::recces , basic::options::OptionKeys::rot_anl
• dump_pdbs : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::legacy_sewing
• dump_peptide_pose : basic::options::OptionKeys::peptide_deriver
• dump_pocketGrid : basic::options::OptionKeys::pocket_grid
• dump_prepared_pose : basic::options::OptionKeys::peptide_deriver
• dump_report_file : basic::options::OptionKeys::peptide_deriver
• dump_rotamer_sets : basic::options::OptionKeys::packing
• dump_rotamers : basic::options::OptionKeys::ralford::dump_rotamers
• dump_silent : basic::options::OptionKeys::recces
• dump_stems : basic::options::OptionKeys::rna::denovo
• dump_templates : basic::options::OptionKeys::tcrmodel
• dump_trajectory : basic::options::OptionKeys::dump_trajectory
• dump_transfac : basic::options::OptionKeys::mean_field
• dump_weight_trajectory : basic::options::OptionKeys::rdc
• dumpPDB_abinitio : basic::options::OptionKeys::flexPepDocking
• dumpPDB_hires : basic::options::OptionKeys::flexPepDocking
• dumpPDB_lowres : basic::options::OptionKeys::flexPepDocking
• dun02_file : basic::options::OptionKeys::corrections::score
• dun10 : basic::options::OptionKeys::corrections::score
• dun10_dir : basic::options::OptionKeys::corrections::score
• dun_entropy_correction : basic::options::OptionKeys::corrections::score
• dun_normsd : basic::options::OptionKeys::corrections::score
• dunbrack_prob_buried : basic::options::OptionKeys::packing
• dunbrack_prob_nonburied : basic::options::OptionKeys::packing
• duplicate_angle_cutoff : basic::options::OptionKeys::motifs
• duplicate_dist_cutoff : basic::options::OptionKeys::motifs
• duplicate_motif_cutoff : basic::options::OptionKeys::motifs
• dwell_cutoff : basic::options::OptionKeys::corrections::water
• dwkulp : basic::options::OptionKeys::dwkulp
• dyepos : basic::options::OptionKeys::AnchoredDesign::akash
• dynamic_grid_refinement : basic::options::OptionKeys::match
• dynamic_prof_calls : basic
• dynamic_prof_total : basic