- d -

d2h_sa_reweight : basic::options::OptionKeys::in::file
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
data_file : basic::options::OptionKeys::motifs
data_in : basic::options::OptionKeys::optE
data_out : basic::options::OptionKeys::optE
database : 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 : basic::options::OptionKeys::in
database_protocol_id : basic::options::OptionKeys::out
db_path : basic::options::OptionKeys::lh
db_prefix : 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_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::loops , basic::options::OptionKeys::membrane , basic::options::OptionKeys::patterson , basic::options::OptionKeys::run , basic::options::OptionKeys::smhybrid
debug_derivatives : basic::options::OptionKeys::edensity
debug_loop_closure : basic::options::OptionKeys::loops
debug_output : basic::options::OptionKeys::ddg
debug_structures : basic::options::OptionKeys::abinitio
decoy : basic::options::OptionKeys::casp
decoystats : basic::options::OptionKeys::run
default_buffer_size : utility::io::mpi_stream
default_max_cycles : basic::options::OptionKeys::optimization
default_movement_params : basic::options::OptionKeys::RBSegmentRelax
default_repeats : basic::options::OptionKeys::relax
define_match_by_single_downstream_positioning : basic::options::OptionKeys::match
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
denied_pdb : basic::options::OptionKeys::frags
DenovoProteinDesign : basic::options::OptionKeys::DenovoProteinDesign
density : basic::options::OptionKeys::hotspot
depth : basic::options::OptionKeys::frags
deriv_check : basic::options::OptionKeys::rna
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
design_all : basic::options::OptionKeys::remodel::design
design_cdrs : basic::options::OptionKeys::antibody::design
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_hydrophobic : basic::options::OptionKeys::smhybrid
design_interface : basic::options::OptionKeys::willmatch
design_linker : basic::options::OptionKeys::smhybrid
design_method : basic::options::OptionKeys::antibody::design
design_min_cycles : basic::options::OptionKeys::enzdes
design_neighbors : basic::options::OptionKeys::remodel::design
design_peptide : basic::options::OptionKeys::flexPepDocking
design_post_graft : basic::options::OptionKeys::antibody::design
design_res_files : basic::options::OptionKeys::smhybrid
design_rounds : basic::options::OptionKeys::antibody::design
design_scorefxn : basic::options::OptionKeys::antibody::design
design_with_minpack : basic::options::OptionKeys::optE
designable_second_shell : basic::options::OptionKeys::dna::design
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_to_min : basic::options::OptionKeys::rot_anl
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
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_backbone_sampling : basic::options::OptionKeys::stepwise::protein
disallow_native_aa : basic::options::OptionKeys::DenovoProteinDesign
dist_cut_off : basic::options::OptionKeys::fingerprint
dist_cutoff : basic::options::OptionKeys::bunsat_calc2
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
distinguish_pucker : basic::options::OptionKeys::stepwise::rna
disulf_landing_range : basic::options::OptionKeys::remodel
disulf_matching_probe : basic::options::OptionKeys::score
disulfide_scorer : basic::options::OptionKeys::blivens::disulfide_scorer
diversify_lvl : basic::options::OptionKeys::pepspec
diversify_pep_seqs : basic::options::OptionKeys::pepspec
dna : basic::options::OptionKeys::dna
dna_defs : basic::options::OptionKeys::dna::design
dna_defs_file : basic::options::OptionKeys::dna::design
dna_move : basic::options::OptionKeys::relax
do_final_repack : basic::options::OptionKeys::relax::centroid
do_graft_design : basic::options::OptionKeys::antibody::design
do_not_sample_multiple_virtual_sugar : basic::options::OptionKeys::stepwise::rna
do_post_design_modeling : basic::options::OptionKeys::antibody::design
do_post_graft_design_modeling : basic::options::OptionKeys::antibody::design
do_sequence_design : basic::options::OptionKeys::antibody::design
dock : basic::options::OptionKeys::matdes::dock
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_pert : basic::options::OptionKeys::docking
dock_post_graft : basic::options::OptionKeys::antibody::design
dock_ppk : basic::options::OptionKeys::docking
dock_rounds : basic::options::OptionKeys::antibody::design
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_interface_score : basic::options::OptionKeys::score
docking_local_refine : basic::options::OptionKeys::docking
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_minimize_omega : basic::options::OptionKeys::chemically_conjugated_docking
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_lazy_ig_mem_limit : basic::options::OptionKeys::packing
downweight_by_sasa : basic::options::OptionKeys::ddg
dr_cycles : basic::options::OptionKeys::fldsgn , 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::stepwise::protein
dump_cg_bb : basic::options::OptionKeys::pepspec
dump_chainA_only : basic::options::OptionKeys::matdes::dock
dump_connect_info : basic::options::OptionKeys::inout
dump_coord_cst_weight_array : basic::options::OptionKeys::loopfcst
dump_cst_set : basic::options::OptionKeys::constraints
dump_final_repack_without_ligand_pdb : basic::options::OptionKeys::enzdes
dump_frags : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::jumps
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_matching_motifs_cutoff : basic::options::OptionKeys::mh
dump_motif_pdbs : basic::options::OptionKeys::mh
dump_motif_pdbs_min_counts : basic::options::OptionKeys::mh
dump_motifs : basic::options::OptionKeys::motifs
dump_pdb : basic::options::OptionKeys::matdes::dock , basic::options::OptionKeys::rot_anl
dump_pdbs : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::specificity
dump_post_graft_designs : basic::options::OptionKeys::antibody::design
dump_rotamer_sets : basic::options::OptionKeys::packing
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
dunbrack_prob_nonburied_semirotameric : 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
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