- d -

• d2h_sa_reweight() : basic::options::OptionKeys::in::file , in::file
• d_max() : score::saxs
• d_min() : score::saxs
• d_step() : score::saxs
• da_eval_pose_map() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_linker_file() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_linker_file_rna() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_nruns() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_require_buried() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_setup() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_setup_option_file() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_setup_output_pdb() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_start_pdb() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• da_start_pdb_num() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• dalphaball() : basic::options::OptionKeys::holes , holes
• data_file() : basic::options::OptionKeys::motifs , motifs
• data_in() : basic::options::OptionKeys::optE , optE
• data_out() : basic::options::OptionKeys::optE , optE
• database() : basic::options::OptionKeys::in::path , in::path
• database_filter() : out
• database_mode_from_name() : utility::sql_database
• database_name() : basic::options::OptionKeys::inout::dbms , inout::dbms
• database_partition() : basic::options::OptionKeys::inout::dbms , inout::dbms
• database_protocol() : basic::options::OptionKeys::in , in
• database_protocol_id() : out
• Dawson() : numeric::statistics
• db_partition_from_options() : basic::database
• db_path() : basic::options::OptionKeys::lh , lh
• db_prefix() : basic::options::OptionKeys::lh , lh
• dbms() : basic::options::OptionKeys::in::dbms , basic::options::OptionKeys::inout::dbms , in::dbms , inout::dbms
• dc() : basic::options::OptionKeys::dc , basic::options::OptionKeys::in::file , dc , in::file
• dd_parser() : basic::options::OptionKeys::jd2 , jd2
• ddg() : basic::options::OptionKeys::ddg , ddg
• ddg_predictions_file() : basic::options::OptionKeys::in::file , in::file
• debug() : abinitio , AnchoredDesign , 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 , edensity , FloppyTail , holes , james , loops , membrane , patterson , run , smhybrid
• debug_derivatives() : basic::options::OptionKeys::edensity , edensity
• debug_loop_closure() : basic::options::OptionKeys::loops , loops
• debug_output() : basic::options::OptionKeys::ddg , ddg
• debug_structures() : abinitio , basic::options::OptionKeys::abinitio
• decode6bit() : utility
• decode_32_to_24() : utility
• decoy() : basic::options::OptionKeys::casp , casp
• decoystats() : run
• default_max_cycles() : basic::options::OptionKeys::optimization , optimization
• default_movement_params() : RBSegmentRelax
• default_repeats() : relax
• define_match_by_single_downstream_positioning() : basic::options::OptionKeys::match , match
• degrees() : numeric::conversions
• delay() : run
• delete_and_assign() : utility::pointer
• delete_and_assign_array() : utility::pointer
• delete_and_zero() : utility::pointer
• delete_and_zero_array() : utility::pointer
• delete_checkpoints() : run
• delete_interface_native_sidechains() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• delete_old_poses() : basic::options::OptionKeys::jd2 , jd2
• denied_pdb() : basic::options::OptionKeys::frags , frags
• DenovoProteinDesign() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• density() : basic::options::OptionKeys::hotspot , hotspot
• depth() : basic::options::OptionKeys::frags , frags
• deriv_check() : rna
• derive_torsion_string_from_native_pose() : basic::options::OptionKeys::loops , loops
• describe_fragments() : basic::options::OptionKeys::frags , frags
• description_file() : basic::options::OptionKeys::boinc , boinc
• deserialize() : numeric
• design() : antibody::design , basic::options::OptionKeys::antibody::design , basic::options::OptionKeys::dna::design , basic::options::OptionKeys::matdes::design , dna::design , matdes::design , remodel::design , rot_anl , smhybrid
• design_all() : remodel::design
• design_cdrs() : antibody::design , basic::options::OptionKeys::antibody::design
• design_chains() : basic::options::OptionKeys::docking , docking
• design_contrast() : out::file
• design_DNA() : basic::options::OptionKeys::dna::specificity , dna::specificity
• design_first() : basic::options::OptionKeys::optE , optE
• design_hydrophobic() : smhybrid
• design_interface() : willmatch
• design_linker() : smhybrid
• design_method() : antibody::design , basic::options::OptionKeys::antibody::design
• design_min_cycles() : basic::options::OptionKeys::enzdes , enzdes
• design_neighbors() : remodel::design
• design_peptide() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• design_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• design_res_files() : smhybrid
• design_rounds() : antibody::design , basic::options::OptionKeys::antibody::design
• design_scorefxn() : antibody::design , basic::options::OptionKeys::antibody::design
• design_with_minpack() : basic::options::OptionKeys::optE , optE
• designable_second_shell() : basic::options::OptionKeys::dna::design , dna::design
• det3() : numeric::model_quality
• det_3() : numeric::kinematic_closure
• detect_bonds() : symmetry
• detect_design_interface() : basic::options::OptionKeys::enzdes , enzdes
• detect_disulf() : basic::options::OptionKeys::in , in
• detect_disulf_tolerance() : basic::options::OptionKeys::in , in
• detect_disulfide_before_relax() : abinitio , basic::options::OptionKeys::abinitio
• detect_oops() : basic::options::OptionKeys::in , in
• device() : basic::options::OptionKeys::gpu , gpu
• diff_to_min() : rot_anl
• dihedral() : numeric
• dihedral_degrees() : numeric
• dihedral_degrees_double() : numeric
• dihedral_deriv_second() : numeric::deriv
• dihedral_double() : numeric
• dihedral_p1_cosine_deriv() : numeric::deriv
• dihedral_p1_cosine_deriv_first() : numeric::deriv
• dihedral_p2_cosine_deriv() : numeric::deriv
• dihedral_p2_cosine_deriv_first() : numeric::deriv
• dihedral_radians() : numeric
• dihedral_radians_double() : numeric
• disable_all_filters() : basic::options::OptionKeys::filters , filters
• disable_co_filter() : basic::options::OptionKeys::filters , filters
• disable_orientation_dependent_rna_ch_o_bonds() : score
• disable_rg_filter() : basic::options::OptionKeys::filters , filters
• disable_sampling_of_loop_takeoff() : stepwise::protein
• disable_sheet_filter() : basic::options::OptionKeys::filters , filters
• disallow_backbone_sampling() : stepwise::protein
• disallow_native_aa() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• dist_cut_off() : basic::options::OptionKeys::fingerprint , fingerprint
• dist_cutoff() : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• dist_cutoffs() : basic::options::OptionKeys::frags::contacts , frags::contacts
• dist_thresholds() : basic::options::OptionKeys::james , james
• distance() : numeric
• distance_cutoff() : basic::options::OptionKeys::contactMap , contactMap
• distance_f1_f2_deriv() : numeric::deriv
• distance_matrix() : basic::options::OptionKeys::contactMap , contactMap
• distance_squared() : numeric
• distinguish_pucker() : stepwise::rna
• disulf_landing_range() : remodel
• disulf_matching_probe() : score
• disulfide_scorer() : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer
• diversify_lvl() : pepspec
• diversify_pep_seqs() : pepspec
• divide() : numeric
• dixon_eig() : numeric::kinematic_closure
• dixon_sturm() : numeric::kinematic_closure
• dixonResultant() : numeric::kinematic_closure
• dna() : basic::options::OptionKeys::dna , dna
• dna_defs() : basic::options::OptionKeys::dna::design , dna::design
• dna_defs_file() : basic::options::OptionKeys::dna::design , dna::design
• dna_move() : relax
• do_abs() : numeric
• do_add_symbol() : numeric
• do_cos() : numeric
• do_exp() : numeric
• do_final_repack() : relax::centroid
• do_graft_design() : antibody::design , basic::options::OptionKeys::antibody::design
• do_ln() : numeric
• do_log() : numeric
• do_log10() : numeric
• do_log2() : numeric
• do_max() : numeric
• do_mean() : numeric
• do_median() : numeric
• do_min() : numeric
• do_not_sample_multiple_virtual_sugar() : stepwise::rna
• do_post_design_modeling() : antibody::design , basic::options::OptionKeys::antibody::design
• do_post_graft_design_modeling() : antibody::design , basic::options::OptionKeys::antibody::design
• do_pow() : numeric
• do_recursion() : numeric::random
• do_sequence_design() : antibody::design , basic::options::OptionKeys::antibody::design
• do_sin() : numeric
• do_sqrt() : numeric
• do_tan() : numeric
• dock() : basic::options::OptionKeys::matdes::dock , matdes::dock
• dock_lowres_filter() : basic::options::OptionKeys::docking , docking
• dock_mcm_first_cycles() : basic::options::OptionKeys::docking , docking
• dock_mcm_rot_magnitude() : basic::options::OptionKeys::docking , docking
• dock_mcm_second_cycles() : basic::options::OptionKeys::docking , docking
• dock_mcm_trans_magnitude() : basic::options::OptionKeys::docking , docking
• dock_min() : basic::options::OptionKeys::docking , docking
• dock_pert() : basic::options::OptionKeys::docking , docking
• dock_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• dock_ppk() : basic::options::OptionKeys::docking , docking
• dock_rounds() : antibody::design , basic::options::OptionKeys::antibody::design
• dock_rtmin() : basic::options::OptionKeys::docking , docking
• dock_trials() : basic::options::OptionKeys::enzdes , enzdes
• docking() : basic::options::OptionKeys::docking , docking
• docking_centroid_inner_cycles() : basic::options::OptionKeys::docking , docking
• docking_centroid_outer_cycles() : basic::options::OptionKeys::docking , docking
• docking_interface_score() : score
• docking_local_refine() : basic::options::OptionKeys::docking , docking
• docklowres_rot_magnitude() : basic::options::OptionKeys::docking , docking
• docklowres_trans_magnitude() : basic::options::OptionKeys::docking , docking
• DockMetrics() : basic::options::OptionKeys::evaluation , evaluation
• DomainAssembly() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• domainFusion() : remodel::domainFusion
• dont_minimize_omega() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• dont_rewrite_dunbrack_database() : out::file
• dont_use_reference_energies() : basic::options::OptionKeys::optE , optE
• dont_use_symm_in_pcalc() : patterson
• dot() : numeric , numeric::kinematic_closure
• dot_product() : numeric
• dot_product_3x3() : numeric::kinematic_closure
• double_lazy_ig() : packing
• double_lazy_ig_mem_limit() : packing
• down_cast() : utility
• down_pointer_cast() : utility::pointer
• downweight_by_sasa() : basic::options::OptionKeys::ddg , ddg
• dr_cycles() : basic::options::OptionKeys::fldsgn , fldsgn , remodel , ufv
• dry_run() : out , run
• dscore_cutoff() : basic::options::OptionKeys::dna::design::reversion , dna::design::reversion
• dspec_cutoff() : basic::options::OptionKeys::dna::design::reversion , dna::design::reversion
• dssp() : basic::options::OptionKeys::in::file , in::file
• dssp1() : basic::options::OptionKeys::mh::filter , mh::filter
• dssp2() : basic::options::OptionKeys::mh::filter , mh::filter
• dtest() : basic::options::OptionKeys::motifs , motifs
• dualspace() : relax
• dump() : stepwise::protein
• dump_cg_bb() : pepspec
• dump_chainA_only() : basic::options::OptionKeys::matdes::dock , matdes::dock
• dump_connect_info() : basic::options::OptionKeys::inout , inout
• dump_coord_cst_weight_array() : basic::options::OptionKeys::loopfcst , loopfcst
• dump_cst_set() : basic::options::OptionKeys::constraints , constraints
• dump_final_repack_without_ligand_pdb() : basic::options::OptionKeys::enzdes , enzdes
• dump_frags() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::jumps , jumps
• dump_input_pdb() : basic::options::OptionKeys::mh , mh
• dump_inverse_rotamers() : basic::options::OptionKeys::enzdes , enzdes
• dump_loop_samples() : basic::options::OptionKeys::enzdes , enzdes
• dump_loops_only() : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• dump_matching_motifs() : basic::options::OptionKeys::mh , mh
• dump_matching_motifs_cutoff() : basic::options::OptionKeys::mh , mh
• dump_motif_pdbs() : basic::options::OptionKeys::mh , mh
• dump_motif_pdbs_min_counts() : basic::options::OptionKeys::mh , mh
• dump_motifs() : basic::options::OptionKeys::motifs , motifs
• dump_pdb() : basic::options::OptionKeys::matdes::dock , matdes::dock , rot_anl
• dump_pdbs() : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::specificity , ddg , dna::specificity
• dump_post_graft_designs() : antibody::design , basic::options::OptionKeys::antibody::design
• dump_rotamer_sets() : packing
• dump_weight_trajectory() : rdc
• dumpPDB_abinitio() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• dumpPDB_hires() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• dumpPDB_lowres() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• dun02_file() : basic::options::OptionKeys::corrections::score , corrections::score
• dun10() : basic::options::OptionKeys::corrections::score , corrections::score
• dun10_dir() : basic::options::OptionKeys::corrections::score , corrections::score
• dun_entropy_correction() : basic::options::OptionKeys::corrections::score , corrections::score
• dun_normsd() : basic::options::OptionKeys::corrections::score , corrections::score
• dunbrack_prob_buried() : packing
• dunbrack_prob_nonburied() : packing
• dunbrack_prob_nonburied_semirotameric() : packing
• duplicate_angle_cutoff() : basic::options::OptionKeys::motifs , motifs
• duplicate_dist_cutoff() : basic::options::OptionKeys::motifs , motifs
• duplicate_motif_cutoff() : basic::options::OptionKeys::motifs , motifs
• dwkulp() : basic::options::OptionKeys::dwkulp , dwkulp
• dyepos() : AnchoredDesign::akash , basic::options::OptionKeys::AnchoredDesign::akash
• dynamic_grid_refinement() : basic::options::OptionKeys::match , match
• dynamic_pointer_cast() : utility::pointer