Here is a list of all namespace members with links to the namespace documentation for each member:

- d -

• d2h_sa_reweight : basic::options::OptionKeys::in::file , in::file
• d_max : basic::options::OptionKeys::score::saxs , score::saxs
• d_min : basic::options::OptionKeys::score::saxs , score::saxs
• d_step : basic::options::OptionKeys::score::saxs , 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
• dalphaball : basic::options::OptionKeys::holes , holes
• DALPHABALL_DERIV : basic
• data_file : basic::options::OptionKeys::motifs , motifs
• data_in : basic::options::OptionKeys::optE , optE
• data_out : basic::options::OptionKeys::optE , optE
• DATA_STORAGE : basic
• database : basic::options::OptionKeys::in::path , in::path
• database_filter : basic::options::OptionKeys::out , 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_AND_BATCH_ID_TAG : basic::message_listening
• database_protocol_id : basic::options::OptionKeys::out , out
• DatabaseResourceLocatorCOP : basic::resource_manager::locator
• DatabaseResourceLocatorOP : basic::resource_manager::locator
• DatabaseSessionLoaderCOP : basic::database
• DatabaseSessionLoaderOP : basic::database
• DatabaseSessionOptionsCOP : basic::database
• DatabaseSessionOptionsOP : basic::database
• Dawson() : numeric::statistics
• db_partition_from_options() : basic::database
• db_path : basic::options::OptionKeys::lh , lh
• db_prefix : basic::options::OptionKeys::lh , lh
• DbDataTypeCOP : basic::database::schema_generator
• DbDataTypeOP : basic::database::schema_generator
• DbDataTypes : basic::database::schema_generator
• DbMoverMessageListenerCOP : basic::message_listening
• DbMoverMessageListenerOP : basic::message_listening
• 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 , basic::options::OptionKeys::patterson , basic::options::OptionKeys::run , basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::run , run
• default_buffer_size : utility::io::mpi_stream
• default_max_cycles : basic::options::OptionKeys::optimization , optimization
• default_movement_params : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• default_repeats : basic::options::OptionKeys::relax , relax
• define_match_by_single_downstream_positioning : basic::options::OptionKeys::match , match
• deg2rad : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• degrees() : numeric::conversions
• DEGREES : numeric::conversions
• degrees_to_radians : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• delay : basic::options::OptionKeys::run , 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 : basic::options::OptionKeys::run , 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 : basic::options::OptionKeys::rna , 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 , basic::options::OptionKeys::remodel::design , basic::options::OptionKeys::rot_anl , basic::options::OptionKeys::smhybrid , dna::design , matdes::design , remodel::design , rot_anl , smhybrid
• design_all : basic::options::OptionKeys::remodel::design , remodel::design
• design_cdrs() : antibody::design , basic::options::OptionKeys::antibody::design
• design_chains : basic::options::OptionKeys::docking , docking
• design_contrast : basic::options::OptionKeys::out::file , out::file
• design_DNA : basic::options::OptionKeys::dna::specificity , dna::specificity
• design_first : basic::options::OptionKeys::optE , optE
• design_hydrophobic : basic::options::OptionKeys::smhybrid , smhybrid
• design_interface : basic::options::OptionKeys::willmatch , willmatch
• design_linker : basic::options::OptionKeys::smhybrid , smhybrid
• design_method() : antibody::design , basic::options::OptionKeys::antibody::design
• design_min_cycles : basic::options::OptionKeys::enzdes , enzdes
• design_neighbors : basic::options::OptionKeys::remodel::design , remodel::design
• design_peptide : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• design_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• design_res_files : basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::symmetry , 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
• DFUNC : basic
• DiagnosticDataAP : basic::datacache
• DiagnosticDataCAP : basic::datacache
• DiagnosticDataCOP : basic::datacache
• DiagnosticDataOP : basic::datacache
• diff_to_min : basic::options::OptionKeys::rot_anl , 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 : basic::options::OptionKeys::score , score
• disable_rg_filter : basic::options::OptionKeys::filters , filters
• disable_sampling_of_loop_takeoff : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• disable_sheet_filter : basic::options::OptionKeys::filters , filters
• disallow_backbone_sampling : basic::options::OptionKeys::stepwise::protein , 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 : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• disulf_landing_range : basic::options::OptionKeys::remodel , remodel
• disulf_matching_probe : basic::options::OptionKeys::score , score
• disulfide_scorer : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer
• diversify_lvl : basic::options::OptionKeys::pepspec , pepspec
• diversify_pep_seqs : basic::options::OptionKeys::pepspec , pepspec
• divide() : numeric
• DIVIDE_SYMBOL : numeric::expression_parser
• DivideExpressionCOP : numeric::expression_parser
• DivideExpressionOP : numeric::expression_parser
• 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 : basic::options::OptionKeys::relax , relax
• do_abs() : numeric
• do_add_symbol() : numeric
• do_cos() : numeric
• do_exp() : numeric
• do_final_repack : basic::options::OptionKeys::relax::centroid , 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 : basic::options::OptionKeys::stepwise::rna , 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 : basic::options::OptionKeys::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 : basic::options::OptionKeys::remodel::domainFusion , remodel::domainFusion
• dont_minimize_omega() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• dont_rewrite_dunbrack_database : basic::options::OptionKeys::out::file , out::file
• dont_use_reference_energies : basic::options::OptionKeys::optE , optE
• dont_use_symm_in_pcalc : basic::options::OptionKeys::patterson , patterson
• dot() : numeric , numeric::kinematic_closure
• dot_product() : numeric
• dot_product_3x3() : numeric::kinematic_closure
• double_lazy_ig : basic::options::OptionKeys::packing , packing
• double_lazy_ig_mem_limit : basic::options::OptionKeys::packing , packing
• down_cast() : utility
• down_pointer_cast() : utility::pointer
• downweight_by_sasa() : basic::options::OptionKeys::ddg , ddg
• dr_cycles : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::remodel , basic::options::OptionKeys::ufv , fldsgn , remodel , ufv
• dry_run : basic::options::OptionKeys::out , basic::options::OptionKeys::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 : basic::options::OptionKeys::relax , relax
• dump : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• dump_cg_bb : basic::options::OptionKeys::pepspec , 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 , basic::options::OptionKeys::rot_anl , 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 : basic::options::OptionKeys::packing , packing
• dump_weight_trajectory : basic::options::OptionKeys::rdc , 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 : basic::options::OptionKeys::packing , packing
• dunbrack_prob_nonburied : basic::options::OptionKeys::packing , packing
• dunbrack_prob_nonburied_semirotameric : basic::options::OptionKeys::packing , 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
• dynamic_prof_calls : basic
• dynamic_prof_total : basic