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_alpha_comp_file
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- D_beta_comp_file
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- 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
- darc_components
: basic::options::OptionKeys::fingerprint
, fingerprint
- darc_elsts_only
: basic::options::OptionKeys::fingerprint
, fingerprint
- darc_shape_only
: basic::options::OptionKeys::fingerprint
, fingerprint
- data
: app::delta_score_per_mutation
- Data
: fmt::internal
- data_file
: basic::options::OptionKeys::motifs
, basic::options::OptionKeys::rna
, motifs
, rna
- data_filename
: app::delta_score_per_mutation
- 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
, pyrosetta::toolbox::load_ligand
, toolbox::load_ligand
- database_cache_dir
: 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_AND_BATCH_ID_TAG
: basic::mpi
- 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
- date()
: ObjexxFCL
- Dawson()
: numeric::statistics
- db
: basic::options::OptionKeys::out::path
, basic::options::OptionKeys::rna::farna::db
, out::path
, rna::farna::db
- db_partition_from_options()
: basic::database
- db_path
: basic::options::OptionKeys::lh
, lh
- DbDataTypeCOP
: basic::database::schema_generator
- DbDataTypeOP
: basic::database::schema_generator
- DbDataTypes
: basic::database::schema_generator
- DbMoverMessageListenerCOP
: basic::mpi
- DbMoverMessageListenerOP
: basic::mpi
- 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_cutoff
: protocols::pmut_scan
- ddg_cycles
: revert_app
- 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::loodo
, basic::options::OptionKeys::loops
, basic::options::OptionKeys::membrane
, basic::options::OptionKeys::run
, basic::options::OptionKeys::smhybrid
, edensity
, FloppyTail
, holes
, james
, loodo
, loops
, membrane
, run
, smhybrid
- debug_derivatives
: basic::options::OptionKeys::edensity
, edensity
- debug_inaccurate_G
: basic::options::OptionKeys::optimization
, optimization
- 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_num
: app::surface_docking::surface_docking
- decoystats
: basic::options::OptionKeys::run
, run
- default
: app::pyrosetta_toolkit::modules::DesignBreakdown
- DEFAULT
: app::pyrosetta_toolkit::modules::prettytable::prettytable
- 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
, setup_pyrosetta
, toolbox::adjust_library_path
- default_buffer_size
: utility::io::mpi_stream
, zlib_stream
- default_max_cycles
: basic::options::OptionKeys::optimization
, optimization
- default_movement_params
: basic::options::OptionKeys::RBSegmentRelax
, RBSegmentRelax
- default_rama_sampling_table
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- default_repeats
: basic::options::OptionKeys::relax
, relax
- DefaultStrategy
: zlib_stream
- define_match_by_single_downstream_positioning
: basic::options::OptionKeys::match
, match
- define_xml_schema_group()
: utility::tag
- defineEnergyMethodCreator()
: pyrosetta
, src
- 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_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
- delLoop()
: app::pyrosetta_toolkit::modules::tools::loops
- delphi_grid
: basic::options::OptionKeys::fingerprint
, fingerprint
- deltaE
: test::Workshop4test
- 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
- depth_first_search_sort()
: utility::graph
- depth_first_visit()
: utility::graph
- depth_first_visit_sort_impl()
: utility::graph
- deriv_check
: basic::options::OptionKeys::rna::farna::minimize
, rna::farna::minimize
- derive_torsion_string_from_native_pose
: basic::options::OptionKeys::loops
, loops
- describe_fragments
: basic::options::OptionKeys::frags
, frags
- description
: app::pyrosetta_toolkit::modules::prettytable::setup
- 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
, revert_app
, rot_anl
, smhybrid
- design_all
: basic::options::OptionKeys::remodel::design
, remodel::design
- design_antigen()
: antibody::design
, basic::options::OptionKeys::antibody::design
- design_around_ligand
: basic::options::OptionKeys::remodel
, remodel
- 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_framework()
: antibody::design
, basic::options::OptionKeys::antibody::design
- design_H3_stem()
: antibody::design
, basic::options::OptionKeys::antibody::design
- design_hydrophobic
: basic::options::OptionKeys::smhybrid
, smhybrid
- design_interface
: basic::options::OptionKeys::willmatch
, willmatch
- design_linker
: basic::options::OptionKeys::smhybrid
, smhybrid
- design_loop_num
: hbs_design
, oop_design
, peptoid_design
- design_min_cycles
: basic::options::OptionKeys::enzdes
, enzdes
- design_neighbors
: basic::options::OptionKeys::remodel::design
, remodel::design
- design_peptide
: basic::options::OptionKeys::cyclic_peptide
, basic::options::OptionKeys::flexPepDocking
, cyclic_peptide
, flexPepDocking
- design_proline()
: antibody::design
, basic::options::OptionKeys::antibody::design
- design_protocol()
: antibody::design
, basic::options::OptionKeys::antibody::design
- design_res_files
: basic::options::OptionKeys::smhybrid
, smhybrid
- design_with_minpack
: basic::options::OptionKeys::optE
, optE
- designable_second_shell
: basic::options::OptionKeys::dna::design
, dna::design
- desn_mc_temp
: dddm
- dest
: contacts
- det3()
: numeric::model_quality
- 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
- dihedral()
: numeric
- dihedral_cst_weight()
: antibody::design
, basic::options::OptionKeys::antibody::design
- 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
- dir
: app::surface_docking::surface_docking
- dirup()
: pdb_to_molfile
- 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_bps_at_extra_min_res
: basic::options::OptionKeys::rna::farna
, rna::farna
- disregard_num_segment_matches
: basic::options::OptionKeys::sewing
, sewing
- dist()
: coordlib
- 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_sq()
: coordlib
- dist_thresholds
: basic::options::OptionKeys::james
, james
- distance()
: numeric
, ObjexxFCL
- distance_cutoff
: basic::options::OptionKeys::contactMap
, contactMap
- distance_f1_f2_deriv()
: numeric::deriv
- distance_matrix
: basic::options::OptionKeys::contactMap
, contactMap
- distance_squared()
: numeric
, ObjexxFCL
- distance_tolerance
: basic::options::OptionKeys::loodo
, loodo
- distinguish_pucker
: basic::options::OptionKeys::stepwise::rna
, stepwise::rna
- disulf_cutoff_postrelax
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- disulf_cutoff_prerelax
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- disulf_file
: app::surface_docking::surface_docking
- disulf_landing_range
: basic::options::OptionKeys::remodel
, remodel
- disulf_matching_probe
: basic::options::OptionKeys::score
, score
- disulfide_file
: basic::options::OptionKeys::stepwise::protein
, stepwise::protein
- disulfide_partner
: app::delta_score_per_mutation
- 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
- DMS_careful_base_pair_classifier
: basic::options::OptionKeys::score
, score
- DMS_separate_features
: basic::options::OptionKeys::score
, score
- dna
: basic::options::OptionKeys::dna
, dna
- dna_backbone_torsion_sdevs
: basic::options::OptionKeys::dna::specificity
, dna::specificity
- dna_chi_torsion_sdev
: basic::options::OptionKeys::dna::specificity
, dna::specificity
- 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
- dna_p
: test::T880_Other
- dna_sugar_torsion_sdev
: basic::options::OptionKeys::dna::specificity
, dna::specificity
- dncase()
: ObjexxFCL
- do_abs()
: numeric
- do_add_symbol()
: numeric
- do_cos()
: numeric
- do_dock()
: antibody::design
, basic::options::OptionKeys::antibody::design
- do_exp()
: numeric
- do_final_repack
: basic::options::OptionKeys::relax::centroid
, relax::centroid
- 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_minimize
: basic::options::OptionKeys::peptide_deriver
, peptide_deriver
- do_not_count_adjacent_res_hbonds
: basic::options::OptionKeys::cyclic_peptide
, cyclic_peptide
- do_not_remove_connection_inconsistencies
: basic::options::OptionKeys::sewing
, sewing
- do_not_sample_multiple_virtual_sugar
: basic::options::OptionKeys::stepwise::rna
, stepwise::rna
- do_pow()
: numeric
- do_rb_min()
: antibody::design
, basic::options::OptionKeys::antibody::design
- do_recursion()
: numeric::random
- do_sin()
: numeric
- do_sqrt()
: numeric
- do_tan()
: numeric
- dock
: basic::options::OptionKeys::matdes::dock
, basic::options::OptionKeys::mp::dock
, matdes::dock
, mp::dock
- dock_cycle_rounds()
: antibody::design
, basic::options::OptionKeys::antibody::design
- dock_hires
: test::Workshop7test
- dock_jump
: docking
, test::T600_Docking
- dock_lowres
: test::Workshop7test
- 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_min_dock()
: antibody::design
, basic::options::OptionKeys::antibody::design
- dock_p
: test::T600_Docking
- dock_pert
: basic::options::OptionKeys::docking
, docking
, test::T600_Docking
- dock_ppk
: basic::options::OptionKeys::docking
, docking
- dock_prot
: docking
- 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_frequency
: basic::options::OptionKeys::stepwise::monte_carlo
, stepwise::monte_carlo
- docking_highres
: docking
- docking_interface_score
: basic::options::OptionKeys::score
, score
- docking_local_refine
: basic::options::OptionKeys::docking
, docking
- docking_lowres
: docking
, test::T600_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_mutate_correct_charge
: local
- dont_mutate_glyprocys
: local
- dont_mutate_hbonded_sidechains
: local
- 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()
: coordlib
, numeric
, numeric::kinematic_closure
, ObjexxFCL
- dot_product()
: app::surface_docking::surf_param
, Equations
, numeric
, ObjexxFCL
, PhiPsi
- double_lazy_ig
: basic::options::OptionKeys::packing
, packing
- double_mutant_scan
: protocols::pmut_scan
- double_of()
: ObjexxFCL
- down_cast()
: utility
- dr_cycles
: basic::options::OptionKeys::remodel
, basic::options::OptionKeys::ufv
, remodel
, ufv
- DRange
: ObjexxFCL
- draw_membrane_planes()
: PyMOLPyRosettaServer
- 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::magnesium::montecarlo
, basic::options::OptionKeys::mh::dump
, basic::options::OptionKeys::mh::harvest
, basic::options::OptionKeys::rna::farna
, basic::options::OptionKeys::stepwise
, magnesium::montecarlo
, mh::dump
, mh::harvest
, rna::farna
, stepwise
, yaml
- dump_all()
: yaml
- dump_all_As
: basic::options::OptionKeys::loodo
, loodo
- dump_all_Bs
: basic::options::OptionKeys::loodo
, loodo
- dump_cg_bb
: basic::options::OptionKeys::pepspec
, pepspec
- dump_chainA_only
: basic::options::OptionKeys::matdes::dock
, matdes::dock
- dump_connollySurface
: basic::options::OptionKeys::pocket_grid
, pocket_grid
- dump_coord_cst_weight_array
: basic::options::OptionKeys::loopfcst
, loopfcst
- dump_cst_set
: basic::options::OptionKeys::constraints
, constraints
- dump_cyclic_poses
: basic::options::OptionKeys::peptide_deriver
, peptide_deriver
- dump_espGrid
: basic::options::OptionKeys::pocket_grid
, pocket_grid
- dump_every_model
: basic::options::OptionKeys::sewing
, sewing
- dump_final_repack_without_ligand_pdb
: basic::options::OptionKeys::enzdes
, enzdes
- dump_frags()
: abinitio
, basic::options::OptionKeys::abinitio
, basic::options::OptionKeys::jumps
, jumps
- dump_Grid
: basic::options::OptionKeys::pocket_grid
, pocket_grid
- 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_motif_pdbs
: 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
, basic::options::OptionKeys::sewing
, ddg
, dna::specificity
, sewing
- dump_peptide_pose
: basic::options::OptionKeys::peptide_deriver
, peptide_deriver
- dump_pocketGrid
: basic::options::OptionKeys::pocket_grid
, pocket_grid
- dump_prepared_pose
: basic::options::OptionKeys::peptide_deriver
, peptide_deriver
- dump_report_file
: basic::options::OptionKeys::peptide_deriver
, peptide_deriver
- dump_rotamer_sets
: basic::options::OptionKeys::packing
, packing
- dump_weight_trajectory
: basic::options::OptionKeys::rdc
, rdc
- dumpPDB()
: app::pyrosetta_toolkit::modules::tools::output
- 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
- 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
- dx_ddelta_omega1()
: numeric::crick_equations
- dx_ddelta_z1()
: numeric::crick_equations
- dx_ddz1()
: numeric::crick_equations
- dx_domega1()
: numeric::crick_equations
- dx_dr1()
: numeric::crick_equations
- dy_ddelta_omega1()
: numeric::crick_equations
- dy_ddelta_z1()
: numeric::crick_equations
- dy_ddz1()
: numeric::crick_equations
- dy_domega1()
: numeric::crick_equations
- dy_dr1()
: numeric::crick_equations
- dyepos()
: AnchoredDesign::akash
, basic::options::OptionKeys::AnchoredDesign::akash
- dynamic_grid_refinement
: basic::options::OptionKeys::match
, match
- dynamic_prof_calls
: basic
- dynamic_prof_total
: basic
- dz_ddelta_omega1()
: numeric::crick_equations
- dz_ddelta_z1()
: numeric::crick_equations
- dz_ddz1()
: numeric::crick_equations
- dz_domega1()
: numeric::crick_equations
- dz_dr1()
: numeric::crick_equations