- d -

• d2r() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• d_array_scale() : core::scoring::fiber_diffraction
• dD_dv1() : protocols::pockets
• dD_dv2() : protocols::pockets
• dD_dv3() : protocols::pockets
• dD_dv4() : protocols::pockets
• dD_dv5() : protocols::pockets
• dD_dv6() : protocols::pockets
• ddG_main() : protocols
• debug_dump_pose() : protocols::anchored_design
• debug_dump_rotamers() : core::pack::rotamer_set
• decide_on_beta_jumping_from_frags() : protocols::abinitio
• decompose() : protocols::nonlocal
• default_jump_atom() : core::chemical::rna
• default_stub() : core::kinematics
• define_chains() : protocols::stepwise::setup
• define_cut_point_stochasticly() : protocols::seeded_abinitio
• define_mainchain_atoms() : core::chemical
• define_movemap_chains() : protocols::seeded_abinitio
• define_scorable_core_from_secondary_structure() : protocols::loops
• definite_terminal_root() : protocols::stepwise::modeler
• defs2allowedtypes() : protocols::motifs
• defs2map() : protocols::motifs
• defs2vector() : protocols::motifs
• delete_all_intragroup_edges() : core::graph
• delete_carbohydrate_branch() : core::pose::carbohydrates
• delete_comment() : core::pose
• delete_leaf() : core::pose::carbohydrates
• delete_overhang_residues() : protocols::grafting
• delete_region() : protocols::grafting
• delete_this_struct_id() : protocols::features::strand_assembly
• delete_this_sw_can_by_sh_id_from_sw_by_comp() : protocols::features::strand_assembly
• delete_virtual_residues() : protocols::relax
• dellinte_dm() : core::scoring::rna::chemical_shift
• dellintk_dm() : core::scoring::rna::chemical_shift
• delta_magnetic_anisotropy() : core::scoring::rna::chemical_shift
• delta_ring_current() : core::scoring::rna::chemical_shift
• delta_ring_current_term() : core::scoring::rna::chemical_shift
• denom() : protocols::cryst
• derive_sc_sc_restraints() : protocols::relax
• deserialize_db_listener_data() : protocols::features
• deserialize_xyz_coords() : protocols::features
• design_protocol_to_enum() : protocols::antibody::design
• design_protocol_to_string() : protocols::antibody::design
• design_residues_list() : protocols::dna
• detect_base_contacts() : protocols::stepwise::modeler::rna::bulge
• detect_ld_chirality_from_polymer_residue() : core::chemical
• detect_phosphate_contacts() : protocols::stepwise::modeler::rna::phosphate
• detect_sugar_contacts() : protocols::stepwise::modeler::rna::sugar
• determinant() : protocols::simple_filters
• determinant_sign() : protocols::simple_filters
• determine_core_heading_surface_heading_by_distance() : protocols::features::strand_assembly
• determine_crossover_behavior() : core::scoring::lkball
• determine_file_type() : core::import_pose
• determine_frag_size() : protocols::abinitio::abscript
• determine_heading_direction_by_vector() : protocols::features::strand_assembly
• dexponential() : core::scoring::constraints
• dfour1_plan() : core::scoring::fiber_diffraction
• dgaussian() : core::scoring::constraints
• dihedral_bin() : core::scoring::dna
• dihedral_distance() : protocols::idealize
• dimer_pairing_pointer_sorter() : core::scoring
• dir_jump() : core::kinematics
• dis_get_coordinate_system() : protocols::jumping
• dis_get_ncac() : protocols::jumping
• dis_RT_from_epos() : protocols::jumping
• disable_conserved_framework_positions() : protocols::antibody::design
• disable_constraint_scoreterms() : protocols::enzdes::enzutil
• disable_design_antigen() : protocols::antibody::design
• disable_design_cdr() : protocols::antibody::design
• disable_design_cdrs() : protocols::antibody::design
• disable_design_framework() : protocols::antibody::design
• disable_design_region() : protocols::antibody::design
• disable_h3_stem_positions() : protocols::antibody::design
• discontinued_lower() : protocols::hybridization
• discontinued_upper() : protocols::hybridization
• dist_score() : protocols::sic_dock
• distance() : core::kinematics , core::kinematics::tree
• distance_squared() : core::kinematics::tree
• disulfide_bonds() : core::conformation
• dna_aa_from_oneletter_code() : core::scoring::dna
• dna_base_partner() : protocols::dna
• dna_comp_name_str() : protocols::dna
• dna_deriv_atom() : core::scoring::methods
• dna_full_name3() : protocols::dna
• DNA_INT_WTS() : core::scoring
• DNA_INT_WTS_GB() : core::scoring
• do_I_skip() : protocols::scoring::methods::pcs2
• do_not_edit_warning() : update_ResidueType_enum_files
• do_one_line() : protocols::frag_picker::scores
• do_scoring() : protocols::toolbox::sample_around
• do_set_xyz() : protocols::stepwise::sampler::protein
• do_xy_scan() : protocols::toolbox::sample_around
• DOCK_LOW_PATCH() : core::scoring
• DOCK_PATCH() : core::scoring
• dock_waters_to_atom() : protocols::toolbox::pose_metric_calculators
• dockPoseIntoMap() : protocols::electron_density
• DOF_bin_size() : protocols::stepwise::modeler::rna::rigid_body
• DOF_bin_value() : protocols::stepwise::modeler::rna::rigid_body
• dof_id_to_string() : protocols::environment
• DOF_Node_sorter() : core::optimization , core::optimization::symmetry
• DOF_type_is_rb() : core::id
• downstream_centroid_by_jump() : protocols::geometry
• downstream_residues_from_jump() : protocols::hybridization
• Doxygen_info() : update_ResidueType_enum_files
• drop_constraints() : core::scoring::constraints
• dround() : core::scoring::rna::chemical_shift
• dssp() : protocols::simple_filters
• DUMMY_BOOL() : core::scoring::hbonds
• DUMMY_DERIV() : core::scoring::hbonds
• DUMMY_HBGEODIMTYPE() : core::scoring::hbonds
• dummy_nodeop() : core::pack::scmin
• dump_as_pdb() : protocols::toolbox
• dump_atom_tree_diff() : core::import_pose::atom_tree_diffs
• dump_atomtree_kinemage() : protocols::viewer
• dump_chis() : protocols::metal_interface
• dump_cif() : core::io::mmcif
• dump_comment_pdb() : core::pose
• dump_cutpoint_info() : protocols::anchored_design
• dump_foldtree_kinemage() : protocols::viewer
• dump_frames_as_pdb() : core::fragment
• dump_graph() : core::chemical::sdf
• dump_gws() : core::io::carbohydrates
• dump_gws_chain() : core::io::carbohydrates
• dump_library() : core::pack::rotamers
• dump_loophash_linkers() : protocols::sic_dock
• dump_matrix() : protocols::evaluation , protocols::toolbox
• dump_matrix_no() : protocols::evaluation , protocols::toolbox
• dump_movemap() : protocols::abinitio
• dump_pdb() : core::io::pdb
• dump_pdb_residue() : core::io::pdb
• dump_points_pdb() : protocols::sic_dock
• dump_pose_kinemage() : protocols::viewer
• dump_reference_pose() : core::import_pose::atom_tree_diffs
• dump_residue_kinemage() : protocols::viewer
• dump_score_line() : core::import_pose::atom_tree_diffs
• dump_structure_kinemage() : protocols::viewer
• dump_tags_() : protocols::jumping
• dump_vall_fasta() : protocols::frags
• dumpcgo() : protocols::kinmatch
• dunbrack_print() : protocols::make_rot_lib
• dup_residue() : core::pack::rotamer_set , core::pack::rotamers