- d -

• D2LChiralMap() : protocols::simple_moves::chiral
• d2r() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::electron_density
• 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::scoring::rna
• default_stub() : core::kinematics
• define_cut_point_stochasticly() : protocols::seeded_abinitio
• define_movemap_chains() : protocols::seeded_abinitio
• define_scorable_core_from_secondary_structure() : protocols::loops
• defs2allowedtypes() : protocols::motifs
• defs2map() : protocols::motifs
• defs2vector() : protocols::motifs
• delete_all_intragroup_edges() : core::graph
• delete_comment() : core::pose
• delete_region() : protocols::grafting
• 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
• DEPROTONATED() : core::chemical
• derive_sc_sc_restraints() : protocols::relax
• deserialize_db_listener_data() : protocols::features
• design_residues_list() : protocols::dna
• determine_crossover_behavior() : core::scoring::methods
• dexponential() : core::scoring::constraints
• dgaussian() : core::scoring::constraints
• dihedral_bin() : core::scoring::dna
• dihedral_distance() : protocols::idealize
• DIIODINATION() : core::chemical
• dimer_pairing_pointer_sorter() : core::scoring
• DIMETHYLATION() : core::chemical
• dir_jump() : core::kinematics
• dis_get_coordinate_system() : protocols::jumping
• dis_get_ncac() : protocols::jumping
• dis_RT_from_epos() : protocols::jumping
• disable_constraint_scoreterms() : protocols::enzdes::enzutil
• discontinued_lower() : protocols::hybridization
• discontinued_upper() : protocols::hybridization
• dist_score() : protocols::sic_dock
• distance() : core::kinematics , core::kinematics::tree
• distance_4d() : protocols::rna
• distance_7d() : protocols::rna
• distance_squared() : core::kinematics::tree
• DISULFIDE() : core::chemical
• disulfide_bonds() : core::conformation
• 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_one_line() : protocols::frag_picker::scores
• do_set_xyz() : protocols::swa::protein
• 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::swa::rna
• DOF_bin_value() : protocols::swa::rna
• 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
• drop_constraints() : core::scoring::constraints
• dround() : core::scoring::rna::chemical_shift
• 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_bfactor_pdb() : core::io::pdb
• dump_connect_info() : core::io::pdb
• dump_cutpoint_info() : protocols::anchored_design
• dump_foldtree_kinemage() : protocols::viewer
• dump_frames_as_pdb() : core::fragment
• dump_library() : core::pack::dunbrack
• dump_loophash_linkers() : protocols::sic_dock
• dump_matrix() : protocols::evaluation , protocols::toolbox
• dump_matrix_no() : protocols::toolbox , protocols::evaluation
• 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
• dumpcgo() : protocols::kinmatch
• dunbrack_print() : protocols::MakeRotLib
• dup_residue() : core::pack::dunbrack , core::pack::rotamer_set