- d -

d2r() : core::scoring::electron_density , core::scoring::electron_density_atomwise
debug_dump_rotamers() : core::pack::rotamer_set
default_jump_atom() : core::chemical::rna
default_stub() : core::kinematics
define_mainchain_atoms() : core::chemical
delete_all_intragroup_edges() : core::graph
delete_comment() : core::pose
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
determine_crossover_behavior() : core::scoring::methods
dexponential() : core::scoring::constraints
dgaussian() : core::scoring::constraints
dihedral_bin() : core::scoring::dna
DIIODINATION() : core::chemical
dimer_pairing_pointer_sorter() : core::scoring
DIMETHYLATION() : core::chemical
distance() : core::kinematics , core::kinematics::tree
distance_squared() : core::kinematics::tree
DISULFIDE() : core::chemical
disulfide_bonds() : core::conformation
dna_deriv_atom() : core::scoring::methods
DNA_INT_WTS() : core::scoring
DNA_INT_WTS_GB() : core::scoring
DOCK_LOW_PATCH() : core::scoring
DOCK_PATCH() : core::scoring
DOF_Node_sorter() : core::optimization , core::optimization::symmetry
DOF_type_is_rb() : core::id
drop_constraints() : core::scoring::constraints
dround() : core::scoring::rna::chemical_shift
DUMMY_HBGEODIMTYPE() : core::scoring::hbonds
dummy_nodeop() : core::pack::scmin
dump_atom_tree_diff() : core::import_pose::atom_tree_diffs
dump_bfactor_pdb() : core::io::pdb
dump_comment_pdb() : core::pose
dump_connect_info() : core::io::pdb
dump_frames_as_pdb() : core::fragment
dump_library() : core::pack::dunbrack
dump_pdb() : core::io::pdb
dump_pdb_residue() : core::io::pdb
dump_reference_pose() : core::import_pose::atom_tree_diffs
dump_score_line() : core::import_pose::atom_tree_diffs
dup_residue() : core::pack::dunbrack , core::pack::rotamer_set