- d -

• D : core::id
• d2h_sa : core::scoring
• D_AA : core::chemical
• D_CHIRALITY : protocols::simple_moves::chiral
• D_RNA : core::chemical
• D_SUGAR : core::chemical
• dab_sasa : core::scoring
• dab_sev : core::scoring
• DATABASE : protocols::jd2::JobInputterInputSource
• Db : core::chemical::element
• DBREF : core::io::pdb
• DBREF1 : core::io::pdb
• DBREF2 : core::io::pdb
• dc : core::scoring
• DCV_ALREADY_CYCLIZED : protocols::simple_moves
• DCV_CYCLIZABLE : protocols::simple_moves
• DCV_NOT_CYCLIZABLE : protocols::simple_moves
• ddG_bind_correlation : protocols::optimize_weights
• ddG_mutation_correlation : protocols::optimize_weights
• ddG_mutation_correlation_with_unfolded_energy : protocols::optimize_weights
• DEFAULT_t : core::chemical
• DELETE : protocols::stepwise::monte_carlo::mover
• DELETE_DOWNSTREAM : protocols::indexed_structure_store
• DELETE_EDGE : protocols::legacy_sewing
• DELETE_LOOP_RES : protocols::stepwise::monte_carlo::mover
• DELETE_PREVIOUS_ROTAMER : core::pack::rotamer_set
• DELETE_ROTAMER : core::pack::rotamer_set
• DELETE_UPSTREAM : protocols::indexed_structure_store
• DeleteBondOrder : core::chemical
• DELTA : core::chemical::rna , core::scoring::dna
• DELTA_ATOM : core::chemical
• DEOXY_O2PRIME : core::chemical
• DEOXY_SUGAR : core::chemical
• DEPROTONATED : core::chemical
• DesignProtocolEnum_total : protocols::antibody::design
• deterministic_graft : protocols::antibody::design
• DFIRE : core::scoring , core::scoring::methods
• DFr : protocols::fldsgn::topology
• DFr_BAB : protocols::fldsgn::topology
• DFr_HPN : protocols::fldsgn::topology
• dG_binding_correlation : protocols::optimize_weights
• diagonal : core::sequence
• DIAMAGNETIC : core::chemical
• DID_NOT_ADD_STRUCTURE : protocols::optimize_weights
• dihedral_constraint : core::scoring
• dihedralA : protocols::jumping
• dihedralAB : protocols::jumping
• dihedralB : protocols::jumping
• DIIODINATION : core::chemical
• DIMETHYLATED_CTERMINUS : core::chemical
• DIMETHYLATED_CTERMINUS_VARIANT : core::chemical
• DIMETHYLATION : core::chemical
• disAB : protocols::jumping
• discard_old_entity : protocols::pack_daemon
• distance_chainbreak : core::scoring
• DISULFIDE : core::chemical , core::pose::full_model_info
• DISULFIDE_BONDED : core::chemical
• disulfide_matching_energy : core::scoring::methods
• DMS : core::pose::rna
• DNA : core::chemical
• dna_base_distance : core::scoring
• dna_bb_torsion : core::scoring
• dna_bp : core::scoring
• dna_bs : core::scoring
• dna_chi : core::scoring
• dna_dihedral_bb : core::scoring
• dna_dihedral_chi : core::scoring
• dna_dihedral_sugar : core::scoring
• dna_dr : core::scoring
• dna_env : core::scoring
• dna_pair : core::scoring
• dna_ref : core::scoring
• dna_sugar_close : core::scoring
• DOCK_DOMAIN : core::pose::full_model_info
• dock_ens_conf : core::scoring
• DockingHighResLegacy : protocols::docking
• DockingPrepackProtocol : protocols::docking
• DockMCMProtocol : protocols::docking
• DockMinMover : protocols::docking
• DOES_NOT_CONTROL : protocols::environment::claims
• dof_constraint : core::scoring
• DOUBLE_T_LOOP : core::scoring::rna
• DoubleBond : core::chemical
• DoubleBondOrder : core::chemical
• DOWN : protocols::denovo_design::components
• Ds : core::chemical::element
• dslf_ca_dih : core::scoring
• dslf_cbs_ds : core::scoring
• dslf_cs_ang : core::scoring
• dslf_fa13 : core::scoring
• dslf_fa13_ref : core::scoring
• dslf_ss_dih : core::scoring
• dslf_ss_dst : core::scoring
• dslfc_ang : core::scoring
• dslfc_bb_dih : core::scoring
• dslfc_cb_dih : core::scoring
• dslfc_cb_dst : core::scoring
• dslfc_cen_dst : core::scoring
• dslfc_rot : core::scoring
• dslfc_RT : core::scoring
• dslfc_trans : core::scoring
• dualspace : protocols::antibody::design
• dummy_score_type : core::scoring
• dump_trajectory : core::scoring
• dunbrack_constraint : core::scoring
• dunbrack_method : core::scoring::methods
• Dy : core::chemical::element
• DY3_COORDINATION : core::chemical