- d -

• dab_sasa() : sasa_test.cc
• dat_a_a_r_ang() : gen_env_dep_orient.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• ddg() : genI213_2comp.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc , cryst_reporters.hh
• decompose() : decompose_GDT.cc
• dedup() : cryst_gen.cc
• define_cut_points() : fold_from_loops.cc
• define_interface() : david_recompute_score_and_rmsd.cc , minimize_ppi.cc , simon_darc_minimize.cc , ragul_darc_minimize.cc , johnk_interface_recompute_score_and_rmsd.cc , johnk_interface_geosol_minimization.cc , david_find_contacts.cc , david_find_complex_contacts.cc , david_find_best_contact_pocket.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_align_and_recompute_score_and_rmsd.cc
• define_movemap_extending_chain() : fold_from_loops.cc
• define_states_test() : turner_rules_test.cc , turner_rules_test_WORKS.cc
• define_variables() : ResidueDisorder.cc
• delete_protein_from_pose() : rnp_ddg.cc
• delete_RNA_from_pose() : rnp_ddg.cc
• delete_test() : test1.cc
• deleteEdge() : CycDsulf.cc
• delta_chi_correction_test() : turner_rules_test.cc
• denom() : spacegroup.hh
• density_grid_search() : place_fragments_into_density.cc
• densityTools() : density_tools.cc
• derive() : PeptideDeriver.cc
• derive_MoveMap_from_cluster_lst() : design_tight_clusters.cc , detect_tight_clusters.cc
• describe_move() : kick_cyclic_pose.cc
• design() : gen_d2_hhhc.cc , gen_disulf_homodimer.cc , dubois.cc , genI213.cc , genmatch.cc , genmatch_3bpy.cc , genmatch_m8.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , organopv.cc , pentcb_design.cc , smhybrid.cc , spiro.cc , ward_design.cc , will_mutalyze.cc , design_symm.bak.110314.cc , gen_d2_4his.cc , cxdesign.cc , char_native.cc , des_pos_ddG.cc , design_symm.cc , design_symm_110330_good.cc , design_symm_no_hack_elec.cc , matdes_design_2comp.cc , gen_d2_3his_ooc.cc , gen_d2.cc , crossmatch_d2.cc , crossmatch.cc , bpy.cc , matdes_mutalyze.cc , matdes_design.cc
• design_1comp() : genI213_2comp.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc
• design_AFILV() : coiled_coil.cc , coiled_coil_zn.cc
• design_AFILVEK() : coiled_coil.cc , coiled_coil_zn.cc
• design_AL() : coiled_coil.cc , coiled_coil_zn.cc
• design_all() : coiled_coil.cc , coiled_coil_zn.cc
• design_cluster() : design_tight_clusters.cc
• design_dyad() : genmatch.cc , genmatch_m8.cc
• design_FILV() : coiled_coil.cc , coiled_coil_zn.cc
• design_FILVEK() : coiled_coil.cc , coiled_coil_zn.cc
• design_hits() : genI213.cc
• design_homodimer() : crossmatch_3e.cc , crossmatch_d2.cc , crossmatch.cc
• design_pose_motifs_only() : scheme_v0_score.cc
• design_target() : coiled_coil.cc , coiled_coil_zn.cc
• design_test() : dna_design_test.cc , dna_spec_test.cc , simple_dna_regression_test.cc
• design_using_resfile() : matdes_design_2comp.cc , matdes_mutalyze.cc , will_mutalyze.cc
• designloop() : design_truecycpeptide_fromstub.cc
• destroy_pseudo_commandline() : init_util.hh
• detail::locale_ref::get< std::locale >() : format.cc
• detect_neighbors() : detect_tight_clusters.cc , design_tight_clusters.cc
• determine_allowed_dofs() : plot_scoreterm.cc
• determine_delx_dely_delz_alpha_beta_gamma() : coarse_rna_test.cc
• determine_if_at_local_minimum_analytic() : sweep_respair_energies.cc
• determine_if_at_local_minimum_numeric() : sweep_respair_energies.cc
• determine_output_name() : restype_converter.cc
• determine_residues_to_rebuild() : erraser2.cc
• devel_main() : kick_n_terminus.cc
• dih_table() : load_angle_r_table.m
• dimer_rms() : gensym_3bpy_from_dimer.cc
• dinucleotide_test() : turner_rules_test.cc , rna_test.cc
• disp_symmop() : cryst_gen.cc
• dist() : kcluster.cc
• dist_matrix_test() : entropy_test.cc
• distance() : iterhybrid_selector.cc , torsional_potential_corrections.cc
• distance_from_line2D() : mpframework_test2.cc
• distribute_jobs() : CycPepMain.cc
• diversify_sam_loop_test() : capri15.cc
• dna_aa_from_oneletter_code() : phil.hh
• dna_chain_check() : simple_dna_regression_test.cc , dna_spec_test.cc
• dna_coupled_rotamer_design_test() : test1.cc
• dna_deriv_test() : test1.cc
• dna_deriv_test_old() : test1.cc
• dna_design_test() : test1.cc
• dna_design_test_old() : test1.cc
• dna_dr_loop_test() : dna_dr_test.cc
• dna_dr_test() : dna_spec_test.cc , simple_dna_regression_test.cc , dna_dr_test.cc
• dna_geometry() : analyze_dna.cc
• dna_io_test() : test1.cc
• dna_motif_matcher() : dna_motif_matcher.cc
• dna_nbr_radii_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• dna_specificity_test() : dna_spec_test.cc , simple_dna_regression_test.cc , dna_spec_test.cc
• dna_stats() : dna_relax.cc
• dna_test() : dna_test.cc
• dnabase_test() : test_multithreaded_ramapp_load.cc
• do_align() : bb_cluster.cc
• do_backrub() : chet_trp_to_gly.cc
• do_centroid_stuff() : coiled_coil.cc , coiled_coil_zn.cc
• do_clustering() : test_cluster.cc
• do_color_by_score() : rna_score.cc
• do_cyclic_permutation() : count_cycpep_sequences.cc
• do_cycpep_analysis() : cycpep_analysis.cc
• do_disorder_prediction() : ResidueDisorder.cc
• do_erraser2() : erraser2.cc
• do_event_prediction() : ResidueDisorder.cc
• do_initial_checks() : design_truecycpeptide_fromstub.cc
• do_KIC() : chet_trp_to_gly.cc
• do_main() : crash_report_test.cc
• do_minimization() : chet_trp_to_gly.cc
• do_one() : crash_report_test.cc
• do_oom() : crash_report_test.cc
• do_options_checks() : count_cycpep_sequences.cc
• do_postload_checks() : design_truecycpeptide_fromstub.cc
• do_refinement() : dgdp.cc
• do_rtmin() : params_opt.cc
• do_sc_min() : cryst_reporters.hh
• do_sc_relax() : cryst_reporters.hh
• do_search() : dgdp.cc
• do_terminal_opt() : ResidueDisorder.cc
• do_the_match() : turner_rules_test.cc
• do_tmalign() : tmalign_cluster.cc
• do_tmscore() : tmalign_cluster.cc
• do_two() : crash_report_test.cc
• do_work() : test_leerichards.cc
• dock() : sicdock.cc , pentcb_test.cc , pentcb.cc , heterodock.cc , hczndimer.cc , genP23.cc , genI213_nocontacts.cc , genI213_gensym.cc , genI213_2comp.cc , gen_xtal_dimer_from_trimer.cc , dxdock_movie.cc , dxdock.cc , dock_asym.cc , d3_bpy_linker.cc , CXdock_TMP.cc , cxdock_sheet.cc , CXdock.cc , cxdock.cc , genI213.cc
• doit() : rblinker.cc , smhybrid.cc , rblinker2_test.cc , rblinker2_overlay_bound.cc , rblinker2.cc , organopv.cc , cycsamp.cc
• doit_refine() : smhybrid.cc
• don_store_hbs() : cnl_env_lost_hbs.cc
• dostuff() : calc_ddG.cc , will_mutalyze.cc , relax_building_block.cc , matdes_mutalyze.cc , matdes_design_2comp.cc , matdes_design.cc , design_symm_no_hack_elec.cc , design_symm_110330_good.cc , design_symm.cc , design_symm.bak.110314.cc , des_pos_ddG.cc , char_native.cc
• dot_sasa() : sasa_test.cc
• dotpdt() : make_a3b_bundle.cc , make_betahelicalbundle.cc , make_helicalbundle.cc
• dotvv() : gpu_mat_vec.hh
• double_helix_test() : turner_test_double_helix.cc
• double_linked_fold_tree() : mike_linker_test.cc
• double_unlinked_fold_tree() : mike_linker_test.cc
• download_url() : node_test.cpp , functor_test.cpp
• drrafter_error_estimation() : drrafter_error_estimation.cc
• dump_bundle_pose() : BundleDumper.cc , CompareBundleToNative.cc
• dump_clash_pdb() : dna_spec_test.cc , simple_dna_regression_test.cc
• dump_coords() : density_res_zscores.cc
• dump_curve_to_db() : roc_optimizer.cc
• dump_data() : johnk_exact_geometric_solvation.cc
• dump_ddg_pdb() : compute_ddgs.cc
• dump_dna_kinemage() : dna_spec_test.cc , simple_dna_regression_test.cc
• dump_efactor_pdb() : pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_spec.06-23.cc , pep_spec.03-11.cc , pep_prepspec.cc , pep_ref.cc , pep_rama.cc , pep_paapp.cc , pep_opt_parallel.cc , pep_opt.cc , pep_gly.cc , pep_analysis.cc
• dump_energy_kinemage() : ligand_evis.cc
• dump_grid_pdb() : johnk_parametrize_geometric_solvation.cc
• dump_hbond_pdb() : dna_spec_test.cc , simple_dna_regression_test.cc , test1.cc
• dump_hbonds() : hbonds_test.cc
• dump_insert_pdb_and_remodel_blueprint() : domain_assemble.cc
• dump_movemap() : r_frag_picker.cc
• dump_multivec() : params_opt.cc
• dump_pair_pose() : BundleDumper.cc
• dump_pdb_atom() : motif_denovo_hb.cc
• dump_points_pdb() : cxdock.cc , dock_asym.cc , dxdock.cc , gpu_linker.cc , symdock_enum_3_1.cc , xyzStripeHash_test.cc
• dump_points_pdb_contacts() : cxdock.cc
• dump_pose() : jdock.cc
• dump_pose_diff() : docking_parallel.cc
• dump_residue_kinemage() : ligand_evis.cc
• dump_rotamerset_pdb() : find_position_matches_using_inverse_rotamers.cc
• dump_sequences() : r_frag_picker.cc
• dump_structure_kinemage() : ligand_evis.cc
• dump_table() : torsional_potential_corrections.cc
• dump_unique_atoms() : dump_unique_atoms.hh
• dump_water_grid_file() : johnk_parametrize_geometric_solvation.cc
• dumpcgo() : FunGroupTK.cc
• dumpsym() : gen_xtal_dimer_from_trimer.cc , genI213.cc , genI213_2comp.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc
• dumpsym2() : gen_xtal_dimer_from_trimer.cc , genI213.cc
• dumpsym6() : gen_xtal_dimer_from_trimer.cc , genI213.cc
• dynamic_bitset_to_hex_string() : compare_features.cc