- r -

• rad2deg() : print_phipsi.cc
• rama2b_test() : test_multithreaded_ramapp_load.cc
• rama_list_pred() : mirrorsymm_test.cc , min_test.cc
• rama_prepro_test() : test_multithreaded_ramapp_load.cc
• rama_test() : test_multithreaded_ramapp_load.cc
• rand_rot() : test_leerichards.cc
• rand_Vec() : Vec.hh
• rand_Vec_condition() : filter.cc
• randangle() : make_ideal_betapeptide.cc , test_KIC_betapeptide.cc
• random_alignment_move() : anneal_align.cc
• random_angle() : turner_two_chain.cc
• random_delta() : turner_two_chain.cc
• random_element() : phil.hh
• random_torsions() : gpu_linker.cc
• random_unit_vector() : cryst_reporters.hh
• randomly_open_pose_loop() : test_CCD_loop_closure.cc
• randomly_shift_and_tilt_pose() : cryst_reporters.hh
• randomly_shift_and_tilt_poses() : cryst_reporters.hh
• randvec() : crossmatch.cc , crossmatch_d2.cc , isct_test.cc , test_leerichards.cc
• rb_entropy_test() : rb_entropy.cc
• rb_test() : test1.cc , dock_test.cc
• rBroker_main_local() : r_broker.cc
• RBSegmentRelax_local_main() : RBSegMove.cc
• RBSegmentRelax_test() : RBSegMove_test_viewer.cc
• read_alignment_fasta_file() : easy_target_test.cc
• read_B_vals() : SID_ERMS_prediction.cc
• read_complex_type() : SID_ERMS_prediction.cc
• read_covalent_connections_file() : design_cycpeptide_MPI.cc
• read_ddg_file() : pack_ddg.cc
• read_distances() : hierarchical_clustering.cc
• read_embeddings() : mp_parameters.cc
• read_equivalent_position_file() : design_cycpeptide_MPI.cc
• read_ERMS() : SID_ERMS_prediction.cc
• read_fasta() : helix_from_sequence.cc
• read_FileVector() : buns.cc , read_l_print_pdbinfo.cc , sasa_buns.cc , vsasa_pdbcode_res.cc
• read_fold_tree_from_file() : backrub_pilot.cc
• read_fragdata() : bpy.cc , spiro.cc , smhybrid.cc , rblinker.cc , frag_util.hh , dubois.cc
• read_frags() : coiled_coil_zn.cc
• read_ignore_comments() : hubdenovo.cc
• read_in_cl_data() : cl_complex_rescore.cc
• read_in_extension() : Extender.cc
• read_in_flexible_regions() : incorporate_motifs.cc
• read_in_mutations() : cartesian_ddg.cc , ddg_monomer.cc
• read_in_pdbs() : SID_rescore.cc , cl_complex_rescore.cc
• read_input_weights() : ensemble_analysis.cc , fast_clustering.cc
• read_jumpcut_file() : smhybrid.cc
• read_library_simple() : iterhybrid_selector.cc
• read_library_w_simpose() : iterhybrid_selector.cc
• read_list_file() : dna_spec_test.cc , simple_dna_regression_test.cc , test1.cc
• read_list_pose_range() : Superimpose_Pdbs.cc
• read_loops_from_text_file() : graphics_demo.cc , long_loop.cc
• read_master_pose_range() : Superimpose_Pdbs.cc
• read_membrane() : mp_parameters.cc , helix_from_sequence.cc
• read_NACCESS_asa_file() : hydrophobic_patch_stats_calculator.cc
• read_native_pose() : loop_closure_test.cc
• read_native_sequence_for_entity_elements() : mpi_msd.cc
• read_occupancy_data() : consolidate_clusters.cc
• read_options() : mp_parameters.cc
• read_parameters() : mp_parameters.cc
• read_patchdock_entry() : docking_inputpatchdock_mpi.cc
• read_PCAfile() : design_cycpeptide_MPI.cc , PCA_visualizer.cc
• read_pdbs() : util.hh
• read_penalties() : mp_parameters.cc
• read_pose() : spanfile_from_pdb.cc , mp_span_from_pdb.cc , mutate.cc
• read_rama_map_file() : torsional_potential_corrections.cc
• read_RDC_file() : RDCTest.cc
• read_res_list() : gentetra_bpy_from_znhis.cc , smhybrid.cc , gentetra_from_trimer.cc , gentetra.cc , gensym_3bpy_from_dimer.cc , genmatch_m8.cc , genmatch_3bpy.cc , genmatch.cc , gen_disulf_homodimer.cc , gen_d2_hhhc.cc , gen_d2_4his.cc , gen_d2_3his_ooc.cc , gen_d2.cc , crossmatch_d2.cc , crossmatch.cc , gen_homo_hc.cc
• read_rigid_body_settings() : turner_test_double_helix.cc , turner_two_chain.cc , turner_rules_test.cc
• read_silent_input_as_library() : iterhybrid_selector.cc
• read_soft_segment_file() : easy_target_test.cc
• read_sphere() : CXdock.cc , d3_bpy_linker.cc , dxdock_movie.cc , heterodock.cc
• read_structures() : ensemble_analysis.cc , fast_clustering.cc
• read_template_structures() : challenge.cc
• read_tensor_test() : read_tensor.cc
• read_thickness() : spanfile_from_pdb.cc , mp_span_from_pdb.cc
• read_write() : dna_spec_test.cc , simple_dna_regression_test.cc
• ReadCAsFromPDB() : denovo_density.cc
• readFile() : dock_test.cc , PDBTest.cc
• readline() : Svm.cc
• readPDBcoords() : pdb_gen_cryst.cc , density_tools.cc
• readPoseAndData_PDB() : evolution.cc
• readPoseAndData_SILENT() : evolution.cc
• real6_from_rt() : loodo.cc
• real6_similarity() : loodo.cc
• real_test_GA() : GA.cc
• reasonable_disulfide_orientation() : disulfides.hh
• reavrg() : avrg_silent.cc
• rebuild() : atom_tree_check.cc
• rebuild_centroid_test() : stepwise_centroid_test.cc
• rebuild_test() : swa_protein_main.cc , TRIAL_protein_helix_assemble.cc , repeat_demo.cc , stepwise_test.cc
• rebuild_trimmed_loops() : capri15.cc
• receive_silent_struct() : design_cycpeptide_MPI.cc
• receive_string_from_node() : pep_opt_parallel.cc
• recenter_with_missing() : ca_to_allatom.cc
• reconstruct_lattice_pose_info() : cryst_reporters.hh
• recover_clustered_frags() : r_local_rdc.cc
• reduce_fa_rep() : minimize_with_cst.cc , ensemble_generator_score12_sidechain_ver2.cc , ensemble_generator_score12_sidechain.cc , ensemble_generator.cc
• reference_sasa() : sasa.cc
• referenceRDC() : RDCTest.cc
• refine() : gensym_3bpy_from_dimer.cc , hczndimer.cc , willmatch_d6_bpy.cc
• refine_fa_pep_bb() : pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.06-23.cc , pep_prepspec.cc , pep_spec.cc
• refine_pose() : pack_ddg.cc
• refold_first() : gpu_refold_test_cpu.hh
• refold_gpu() : gpu_linker.cc
• refold_ros() : gpu_linker.cc
• refold_second() : gpu_refold_test_cpu.hh
• refold_third() : gpu_refold_test_cpu.hh
• refresh_cutpoints() : fold_from_loops.cc
• region_constraint_score() : unalignedEvaluate.cc
• region_density_score() : unalignedEvaluate.cc
• region_for_string() : measure_sequence_similarity_to_native.cc
• region_rmsd() : calcFractionFolded.cc , unalignedEvaluate.cc
• region_rmsd_structures_aligned() : unalignedEvaluate.cc
• region_score() : unalignedEvaluate.cc
• register_calcs() : byres_data.cc
• register_metrics() : hotspot_test.cc , AlanineScanner.cc , metrics_test.cc , david_find_surface_residues.cc , noah_score_interface.cc
• register_options() : test_trRosettaProtocolMover.cc , gpu_score.cc , cluster_cyc_disulf.cc , CXdock.cc , cxdock_sheet.cc , d3_bpy_linker.cc , designability_stats.cc , disulf_frag_match.cc , disulf_frag_search.cc , dock_asym.cc , dxdock.cc , dxdock_movie.cc , flail.cc , gen_trimer_disulf.cc , gensym_3bpy_from_dimer.cc , gpu_linker.cc , test_cyclic_rama.cc , test_multithreaded_pdb_load.cc , make_betahelicalbundle.cc , test_D_scoring.cc , test_KIC_betapeptide.cc , test_makebundle_mover.cc , test_makebundlehelix_mover.cc , test_metalloproteins.cc , test_multithreaded_ig_correctness.cc , test_multithreaded_packing_performance.cc , test_trRosettaConstraintGenerator.cc , test_multithreaded_ramapp_load.cc , test_pose_copy.cc , test_rosetta_thread_manager_advanced_API.cc , test_rosetta_thread_manager_basic_API.cc , test_sidechainKIC.cc , test_tensorflow_graph_convolutional_nn.cc , test_trRosetta.cc , count_cycpep_sequences.cc , r_rmsf.cc , cst_info.cc , ensemble_analysis.cc , fast_clustering.cc , HDXEnergy.cc , antibody_numbering_converter.cc , glycan_clash_check.cc , glycan_info.cc , extract_replica.cc , fragment_picker.cc , helical_bundle_predict.cc , idealize_jd2.cc , r_noe_assign.cc , remodel.cc , restype_converter.cc , struc_set_fragment_picker.cc , trRosetta.cc , sicdock.cc , helix_assembly.cc , heterodock.cc , hubabinitio.cc , hubdenovo.cc , hubfragdesign.cc , motif_denovo_hb.cc , pentcb_design.cc , scheme_v0_score.cc , gpu_test.cc , symdock_enum_3_1.cc , tcdock.cc , test_loop_hash.cc , xyzStripeHash_dump.cc , xyzStripeHash_test.cc , ufv.cc , extract_CA_coords.cc , rescore_fragments.cc , TryScoreFilter.cc , welde_chains.cc , Features.cc , diverse_fragments.cc , fragmentpicker_integration_demo.cc , picker.cc , PickSSE.cc , quotapicker_demo.cc , read_profile.cc , hierarchical_clustering.cc , call_saxs_score.cc , ComputeSAXSSpectrum.cc , linker_sampler.cc , RescorePDDF.cc , RescoreSAXS.cc , RotateSAXS.cc , convert_frags.cc , rotamer_recovery.cc , make_a3b_bundle.cc , basic_glycan_sampler.cc , make_retroinverso.cc , DisulfideTest.cc , DomainAssemblerNDocker.cc , AllCrmsd.cc , call_rdc.cc , symmetrize_old_ramamap.cc , CreatePose.cc , DetailedScores.cc , DisulfideBondEnergy.cc , DumpConstraints.cc , GunnTest.cc , print_options.cc , RDCTest.cc , make_ideal_betapeptide.cc , assemble_placed_fragments.cc , match_disulfide_to_scaffold.cc , HECT.hh , bettercluster.cc , design_cycpeptide_MPI.cc , design_truecycpeptide_fromstub.cc , fit_helixparams.cc , make_helicalbundle.cc , tnm_sampler.cc , make_mainchain_potential.cc , make_truecyclicpeptide.cc , PCA_internal_test.cc , plot_scoreterm.cc , symmetrize_3d_ramamap.cc , symmetrize_new_ramamap.cc , symmetrize_rotlib.cc , build_repeats.cc , SaxsSampler.cc , test_chain_sequence.cc , cxdock.cc , test_neighborhood_selector.cc , test_symmetry.cc , jidealize.cc , matdes_design_2comp.cc , r_assign_clusters.cc , r_build_hotspot_loops.cc , r_convert_frags.cc , r_min_check.cc , r_mpi.cc , r_rmsf.cc , r_score.cc , r_score_rdc.cc , helical_param.cc
• register_options_broker() : r_abrelax.cc
• rel_sasa_score() : HDXEnergy.cc
• relax_cenrot_pose() : cenrot_bbsc_demo.cc , fa_to_cenrot_score.cc
• relax_main_local() : relax_viewer.cc
• relax_test() : capri15.cc , relax_viewer.cc
• relax_with_restraints_on_constres() : avrg_silent.cc
• relaxloop() : design_truecycpeptide_fromstub.cc
• remove_all_virtual_residues() : rms_util.hh
• remove_dashes() : rna_thread.cc , rna_thread_and_minimize.cc
• remove_drift() : cryst_gen.cc
• remove_duplicate_motifs() : remove_duplicate_motifs.cc
• remove_membrane_residue() : mpframework_test.cc
• remove_pep_buffer_res() : pep_prepspec.cc , pep_gly.cc
• remove_pep_res() : pep_spec.06-23.cc , pep_spec.cc , pep_spec_flx.cc , pep_spec_flx.mov.cc , pepspec.cc
• remove_pose_water() : byres_data.cc
• removeConstraintsNearGap() : minimalCstHomology.cc
• reorder_foldtree() : InterfaceMutMaker.cc
• reorient_to_base_pair_coordinate_system() : coarse_rna_test.cc
• rep_hb_atom() : cnl_env_lost_hbs.cc , lig_polar_sat.cc
• repack() : gen_disulf_homodimer.cc , genmatch.cc , genmatch_3bpy.cc , genmatch_m8.cc , gensym_3bpy_from_dimer.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , pentcb_design.cc , smhybrid.cc , spiro.cc , test_ikrs.cc , test_ikrs2.cc , test_ikrs_flymake.cc , will_mutalyze.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , cxdesign.cc , des_pos_ddG.cc , design_symm.cc , design_symm_110330_good.cc , matdes_design.cc , matdes_design_2comp.cc , matdes_mutalyze.cc , easy_target_test.cc , coiled_coil_zn.cc , crossmatch.cc , crossmatch_d2.cc , dubois.cc , gen_d2.cc , gen_d2_3his_ooc.cc , coiled_coil.cc
• repack_all() : genI213.cc
• repack_cluster() : detect_tight_clusters.cc
• repack_iface() : genI213.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc
• repack_minimize_test() : gcc185_test.cc
• repack_pose() : rss_energy_calculator.cc , surfacescore.cc
• repack_step() : design_tight_clusters.cc
• repack_test() : simple_dna_regression_test.cc , stepwise_test.cc , beta_peptide_modeling.cc
• repackmin() : gen_trimer_disulf.cc
• replace_nat_seq() : genI213_2comp.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc
• replace_string() : smhybrid.cc
• replace_torsion_angles() : rna_test.cc
• report() : spiro.cc , avrg_silent.cc , dubois.cc , smhybrid.cc , bpy.cc
• report_and_dump() : iterhybrid_selector.cc
• report_system_error() : format.h , format-inl.h
• ReportStubIdentity() : dumpstubinteractions.cc
• ReportStubStubEnergy() : dumpstubinteractions.cc
• ReportStubTargetEnergy() : dumpstubinteractions.cc
• reroot_restype() : atom_tree_check.cc
• res2stub() : gen_d2_hhhc.cc , gen_homo_hc.cc , gen_d2_4his.cc , gen_d2_3his_ooc.cc , gen_d2.cc
• res_lvl_analysis() : rotamer_repack.cc
• res_type_score() : armEval.cc , evalRepeats.cc
• resample_full_model() : erraser2.cc
• resample_full_model_test() : resample_full_model.cc
• rescale_phosphate_charges() : dna_design_test.cc
• rescore() : rescore_i213.cc
• rescore_pose() : fa_to_cenrot_score.cc
• rescore_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• reset_sfxn() : design_truecycpeptide_fromstub.cc
• residue_distance() : disulfides.hh
• residue_types_from_sequence() : adding_peptoids.cc
• residues_too_distant() : rna_design.cc
• reslist() : gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• restore_hack() : fast_gap.cc , full_length_model.cc
• results_to_pdb() : dgdp.cc
• retag() : iterhybrid_selector.cc
• retrieve_capri_data_from_pose() : capri15_scoring.hh
• retrieve_residue_pair_energies() : dna_spec_test.cc , simple_dna_regression_test.cc
• retrieve_rms_and_clash_scores_from_gpu() : SmotifPairRmsdCalculatorGPU.CC , BundlePairRmsdCalculatorGPU.cc
• return_zero() : crash_report_test.cc
• reverse() : turner_rules_test.cc
• reverse_convert() : multistage_rosetta_scripts.cc , reverse_conversion_util.hh
• reverse_doublet_test() : turner_rules_test.cc
• reverse_rbs_test() : turner_rules_test.cc
• rg2d() : coiled_coil.cc , coiled_coil_zn.cc
• rhiju_pack() : gcc185_test.cc
• rhiju_pdbstats() : pdbstats_test.cc , rna_features.cc , pdbstats_rnahelix.cc
• rmsd_base_doublet() : turner_rules_test.cc
• rmsd_base_doublet_symmetric() : turner_rules_test.cc
• rmsd_compute() : turner_test_double_helix.cc , turner_test_one_chain.cc
• rmsd_over_base() : turner_rules_test.cc
• rna_assemble_all_combinations_test() : rna_assemble_test.cc
• rna_assemble_test() : rna_assemble_test.cc
• rna_backbone_rebuild_test() : rna_test.cc
• rna_build_helix_test() : rna_helix.cc
• rna_build_helix_test_OLD() : rna_assemble_test.cc
• rna_build_helix_test_precompute() : rna_assemble_test.cc
• rna_chain_closure_test() : rna_test.cc
• rna_close_chainbreaks_test() : rna_test.cc
• rna_close_loop_test() : turner_rules_test.cc
• rna_denovo() : rna_denovo.cc
• rna_denovo_legacy() : rna_denovo.cc
• rna_denovo_test() : rna_test.cc
• rna_design_gap_test() : rna_test.cc
• rna_design_test() : trial_rna_mutants.cc , rna_design.cc , rna_test.cc
• rna_features_from_pose() : rna_features.cc
• rna_fullatom_minimize_silent_test() : rna_test.cc
• rna_fullatom_minimize_test() : rna_minimize.cc
• rna_fullatom_multiscore_test() : rna_test.cc
• rna_fullatom_score_test() : rna_test.cc
• rna_helix_pdbstats_from_pose() : pdbstats_rnahelix.cc
• rna_idealize_test() : rna_test.cc , parin_test.cc
• rna_lores_score_silent_test() : rna_test.cc
• rna_lores_score_test() : rna_test.cc
• rna_motif_test() : rna_motif.cc
• rna_o2prime_test() : rna_test.cc
• rna_protein_pdbstats_test() : rna_protein_test.cc
• rna_protein_prepack_test() : rna_protein_test.cc
• rna_protein_rb_test() : rna_protein_test.cc
• rna_protein_repack_test() : rna_protein_test.cc
• rna_resample_test() : swa_rna_analytical_closure.cc
• rna_sample_virtual_sugar() : swa_rna_main.cc
• rna_sequence_recovery_metrics() : rna_design.cc
• rna_stack_pdbstats_from_pose() : pdbstats_test.cc
• rna_stats_test() : rna_test.cc
• rna_suitename() : rna_suitename.cc
• rna_superimpose_and_graft_test() : rna_graft.cc
• rna_thread_test() : rna_thread.cc
• rna_torsion_check_test() : rna_test.cc
• rot() : mixedMC.cc
• rot_pose() : symdock_enum_3_1.cc , sasa_test.cc , nisod.cc , symdock_enum.cc , nisod.cc , coiled_coil_zn.cc , coiled_coil.cc , matdes_design_2comp.cc , symdock_enum.cc , symdock_enum_3_1.cc , coiled_coil.cc
• rotamer_prediction_benchmark() : rotamer_prediction_benchmark.cc
• rotamer_trials_test() : test1.cc
• RotamerAnalysis() : rotamer_repack.cc
• rotamerize() : rotamerize.cc
• rotamerize_rna_test() : rna_test.cc
• rotamerize_structure() : rna_test.cc
• rotate_into_nucleobase_frame() : adenosine_stack_test.cc
• rotatePoint() : get_pharmacophore_without_bound_rna.cc
• rotateUntilCys() : CycDsulf.cc
• rotationMAT() : gpu_mat_vec.hh
• rots_from_pose() : analyze_casp9.cc , angle_recovery_stats.cc
• rottrial_residue() : rotamer_repack.cc
• rottrialmin_residue() : rotamer_repack.cc
• rotx() : gpu_mat_vec.hh
• roty() : gpu_mat_vec.hh
• rotz() : gpu_mat_vec.hh
• round() : ensemble_analysis.cc
• round_minimized_namer() : erraser2.cc
• round_resampled_namer() : erraser2.cc
• rows() : gpu_mat_vec.hh
• RT_from_epos() : create_disulfide_fa_angle_statistics.cc , create_disulfide_distance_statistics.cc , create_disulfide_database.cc , create_disulfide_alldata.cc , compute_disulfide_matching_score.cc , create_disulfide_angle_statistics.cc
• run() : gen_homo_hc.cc , genI213_2dsf.cc , genmatch_3bpy.cc , genmatch_d6_bhhcg.cc , genmatch_d6_bpy.cc , gensym_3bpy_from_dimer.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , hubdenovo.cc , IKFGDB.cc , print_dunscores.cc , willmatch_2d6_bhe.cc , willmatch_chorismate.cc , willmatch_d6_bpy.cc , extract_CA_coords.cc , r_rmsf.cc , ensemble_analysis.cc , mikejd2test.cc , fast_clustering.cc , r_noe_assign.cc , struc_set_fragment_picker.cc , r_assign_clusters.cc , gen_disulf_homodimer.cc , PCS_main.cc , sheet_translate.cc , test.cc , symdock_enum.cc , symdock_enum_3_1.cc , r_broker.cc , r_count_neighbours.cc , r_cst_tool.cc , r_min_check.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , r_mpi.cc , gen_d2_3his_ooc.cc , gen_d2.cc , gen3bpy.cc , FunGroupTK.cc , read_pose_jump_orientation_repack.cc , r_score_rdc.cc , r_score.cc , r_rmsf.cc
• run_3bpy() : genmatch.cc
• run_aio() : dgdp.cc
• run_diiron_glu() : genmatch.cc
• run_hd() : FunGroupTK_test.cc
• run_hh() : FunGroupTK_test.cc
• run_m8() : genmatch_m8.cc
• run_mc() : ensemble_generator.cc , ensemble_generator_score12_sidechain.cc , ensemble_generator_score12_sidechain_ver2.cc
• run_old() : r_noe_assign.cc
• run_parallel_docking() : docking_parallel.cc , docking_inputpatchdock_mpi.cc
• run_pep_prep() : pep_prep.cc , pepspec_anchor_dock.cc
• run_sandbox() : loophash.cc , loophash_cenrelax.cc
• run_sf4h() : sf4_hash.cc
• run_test() : hotspot_stub_constraint_test.cc
• run_tests() : simple_dna_regression_test.cc
• run_trace() : pseudo_ca_trace.cc
• run_tyr_his() : genmatch.cc
• run_zn2his() : genmatch.cc
• RunPepSpec() : pepspec.cc , pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_spec.06-23.cc , pep_spec.03-11.cc , pep_ref.cc , pep_rama.cc , pep_prepspec.cc , pep_paapp.cc , pep_opt_parallel.cc , pep_opt.cc , pep_nrg.cc , pep_gly.cc , pep_analysis.cc