- r -

• rand_rot() : core::scoring::packstat
• random_delay() : core::init
• random_rotation() : core::scoring::motif
• read_additional_pdb_data() : core::import_pose
• read_alignment_file() : core::sequence
• read_all_alignments() : core::sequence
• read_all_poses() : core::import_pose
• read_aln() : core::sequence
• read_binary() : core::io::serialization
• read_bytes() : core::io::serialization
• read_codes_and_roots_from_database_file() : core::chemical::carbohydrates
• read_comment_pdb() : core::pose
• read_conformers_from_database_file_for_ring_size() : core::chemical
• read_ddg_predictions_file() : core::io::PositionDdGInfo
• read_DNA_rotlib() : core::pack::rotamer_set
• read_dunbrack_library() : core::pack::dunbrack
• read_fasta_file() : core::sequence
• read_fasta_file_return_str() : core::sequence
• read_fasta_file_str() : core::sequence
• read_general_aln() : core::sequence
• read_general_aln_file() : core::sequence
• read_grishin_aln_file() : core::sequence
• read_lines_from_file() : update_ResidueType_enum_files
• read_motifs_binary() : core::scoring::motif
• read_pairing_list() : core::scoring::dssp
• read_properties_from_database_file() : core::chemical::carbohydrates
• read_psipred_ss2_file() : core::pose
• read_std_frags_from_cmd() : core::fragment
• read_stoopid() : core::scoring::packstat
• read_topology_file() : core::chemical
• read_xfrag_binary() : core::scoring::motif
• read_xfres_binary() : core::scoring::motif
• readValueOrDie() : core::scoring::func
• real6_to_rt() : core::scoring::motif
• real_to_uint16() : core::scoring::motif
• real_to_uint8() : core::scoring::motif
• rebuild_disulfide() : core::util
• recenter() : core::conformation::symmetry
• regenerate_graph_vertex_index() : core::chemical
• reinitialize_mingraph_neighborhood_for_residue() : core::pack
• remap_cis_omega_torsion_bins_to_trans() : core::conformation
• remap_names_on_geometry() : core::io::pdb
• remodel_fold_tree_to_account_for_insertion() : core::kinematics
• remove_constraint_from_residue_constraints() : core::scoring::constraints
• remove_constraints_of_type() : core::scoring::constraints
• remove_cutpoint_variants() : core::util
• remove_ligand_canonical_residues() : core::pose
• remove_lower_terminus_type_from_conformation_residue() : core::conformation
• remove_lower_terminus_type_from_pose_residue() : core::pose
• remove_nonbb_constraints() : core::scoring::constraints
• remove_nonprotein_residues() : core::pose
• remove_upper_terminus_type_from_conformation_residue() : core::conformation
• remove_upper_terminus_type_from_pose_residue() : core::pose
• remove_variant_type_from_conformation_residue() : core::conformation
• remove_variant_type_from_pose_residue() : core::pose
• remove_variant_type_from_residue() : core::pose
• remove_virtual_residues() : core::pose
• remove_virtual_rna_residue_variant_type() : core::pose::rna
• remove_whitespaces() : core::scoring::rna::chemical_shift
• rename_atoms() : core::chemical
• renumber_pdbinfo_based_on_conf_chains() : core::pose
• reorder_full_model_info_after_append() : core::pose::full_model_info
• reorder_full_model_info_after_delete() : core::pose::full_model_info
• reorder_full_model_info_after_prepend() : core::pose::full_model_info
• reorder_moving_res_list_after_delete() : core::pose::full_model_info
• reorder_moving_res_list_after_insert() : core::pose::full_model_info
• reorder_res_list_after_append() : core::pose::full_model_info
• reorder_res_list_after_delete() : core::pose::full_model_info
• reorder_res_list_after_prepend() : core::pose::full_model_info
• repackable_residues() : core::pack
• repackable_residues_dup() : core::pack
• replace_conformation_residue_copying_existing_coordinates() : core::conformation
• replace_pose_residue_copying_existing_coordinates() : core::pose
• replace_residue_in_atom_tree() : core::conformation
• replace_substr() : core::kinematics
• replaced_symmetric_foldtree_with_new_monomer() : core::conformation::symmetry
• report_application_command() : core::init
• requires_CB_mapping() : core::scoring::constraints
• reroot_restype() : core::chemical
• res1_pointed_at_res2() : core::pack::task::operation::util
• resample() : core::scoring::electron_density
• residue_center_of_mass() : core::conformation::symmetry , core::pose
• residue_fast_pair_energy_attached_H() : core::scoring
• residue_gws_string() : core::io::carbohydrates
• residue_is_bulge() : core::pose::rna
• residue_point_graph_from_conformation() : core::conformation
• residue_range_gws_string() : core::io::carbohydrates
• residue_sc_rmsd_no_super() : core::scoring
• residue_selector_single_from_line() : core::chemical
• residue_type_all_patches_name() : core::chemical
• residue_type_base_name() : core::chemical
• residue_types_from_saccharide_sequence() : core::pose
• residue_types_from_sequence() : core::pose
• residues_interact() : core::scoring::methods
• restrict_prec() : core::io::pdb
• retain_top() : core::fragment
• retrieve_base_partner_from_pose() : core::scoring::dna
• retrieve_base_partner_from_pose_inline() : core::scoring::methods
• retrieve_const_ss_info_from_pose() : core::scoring
• retrieve_coordinates() : core::scoring
• retrieve_CSA_from_pose() : core::scoring
• retrieve_DC_from_pose() : core::scoring
• retrieve_lkb_pairdata() : core::scoring::methods
• retrieve_lkb_resdata() : core::scoring::methods
• retrieve_lkb_resdata_ptr() : core::scoring::methods
• retrieve_lkb_residue_info() : core::scoring::methods
• retrieve_lkb_rotamer_set_info() : core::scoring::methods
• retrieve_nonconst_lkb_pairdata() : core::scoring::methods
• retrieve_nonconst_lkb_resdata() : core::scoring::methods
• retrieve_nonconst_lkb_residue_info() : core::scoring::methods
• retrieve_nonconst_ss_info_from_pose() : core::scoring
• retrieve_RDC_from_pose() : core::scoring
• retrieve_RDC_ROHL_from_pose() : core::scoring
• return_nearest_residue() : core::conformation::symmetry , core::pose
• retype_is_aromatic() : core::chemical
• revert_to_pre_talaris_2013_defaults() : core::init
• ring_current_effect() : core::scoring::rna::chemical_shift
• ring_current_effect_individual_ring() : core::scoring::rna::chemical_shift
• ring_pos() : core::scoring::rna::chemical_shift
• rms_at_all_corresponding_atoms() : core::scoring
• rms_at_corresponding_atoms() : core::scoring
• rms_at_corresponding_atoms_no_super() : core::scoring
• rms_at_corresponding_heavy_atoms() : core::scoring
• rms_error_with_noise() : core::import_pose::atom_tree_diffs
• rmsd_no_super() : core::scoring
• rmsd_no_super_subset() : core::scoring
• rmsd_with_super() : core::scoring
• rmsd_with_super_subset() : core::scoring
• RNA_HIRES_WTS() : core::scoring
• RNA_LORES_PLUS_HIRES_WTS() : core::scoring
• RNA_LORES_WTS() : core::scoring
• rna_residue_name_to_num() : core::scoring::rna
• rna_scoring_info_from_pose() : core::scoring::rna
• rosetta_recharge_fullatom() : core::chemical
• rosetta_retype_fullatom() : core::chemical
• rot_sample_from_name() : core::pack::task
• rotamer_from_chi() : core::pack::dunbrack
• rotamer_from_chi_02() : core::pack::dunbrack
• rotamer_trials() : core::pack
• rotate_anchor_to_x_axis() : core::pose::symmetry
• rpm_type1() : core::scoring::motif
• rpm_type2() : core::scoring::motif
• rsd_set_from_cmd_line() : core::chemical
• rt6_rt6_bb_dis2() : core::scoring::motif
• rt6_rt6_bb_dis2_explicit_stupid() : core::scoring::motif
• rt6_rt6_dis2() : core::scoring::motif
• rt_to_real6() : core::scoring::motif