- r -

• R2quat() : protocols::simple_filters
• rama_list_pred() : protocols::relax
• rand_rot() : core::scoring::packstat
• random_conformer_tracer() : protocols::ligand_docking
• random_connection() : protocols::ligand_docking
• random_delay() : core
• random_reorientation_matrix() : protocols::geometry
• randomize_selected_atoms() : protocols::comparative_modeling
• range() : protocols::sic_dock
• rb_grid_rotamer_trials_atr_rep() : protocols::ligand_docking
• rb_grid_score_atr_rep() : protocols::ligand_docking
• rbseg_RG() : protocols::rbsegment_relax
• RBSegmentRelax_main() : protocols
• read1() : protocols::cluster
• 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_ddg_predictions_file() : core::io::PositionDdGInfo
• read_disulf_pairing_list() : protocols::jumping
• read_DNA_rotlib() : core::pack::rotamer_set
• read_dunbrack_library() : core::pack::dunbrack
• read_extra_residues() : protocols::comparative_modeling
• read_fasta_file() : core::sequence
• read_fasta_file_return_str() : core::sequence
• read_fasta_file_str() : core::sequence
• read_fragment_candidates() : protocols::frag_picker
• read_frags() : protocols::topology_broker
• read_general_aln() : core::sequence
• read_general_aln_file() : core::sequence
• read_grishin_aln_file() : core::sequence
• read_H3_cter_fragment() : protocols::antibody
• read_in_mutations() : protocols
• read_loop_fragments() : protocols::loops
• read_pairing_list() : core::scoring::dssp , protocols::jumping
• read_pose_from_pdb() : protocols::enzdes::enzutil
• read_psipred_ss2_file() : core::pose
• read_RBSegment_file() : protocols::rbsegment_relax
• read_std_frags_from_cmd() : core::fragment
• read_stoopid() : core::scoring::packstat
• read_template_scores() : protocols::cluster
• read_topology_file() : core::chemical
• readValueOrDie() : core::scoring::constraints
• RealAngleToShort() : protocols::loophash
• REALLY_BAD_SCORE() : protocols::loops::loop_closure::ccd
• rebuild_disulfide() : core::util
• rebuild_loops_until_closed() : protocols::comparative_modeling
• recenter() : core::conformation::symmetry
• recreate_task() : protocols::enzdes::enzutil
• reduced_size() : protocols::scoring::methods::pcs2
• refine_mindis_with_xyzHash() : protocols::sic_dock
• refold_loop_torsion() : protocols::loops::loop_closure::ccd
• register_cutoff() : protocols::abinitio
• register_options() : protocols::evaluation , protocols::jd2
• register_options_broker() : protocols::abinitio
• register_options_universal_main() : protocols::jobdist
• regular_edges_within_interval() : protocols::forge::methods
• regular_facet_containing_position() : protocols::forge::methods
• reinitialize_mingraph_neighborhood_for_residue() : core::pack
• reinstate_side_chain_angles() : protocols::swa::protein
• Relax_main() : protocols::relax
• relax_pose() : protocols::relax
• remap_rb_segments() : protocols::rbsegment_relax
• remodel_fold_tree_to_account_for_insertion() : core::kinematics
• remodel_generic_taskfactory() : protocols::forge::methods
• remove_all_enzdes_constraints() : protocols::enzdes::enzutil
• remove_all_variant_types() : protocols::swa::rna
• remove_chain_break_jump_point() : protocols::swa::rna
• remove_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• remove_constraint_from_residue_constraints() : core::scoring::constraints
• remove_coordinate_constraints_from_pose() : protocols::protein_interface_design
• remove_cut() : protocols::jumping
• remove_cutpoint() : protocols::forge::methods
• remove_cutpoint_closed() : protocols::rna
• remove_cutpoint_variants() : core::util , protocols::forge::methods , protocols::loops
• remove_cutpoints() : protocols::forge::methods
• remove_cutpoints_closed() : protocols::rna
• remove_end_variants() : protocols::swa::protein
• remove_file() : protocols::swa::rna
• remove_hotspot_constraints_from_pose() : protocols::hotspot_hashing
• 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_missing_density() : protocols::loops
• remove_non_protein_residues() : protocols::toolbox::pose_manipulation
• remove_nonprotein_residues() : core::pose
• remove_remark_header_for_geomcst() : protocols::enzdes::enzutil
• remove_residues() : protocols::hybridization
• remove_short_chunks() : protocols::loops
• remove_small_gaps() : protocols::loops
• 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_O2Star_hydrogen() : protocols::swa::rna
• remove_virtual_residues() : core::pose
• remove_virtual_rna_residue_variant_type() : protocols::swa::rna
• remove_whitespaces() : core::scoring::rna::chemical_shift
• renumber_pdbinfo_based_on_conf_chains() : core::pose
• renumber_with_pdb_info() : protocols::hybridization
• reorder_after_append() : protocols::swa::monte_carlo
• reorder_after_delete() : protocols::swa::monte_carlo
• reorder_after_insert() : protocols::swa::monte_carlo
• reorder_after_prepend() : protocols::swa::monte_carlo
• reorder_sub_to_full_info_after_append() : protocols::swa::monte_carlo
• reorder_sub_to_full_info_after_delete() : protocols::swa::monte_carlo
• reorder_sub_to_full_info_after_prepend() : protocols::swa::monte_carlo
• reorder_with_first_non_mobile_as_root() : protocols::ligand_docking
• reorient_extended_fibril() : protocols::fibril
• repackable_residues() : core::pack
• repackable_residues_dup() : core::pack
• RepGridTracer() : protocols::qsar::scoring_grid
• replace() : protocols::forge::methods
• replace_conformation_residue_copying_existing_coordinates() : core::conformation
• replace_pose_residue_copying_existing_coordinates() : core::pose
• replace_region() : protocols::grafting
• replace_residue_in_atom_tree() : core::conformation
• replace_residue_keeping_all_atom_positions() : protocols::toolbox::match_enzdes_util
• replace_substr() : core::kinematics
• replaced_symmetric_foldtree_with_new_monomer() : core::conformation::symmetry
• REPLONLY() : core::chemical
• report_application_command() : core
• report_batch_inconsistency() : protocols::jd2::archive
• report_tag_error() : protocols::jd2::archive
• report_value_error() : protocols::jd2::archive
• requires_CB_mapping() : core::scoring::constraints
• res1_pointed_at_res2() : core::pack::task::operation::util
• resample() : core::scoring::electron_density
• rescale_scorefxn() : protocols::swa::rna
• reset_x() : protocols::toolbox
• residue_burial_filter_tracer() : protocols::simple_filters
• residue_center_of_mass() : core::conformation::symmetry , protocols::geometry
• residue_cutoff() : protocols::abinitio
• residue_distance_filter_tracer() : protocols::simple_filters
• residue_fast_pair_energy_attached_H() : core::scoring
• residue_is_bulge() : protocols::rna
• residue_list_sort_citeria() : protocols::swa::rna
• residue_packer_states() : protocols::rosetta_scripts
• residue_point_graph_from_conformation() : core::conformation
• residue_sc_rmsd_no_super() : core::scoring , protocols::hotspot_hashing
• residue_selector_single_from_line() : core::chemical
• residue_type_all_patches_name() : core::chemical
• residue_type_base_name() : core::chemical
• residue_type_has_waters() : core::scoring::methods
• residue_types_from_saccharide_sequence() : core::pose
• residue_types_from_sequence() : core::pose
• residues_in_interface_tracer() : protocols::simple_filters
• residues_interact() : core::scoring::methods
• restore_pose_from_rbsegs() : protocols::rbsegment_relax
• restore_residues() : protocols::forge::methods
• restrain_ligand_nbr_atom() : protocols::ligand_docking
• restrict_dna_rotamers() : protocols::dna
• restrict_prec() : core::io::pdb
• restrict_to_canonical_aas() : protocols::multistate_design
• restrict_to_protein_residues() : protocols::ligand_docking
• restrict_to_single_sequence() : protocols::dna
• retain_top() : core::fragment
• retrieve_assignment() : protocols::noesy_assign
• 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_nonconst_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
• retrieve_RDC_segments_from_pose() : protocols::scoring
• retrieve_residue_info() : core::scoring::methods
• retrieve_rotamer_set_info() : core::scoring::methods
• return_nearest_residue() : core::conformation::symmetry , protocols::geometry
• return_region() : protocols::grafting
• RG() : protocols::rigid , core::io::silent , protocols::protein_interface_design::movers , protocols::rna , protocols::loop_build , core::pack::interaction_graph , protocols::jumping , protocols::loops , protocols::ligand_docking , protocols::protein_interface_design::movers , protocols::loophash , protocols::abinitio , protocols::loops , protocols::forge::remodel , protocols::loops::loop_closure::kinematic_closure , protocols::cluster , protocols::enzdes , protocols::simple_moves , protocols::comparative_modeling , protocols::design_opt , protocols::simple_moves , protocols::abinitio , protocols::rna , core::pack , core::pack::annealer , core::optimization , core::io::pdb , protocols::wum , core::fragment::picking_old::vall::eval , core::conformation::symmetry , protocols::loops , core::fragment , protocols::loops::loop_mover::perturb , protocols::loops::loop_mover::refine , core::fragment::picking_old::vall::eval , protocols::loops , protocols::protein_interface_design::movers , protocols::hybridization , protocols::rbsegment_relax , protocols::rigid , protocols::idealize , protocols::simple_moves , protocols::seeded_abinitio , protocols::wum , protocols::simple_moves::symmetry , protocols::toolbox::pose_metric_calculators , protocols::nonlocal , protocols::match , protocols::moves , protocols::rna , protocols::loophash , protocols::loops::loop_mover::perturb , protocols , protocols::jobdist , protocols::loops::loop_mover::refine , protocols::loophash , protocols::loops::loop_mover::refine , protocols::loops::loop_mover , protocols::loops::loop_mover::perturb , protocols::loophash , protocols::loops::loop_closure::ccd , core::fragment::picking_old::vall::eval , core::pack::rotamer_set , protocols::forge::build , protocols::jumping , protocols::protein_interface_design::movers , protocols::frag_picker::scores , protocols::forge::build , protocols::rna , protocols::forge::remodel
• rg() : protocols::simple_moves
• RG() : protocols::forge::methods , core::pose::symmetry , protocols::simple_moves::asym_fold_and_dock , protocols::forge::methods , protocols::ub_e2c , protocols::rosetta_scripts , protocols::ddg , core::scoring , protocols::coarse_rna , protocols::simple_moves , core::kinematics , protocols::flexpack::annealer , protocols::design_opt , core::scoring::constraints , protocols::abinitio
• 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_FRAG_STORE() : protocols::loops::loop_closure::ccd
• rmsd_no_super() : core::scoring
• rmsd_no_super_subset() : core::scoring
• rmsd_over_residue_list() : protocols::swa::rna
• rmsd_with_super() : core::scoring
• rmsd_with_super_subset() : core::scoring
• RMSwrapper() : protocols::simple_filters
• 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
• rolling_score() : protocols::frag_picker::scores
• rot_sample_from_name() : core::pack::task
• rotamer_from_chi() : core::pack::dunbrack
• rotamer_from_chi_02() : core::pack::dunbrack
• rotamer_trials() : core::pack
• rotamers_for_trials() : protocols::ligand_docking
• RotamerTracer() : protocols::RotamerDump
• rotate() : protocols::swa
• rotate_anchor_to_x_axis() : core::pose::symmetry
• rotate_tracer() : protocols::ligand_docking
• rotate_vec() : protocols::toolbox
• rotates_tracer() : protocols::ligand_docking
• rots_from_pose() : protocols::comparative_modeling
• rottrials_RG() : core::pack
• round() : protocols::noesy_assign
• rsd_set_from_cmd_line() : core::chemical
• RT_from_epos() : protocols::jumping
• rtmin_RG() : core::pack
• run_boinc_debug() : protocols::abinitio
• run_calculator() : protocols::forge::remodel