- r -

• R2quat() : protocols::simple_filters
• R3z1() : protocols::sic_dock::scores
• R3z2() : protocols::sic_dock::scores
• R3z3() : protocols::sic_dock::scores
• rama_list_pred() : protocols::relax
• ramp_minpack_loop() : protocols::mpi_refinement
• ramp_minpack_pose() : protocols::mpi_refinement
• random_conformer_tracer() : protocols::ligand_docking
• random_connection() : protocols::ligand_docking
• 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
• RBSegmentRelax_main() : protocols
• read1() : protocols::cluster
• read_biounit() : protocols::sic_dock
• read_disulf_pairing_list() : protocols::jumping
• read_extra_residues() : protocols::comparative_modeling
• read_fragment_candidates() : protocols::frag_picker
• read_frags() : protocols::topology_broker
• read_H3_cter_fragment() : protocols::antibody_legacy
• read_in_mutations() : protocols
• read_loop_fragments() : protocols::loops
• read_minor_helix_params() : protocols::helical_bundle
• read_pairing_list() : protocols::jumping
• read_pose_from_pdb() : protocols::enzdes::enzutil
• read_RBSegment_file() : protocols::rbsegment_relax
• read_rigid_core() : protocols::abinitio::abscript
• read_ss2() : protocols::mpi_refinement
• read_template_scores() : protocols::cluster
• RealAngleToShort() : protocols::loophash
• REALLY_BAD_SCORE() : protocols::loops::loop_closure::ccd
• rebuild_loops_until_closed() : protocols::comparative_modeling
• recreate_task() : protocols::enzdes::enzutil
• recursive_multiple_disulfide_former() : protocols::forge::remodel
• reduced_size() : protocols::scoring::methods::pcs2
• REFINE() : protocols::loops::loop_mover
• refine_mindis_with_xyzHash() : protocols::sic_dock
• 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
• Relax_main() : protocols::relax
• relax_pose() : protocols::relax
• remap_rb_segments() : protocols::rbsegment_relax
• remodel_generic_taskfactory() : protocols::forge::methods
• remove_all_enzdes_constraints() : protocols::enzdes::enzutil
• remove_all_variant_types() : protocols::stepwise::modeler::rna
• remove_all_virtual_phosphates() : protocols::stepwise::modeler::rna
• remove_chain_break_jump_point() : protocols::stepwise::legacy::modeler::rna
• remove_chain_break_variants() : protocols::stepwise::modeler::rna
• remove_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• remove_coordinate_constraints_from_pose() : protocols::protein_interface_design
• remove_cut() : protocols::jumping
• remove_cutpoint() : protocols::forge::methods
• remove_cutpoint_closed() : protocols::farna
• remove_cutpoint_variants() : protocols::forge::methods , protocols::loops
• remove_cutpoint_variants_for_ccd() : protocols::grafting
• remove_cutpoints() : protocols::forge::methods
• remove_cutpoints_closed() : protocols::farna
• remove_file() : protocols::stepwise::modeler::rna
• remove_hotspot_constraints_from_pose() : protocols::hotspot_hashing
• remove_missing_density() : protocols::loops
• remove_non_protein_residues() : protocols::toolbox::pose_manipulation
• remove_remark_header_for_geomcst() : protocols::enzdes::enzutil
• remove_residues() : protocols::hybridization
• remove_short_chunks() : protocols::loops
• remove_silent_file_if_it_exists() : protocols::stepwise::modeler
• remove_small_gaps() : protocols::loops
• remove_terminal_phosphates() : protocols::stepwise::modeler::rna::phosphate
• remove_virtual_O2Prime_hydrogen() : protocols::stepwise::modeler::rna
• renumber_with_pdb_info() : protocols::hybridization
• reorder_membrane_foldtree() : protocols::membrane::geometry
• reorder_root_partition_res() : protocols::stepwise::modeler
• reorder_with_first_non_mobile_as_root() : protocols::ligand_docking
• reorient_extended_fibril() : protocols::fibril
• repack_connection_and_residues_in_movemap() : protocols::grafting
• repack_connection_and_residues_in_movemap_and_piece() : protocols::grafting
• repack_connection_and_residues_in_movemap_and_piece_and_neighbors() : protocols::grafting
• RepGridTracer() : protocols::qsar::scoring_grid
• replace() : protocols::forge::methods
• replace_region() : protocols::grafting
• replace_residue_keeping_all_atom_positions() : protocols::toolbox::match_enzdes_util
• report_batch_inconsistency() : protocols::jd2::archive
• report_heading_directions_of_all_AA_in_a_strand() : protocols::features::strand_assembly
• report_tag_error() : protocols::jd2::archive
• report_value_error() : protocols::jd2::archive
• reroot() : protocols::stepwise::modeler
• reroot_based_on_full_model_info() : protocols::stepwise::modeler
• res_res_min_distance() : protocols::simple_filters
• res_rmsd() : protocols::simple_filters
• rescale_scorefxn() : protocols::stepwise::modeler::rna
• reset_x() : protocols::toolbox
• residue_burial_filter_tracer() : protocols::simple_filters
• residue_center_of_mass() : protocols::membrane::geometry
• residue_cutoff() : protocols::abinitio
• residue_distance_filter_tracer() : protocols::simple_filters
• residue_is_floppy() : protocols::sic_dock
• residue_packer_states() : protocols::rosetta_scripts
• residue_sc_rmsd_no_super() : protocols::hotspot_hashing
• residues_in_interface_tracer() : protocols::simple_filters
• 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_to_canonical_aas() : protocols::multistate_design
• restrict_to_protein_residues() : protocols::ligand_docking
• restrict_to_single_sequence() : protocols::dna
• retrieve_assignment() : protocols::noesy_assign
• retrieve_RDC_segments_from_pose() : protocols::scoring
• retrieve_residue_num_of_rkde() : protocols::features::strand_assembly
• return_nearest_residue() : protocols::membrane::geometry
• return_region() : protocols::grafting
• revise_root_and_moving_res() : protocols::stepwise::modeler
• revise_root_and_moving_res_list() : protocols::stepwise::modeler
• rm_variant() : protocols::environment
• RMSD_FRAG_STORE() : protocols::loops::loop_closure::ccd
• rmsd_over_residue_list() : protocols::stepwise::modeler::rna
• RMSwrapper() : protocols::simple_filters
• rolling_score() : protocols::frag_picker::scores
• rot_mat() : protocols::forge::remodel
• rot_pose() : protocols::matdes , protocols::sic_dock
• rotamers_for_trials() : protocols::ligand_docking
• RotamerTracer() : protocols::RotamerDump
• rotate() : protocols::toolbox::rigid_body
• rotate_into_nucleobase_frame() : protocols::toolbox::sample_around
• rotate_into_phosphate_frame() : protocols::toolbox::sample_around
• rotate_tracer() : protocols::ligand_docking
• rotate_vec() : protocols::toolbox
• rotates_tracer() : protocols::ligand_docking
• rots_from_pose() : protocols::comparative_modeling
• round() : protocols::noesy_assign
• round_to_float() : protocols::features::strand_assembly
• round_to_Real() : protocols::features::strand_assembly
• round_to_Size() : protocols::features::strand_assembly
• RT_from_epos() : protocols::jumping
• run_boinc_debug() : protocols::abinitio