- o -

• O() : protocols::sic_dock::scores
• o2prime_trials() : protocols::stepwise::modeler::rna
• obtain_secstruct_segments() : core::fragment::rna
• off_rotamer_pack() : core::pack
• off_rotamer_pack_optimize() : core::pack
• off_rotamer_pack_setup() : core::pack
• off_rotamer_pack_update_pose() : core::pack
• omega2_torsion() : core::id
• omega_torsion() : core::id
• omega_torsion_beta_aa() : core::id
• omega_torsion_meta_aramid() : core::id
• omega_torsion_oligourea() : core::id
• omega_torsion_ortho_aramid() : core::id
• omega_torsion_para_aramid() : core::id
• omega_torsion_post_methylene_meta_aramid() : core::id
• omega_torsion_post_methylene_ortho_aramid() : core::id
• omega_torsion_post_methylene_para_aramid() : core::id
• omega_torsion_pre_methylene_meta_aramid() : core::id
• omega_torsion_pre_methylene_ortho_aramid() : core::id
• omega_torsion_pre_methylene_para_aramid() : core::id
• omega_torsion_pre_methylene_post_methylene_meta_aramid() : core::id
• omega_torsion_pre_methylene_post_methylene_ortho_aramid() : core::id
• omega_torsion_pre_methylene_post_methylene_para_aramid() : core::id
• on_pose_accept() : protocols::medal
• on_segment() : core::membrane
• one_indexed_chr_chains() : core::chemical
• one_letter_from_rt() : core::import_pose::libraries
• one_network_is_subset_of_other() : protocols::hbnet
• oneletter2aa() : core::chemical
• oneletter_code_from_aa() : core::chemical
• oneletter_code_specifies_aa() : core::chemical
• onError() : core::pack::task
• open_stream() : protocols::noesy_assign
• operator!=() : core::chemical , core::chemical::rings , core::conformation::symmetry , core::io::nmr , core::kinematics , core::pose::full_model_info , core::scoring::hbonds , core::scoring::methods , core::scoring::nmr::pcs , core::scoring::nmr::pre , core::scoring::nmr::rdc , protocols::jd2
• operator&() : protocols::loop_modeling , protocols::network
• operator*() : core::kinematics , core::scoring , protocols::mean_field
• operator*=() : protocols::mean_field
• operator+() : protocols::mean_field
• operator++() : core::chemical , core::scoring::carbohydrates
• operator+=() : protocols::mean_field
• operator-() : protocols::mean_field
• operator-=() : protocols::mean_field
• operator/() : protocols::mean_field
• operator/=() : protocols::mean_field
• operator<() : core::chemical , core::fragment::rna , core::io::nmr , core::kinematics , core::pose::rna , core::scoring::etable , core::scoring::rna , core::sequence , protocols::sewing::data_storage
• operator<<() : core::chemical::carbohydrates , core::chemical::gasteiger , core::chemical , core::chemical::rings , core::conformation::membrane , core::conformation , core::conformation::signals , core::conformation::symmetry , core::environment , core::fragment , core::fragment::picking_old::vall::scores , core::id , core::import_pose::libraries , core::import_pose , core::io::mmtf , core::io , core::io::pdb , core::kinematics , core::optimization , core::pack::interaction_graph , core::pack::rotamer_set , core::pack::task , core::pack_basic , core::pose::full_model_info , core::pose , core::pose::rna , core::scoring::constraints , core::scoring::dssp , core::scoring::elec::electrie , core::scoring::etable::etrie , core::scoring::etable , core::scoring::func , core::scoring::hbonds::hbtrie , core::scoring::hbonds , core::scoring::lkball::lkbtrie , core::scoring::loop_graph , core::scoring::methods , core::scoring::mm::mmtrie , core::scoring::mm , core::scoring::motif , core::scoring , core::scoring::packstat , core::scoring::rna , core::sequence , protocols::aa_composition , protocols::abinitio , protocols::analysis , protocols::antibody , protocols::antibody::snugdock , protocols::backbone_moves::local_backbone_mover , protocols::backbone_moves , protocols::calc_taskop_movers , protocols::canonical_sampling , protocols::carbohydrates , protocols::chemically_conjugated_docking , protocols::constraint_generator , protocols::constraint_movers , protocols::cyclic_peptide , protocols::denovo_design::components , protocols::denovo_design::movers , protocols::denovo_design::task_operations , protocols::dna , protocols::docking , protocols::environment::claims , protocols::enzymatic_movers , protocols::farnesyl , protocols::features::helixAssembly , protocols::fldsgn::topology , protocols::frag_picker , protocols::frags , protocols::genetic_algorithm , protocols::hotspot_hashing , protocols::indexed_structure_store , protocols::jd2::archive , protocols::jd2 , protocols::jd3::chunk_library , protocols::jd3::full_model , protocols::jd3 , protocols::jd3::standard , protocols::jumping , protocols::legacy_sewing , protocols::ligand_docking::ligand_options , protocols::loops::loop_closure::ccd , protocols::loops::loop_closure::jacobi , protocols::loops::loop_mover::perturb , protocols::loops::loop_mover::refine , protocols::loops , protocols::match::output , protocols::mean_field , protocols::membrane , protocols::membrane_benchmark , protocols::minimization_packing , protocols::monte_carlo , protocols::motifs , protocols::moves , protocols::ncbb , protocols::noesy_assign , protocols::optimize_weights , protocols::pdbinfo_manipulations , protocols::pmut_scan , protocols::pose_creation , protocols::quantum_annealing , protocols::recces::scratch , protocols::rigid , protocols::rna::denovo::movers , protocols::rna::denovo , protocols::rna::movers , protocols::rosetta_scripts , protocols::scoring::methods::pcs2 , protocols::scoring::methods::pcs , protocols::scoring::methods::pcsTs1 , protocols::scoring::methods::pcsTs2 , protocols::scoring::methods::pcsTs3 , protocols::scoring::methods::pcsTs4 , protocols::scoring , protocols::sewing::hashing , protocols::sewing::movers , protocols::sic_dock , protocols::simple_moves , protocols::sparta , protocols::stepwise::modeler::rna::phosphate , protocols::stepwise::monte_carlo::mover , protocols::toolbox , protocols::topology_broker::claims , protocols::topology_broker
• operator<=() : core::io::nmr
• operator==() : boost::tuples , core::chemical , core::chemical::rings , core::conformation::symmetry , core::io::nmr , core::kinematics , core::pose::full_model_info , core::pose::rna , core::scoring::etable , core::scoring::hbonds , core::scoring::methods , core::scoring::nmr::pcs , core::scoring::nmr::pre , core::scoring::nmr::rdc , core::scoring , core::scoring::rna , protocols::jd2 , protocols::make_rot_lib , protocols::stepwise::monte_carlo::mover
• operator>() : core::io::nmr
• operator>=() : core::io::nmr
• operator>>() : core::chemical , core::conformation::symmetry , core::fragment , core::id , core::kinematics , core::pose::full_model_info , core::scoring::dssp , core::scoring::motif , core::scoring , core::scoring::packstat , core::sequence , protocols::abinitio , protocols::frags , protocols::hotspot_hashing , protocols::jd2::archive , protocols::noesy_assign , protocols::sasa_scores , protocols::toolbox , protocols::topology_broker
• operator|() : protocols::loop_modeling , protocols::moves , protocols::network
• opposite_designation() : core::chemical::rings
• oprod() : protocols::toolbox
• optimal_connection_point() : protocols::protein_interface_design
• optimal_water_distance() : core::scoring::lkball
• optimize() : protocols::hybridization
• optimize_H_and_notify() : core::pack
• optimizeH() : core::pack
• option_type_from_key() : protocols::jd3::chunk_library , protocols::jd3::full_model , protocols::jd3
• option_vdw_rep_screen_info_user() : protocols::scoring
• optionally_named_move_map_ct_namer() : protocols::rosetta_scripts
• options_for_generate_relax_from_cmd() : protocols::relax
• options_for_get_cst_fa_file_option() : core::scoring::constraints
• options_for_get_cst_file_option() : core::scoring::constraints
• options_for_job() : protocols::jd3
• options_for_set_native_in_mover() : protocols::jd2
• options_from_tag() : protocols::jd3
• OR_combine() : core::select::residue_selector
• order() : protocols::forge::methods
• order_tensor_parameters() : core::scoring::nmr
• orient_array() : protocols::indexed_structure_store
• orient_residue_for_ideal_bond() : core::conformation
• orient_tcr_chain() : protocols::tcr
• orientations_str() : protocols::denovo_design::components
• original_pose_residue_is_in_residue_map() : protocols::generalized_kinematic_closure
• out_of_bounds_memory_access() : protocols::toolbox
• out_pair_constel() : protocols::constel
• out_triple_constel() : protocols::constel
• output_base_pairs() : core::pose::rna
• output_base_stacks() : core::pose::rna
• output_bool_list() : protocols::stepwise::legacy::modeler::rna
• output_boolean() : core::pose::rna , protocols::stepwise::modeler
• output_data() : protocols::stepwise::modeler::rna
• output_error_message() : protocols::scoring::methods::pcs2
• output_fasta_file() : core::sequence
• output_fold_tree_info() : protocols::stepwise::legacy::modeler::rna
• output_interface_deltas() : protocols::ligand_docking
• output_intermediate_pose() : protocols::jd2
• output_is_prepend_map() : protocols::stepwise::legacy::modeler::rna
• output_ligands() : core::pose::rna
• output_motifs_to_pymol() : core::scoring::rna
• output_movemap() : protocols::stepwise::modeler
• output_other_contacts() : core::pose::rna
• output_packstat() : protocols::vip
• output_packstat_pdb() : core::scoring::packstat
• output_pair_size() : protocols::stepwise::legacy::modeler::rna
• output_pose_list() : protocols::stepwise::legacy::modeler::protein
• output_protein_movemap_header() : protocols::stepwise::modeler
• output_res_map() : protocols::stepwise::modeler::rna
• output_residue() : core::chemical::sdf
• output_rna_motif() : core::scoring::rna
• output_rna_motifs() : core::scoring::rna
• output_rna_motifs_detailed() : core::scoring::rna
• output_rna_movemap_header() : protocols::stepwise::modeler
• output_rotamer() : protocols::stepwise::modeler::rna
• output_seq_num_list() : protocols::stepwise::modeler::rna
• output_silent_struct() : protocols::stepwise::legacy::modeler::protein
• output_size_list() : protocols::stepwise::legacy::modeler::rna
• output_stems() : core::pose::rna
• output_title_text() : protocols::stepwise::modeler::rna
• output_to_silent_file() : protocols::stepwise::monte_carlo
• overlap() : core::scoring::packstat
• overlap_chainbreak() : protocols::forge::methods