- o -

• o2prime_packer() : swa_rna_util.cc
• O_annotate_functions() : options.cpp
• O_annotate_includes() : options.cpp
• O_bind() : options.cpp
• O_bind_class_template_specialization() : options.cpp
• O_config() : options.cpp
• O_flat() : options.cpp
• O_include_pybind11_stl() : options.cpp
• O_max_file_size() : options.cpp
• O_prefix() : options.cpp
• O_root_module() : options.cpp
• O_single_file() : options.cpp
• O_skip() : options.cpp
• O_skip_line_number() : options.cpp
• O_suppress_errors() : options.cpp
• O_trace() : options.cpp
• O_verbose() : options.cpp
• obtain_secstruct_segments() : homolog_finder_farna.cc
• obtain_start_pose() : erraser2.cc
• octree_test() : xyzHash_test.hh
• old_simple_conformation_test() : test1.cc
• OMG_BINRANGE() : peptoid_rotlib_test2.cc
• ompA_task() : membrane_ddG.cc
• ompLA_task() : membrane_ddG.cc
• on_segment() : mpframework_test2.cc
• one_chain_MC_sampling() : turner_test_one_chain.cc
• one_chain_ST_MC() : turner_test_one_chain.cc
• oneChainPose() : PeptideDeriver.cc
• operator+() : pep_opt_parallel.cc
• operator<() : pseudo_ca_trace.cc , denovo_density.cc , pseudo_ca_trace.cc
• operator<<() : undirected_graph.cc , serialization.h , Vec.hh , hubdenovo.cc , helix_assembly.cc , hczndimer.cc , gpu_mat_vec.hh , crossmatch_d2.cc , crossmatch.cc , TracerTest.cc , test1.cc , gpu_mat_vec.hh , undirected_graph.cc
• operator>>() : serialization.h , hczndimer.cc
• operator|() : color.h
• OPT_1GRP_KEY() : test_bbmc.org.cc , cxdesign.cc , cenrot_jd2.cc , test_bbmc.cc , calibur.cc , design_tight_clusters.cc , test_bbmc.org.cc , design_tight_clusters.cc , test_bbmc.org.cc , detect_tight_clusters.cc , test_bbmc.cc , test_bbmc.org.cc , test_bbmc.cc
• opt_bicelle_params() : mp_optimize_geometry_params.cc
• opt_double_vesicle_params() : mp_optimize_geometry_params.cc
• OPT_KEY() : design_cycpeptide_MPI.cc , make_ideal_betapeptide.cc , PCA_visualizer.cc , test_KIC_betapeptide.cc , bettercluster.cc , design_cycpeptide_MPI.cc , dock_pdb_into_density.cc , r_count_neighbours.cc , r_cst_tool.cc , parin_test.cc , bettercluster.cc , design_cycpeptide_MPI.cc , bettercluster.cc , design_cycpeptide_MPI.cc , bettercluster.cc
• opt_vesicle_params() : mp_optimize_geometry_params.cc
• opte_num_inner_iterations() : optE_test.cc
• opte_weight_mixing_factor() : optE_test.cc
• optimal_rotation() : mammoth_hack.cc
• optimize_embedding() : helix_from_sequence.cc
• optimize_pose() : minimize_with_cst.cc
• optimize_weights() : optE_test.cc , roc_optimizer.cc
• order_score_score() : HDXEnergy.cc
• OS_VER() : crash_report.cc
• output_alignments() : filterAlignments.cc , filterImperfectAln.cc , minimalCstHomology.cc
• output_all_repeats() : extractNativeRepeats.cc
• output_angles() : coarse_rna_test.cc
• output_backbone_stats() : easy_target_test.cc
• output_benchmark_stuff() : rna_test.cc
• output_caAtomsToConstraint() : minimalCstRelax.cc
• output_canonical_base_pair_steps() : rna_database.cc
• output_centroid_silent_struct() : stepwise_centroid_test.cc
• output_centroid_stats() : pdbstats_test.cc
• output_chainTORS() : loop_closure_test.cc
• output_chi_stats() : easy_target_test.cc
• output_cmp() : elec_dens_rot_recov.cc
• output_connect() : entropy_test.cc
• output_constraints() : easy_target_test.cc
• output_constraints_for_full_length() : easy_target_test.cc
• output_contact_info() : get_info.cc
• output_csts() : get_info.cc
• output_distance_matrix() : entropy_test.cc
• output_general_base_pair_steps() : rna_database.cc
• output_interface_graphviz() : hbond_connect.cc
• output_local_minima() : sweep_respair_energies.cc
• output_minipose_coords_test() : coarse_rna_test.cc
• output_native_ss_info() : get_info.cc
• output_packstat() : packstat.cc , pilot_packstat.cc
• output_packstat_pdb() : pilot_packstat.cc , packstat.cc
• OUTPUT_PATH() : test_coenzymes.cc , test_explicit_membrane_input.cc
• output_PCA() : bettercluster.cc
• output_pdb() : fragpdb.cc
• output_residue_struct() : swa_rna_util.cc
• output_residue_types() : restype_converter.cc
• output_results() : ResidueDisorder.cc , SID_ERMS_prediction.cc , per_residue_solvent_exposure.cc , cl_complex_rescore.cc , SID_rescore.cc , HDXEnergy.cc
• output_sasa() : rna_test.cc
• output_score() : test_carbohydrate_scoring.cc
• output_seq_with_residue_emphasis() : build_full_model.cc
• output_single_motif() : ligand_motifs.cc , dna_motifs_collector.cc , ligand_motifs.cc , extract_motifs.cc
• output_ss_info() : get_info.cc
• output_strand1_strand2_info() : turner_rules_test.cc
• output_struct_type() : rna_test.cc
• output_stuff() : entropy_test.cc , turner_rules_test.cc
• output_sugar_geometry_parameters() : rna_test.cc
• output_sugar_internal_dof() : rna_test.cc
• output_superimposed_pdb() : rna_graft.cc
• output_to_silent() : loop_closure_test.cc
• output_torsion_list() : turner_test_double_helix.cc , turner_rules_test.cc
• output_torsion_M_v_lists() : turner_rules_test.cc
• output_torsions() : coarse_rna_test.cc
• overlap_score() : overlap_score.hh
• overlay_bb_bondangles() : overlay_bb_bondangles.cc