- o -

• o() : out::file
• obey_ENDMDL() : basic::options::OptionKeys::in::file , in::file
• obj_to_map() : utility::json_spirit
• objective_function() : basic::options::OptionKeys::lh , lh
• occupancy() : basic::options::OptionKeys::mh::filter , mh::filter
• old_estat() : basic::options::OptionKeys::docking::ligand , docking::ligand
• omega() : AnchoredDesign::filters , basic::options::OptionKeys::AnchoredDesign::filters
• one_body() : rotamerdump
• oneloop() : basic::options::OptionKeys::mh::filter , mh::filter
• only_enumerate_non_match_redundant_ligand_rotamers() : basic::options::OptionKeys::match , match
• only_repack() : basic::options::OptionKeys::dna::specificity , dna::specificity
• only_stage1() : abinitio , basic::options::OptionKeys::abinitio
• open() : basic::database
• operate() : packing::ex1 , packing::ex2 , packing::ex3 , packing::ex4
• operator!=() : numeric , utility::file , utility::keys , utility , utility::pointer , utility::query::metric_operators
• operator&() : utility::query::filter_operators
• operator*() : numeric::kinematic_closure , numeric , utility::query::metric_operators
• operator*=() : numeric
• operator+() : numeric::kinematic_closure , numeric , utility , utility::options , utility::query::metric_operators
• operator+=() : numeric
• operator-() : numeric::kinematic_closure , numeric , utility , utility::query::metric_operators
• operator-=() : numeric
• operator/() : numeric::kinematic_closure , numeric , utility::query::metric_operators
• operator/=() : numeric
• operator<() : numeric , utility::file , utility::keys , utility , utility::options , utility::pointer , utility::query::metric_operators
• operator<<() : basic::resource_manager , basic::sampling::orientations , numeric::kdtree , numeric::kinematic_closure , numeric , utility::excn , utility::file , utility , utility::options , utility::pointer , utility::tag
• operator<=() : numeric , utility::file , utility::keys , utility , utility::query::metric_operators
• operator==() : numeric , utility::file , utility::json_spirit , utility::keys , utility , utility::pointer , utility::query::metric_operators
• operator>() : numeric , utility::file , utility::keys , utility , utility::query::metric_operators
• operator>=() : numeric , utility::file , utility::keys , utility , utility::query::metric_operators
• operator>>() : numeric , utility::file
• operator^() : numeric , utility::query::metric_operators
• operator|() : utility , utility::query::filter_operators
• operator~() : utility::query::filter_operators
• opt_input_structure() : basic::options::OptionKeys::ddg , ddg
• opt_radius() : basic::options::OptionKeys::casp , basic::options::OptionKeys::ddg , casp , ddg
• optE() : basic::options::OptionKeys::optE , optE
• optE_no_protein_fa_elec() : basic::options::OptionKeys::optE , optE
• optE_soft_rep() : basic::options::OptionKeys::optE , optE
• optH_MCA() : packing
• optH_patch() : score
• optH_weights() : score
• optimization() : basic::options::OptionKeys::optimization , optimization
• optimize_cutpoints_margin() : abinitio , basic::options::OptionKeys::abinitio
• optimize_cutpoints_using_kic() : abinitio , basic::options::OptionKeys::abinitio
• optimize_ddG_bind_correlation() : basic::options::OptionKeys::optE , optE
• optimize_ddGmutation() : basic::options::OptionKeys::optE , optE
• optimize_ddGmutation_boltzman_average() : basic::options::OptionKeys::optE , optE
• optimize_ddGmutation_straight_mean() : basic::options::OptionKeys::optE , optE
• optimize_decoy_discrimination() : basic::options::OptionKeys::optE , optE
• optimize_dGbinding() : basic::options::OptionKeys::optE , optE
• optimize_ligand_discrimination() : basic::options::OptionKeys::optE , optE
• optimize_ligand_rot() : basic::options::OptionKeys::optE , optE
• optimize_loops() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• optimize_nat_aa() : basic::options::OptionKeys::optE , optE
• optimize_nat_rot() : basic::options::OptionKeys::optE , optE
• optimize_only_kic_region_sidechains_after_move() : basic::options::OptionKeys::loops , loops
• optimize_pssm() : basic::options::OptionKeys::optE , optE
• optimize_starting_free_weights() : basic::options::OptionKeys::optE , optE
• option_file() : basic::options::OptionKeys::docking::ligand , docking::ligand
• Option_Group() : options_class
• optional_positive_intafteroption() : basic::options
• orb_orb_stats() : orbitals
• orbitals() : orbitals
• orientation_atoms() : basic::options::OptionKeys::match , match
• origin_res_num() : basic::options::OptionKeys::fingerprint , fingerprint
• other_pose_scorefile() : run
• other_pose_to_scorefile() : run
• other_poses() : basic::options::OptionKeys::full_model , full_model
• out() : basic::options::OptionKeys::canonical_sampling::out , basic::options::OptionKeys::ddg , canonical_sampling::out , ddg , out
• out_path() : basic::options::OptionKeys::lh::fragpdb , lh::fragpdb
• out_pdb_prefix() : basic::options::OptionKeys::ddg , ddg
• outer_cycles() : basic::options::OptionKeys::loops , loops
• outer_iteration_scale() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• outer_product() : numeric
• outeriterations_scaling() : packing
• outlog() : basic::options::OptionKeys::optE::rescore , optE::rescore
• output() : basic::options::OptionKeys::cp , cp , out
• output_all() : basic::options::OptionKeys::frags::contacts , frags::contacts
• output_centroid() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• output_dir() : basic::options::OptionKeys::ddg , ddg
• output_etables() : score
• output_extra_RMSDs() : stepwise::rna
• output_feature_vector() : ProQ
• output_file() : basic::options::OptionKeys::motifs , motifs
• output_format() : basic::options::OptionKeys::match , match
• output_fragfiles() : remodel
• output_frags_pdbs() : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• output_hbond_info() : run
• output_idealized() : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• output_initial_pdb() : basic::options::OptionKeys::dna::design , dna::design
• output_local_prediction() : ProQ
• output_matches_per_group() : basic::options::OptionKeys::match , match
• output_matchres_only() : basic::options::OptionKeys::match , match
• output_only_cluster_transitions() : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• output_orbitals() : out::file
• output_pdb() : basic::options::OptionKeys::loops , loops , stepwise::rna
• output_raw_scores() : pH
• output_residue_energies() : score
• output_score_filter() : basic::options::OptionKeys::cluster , cluster
• output_silent() : basic::options::OptionKeys::ddg , basic::options::OptionKeys::frags::nonlocal , basic::options::OptionKeys::frags , ddg , frags::nonlocal , frags
• output_structures() : basic::options::OptionKeys::dna::design::specificity , dna::design::specificity
• output_tag() : out
• output_top_n_new_decoys() : basic::options::OptionKeys::optE , optE
• output_torsions() : out::file
• output_unbound_pdb() : basic::options::OptionKeys::dna::design , dna::design
• output_virtual() : out::file
• overlap_chainbreak() : basic::options::OptionKeys::jumps , jumps
• overlap_chainbreak_weight() : relax
• override_vdw_all_stages() : abinitio , basic::options::OptionKeys::abinitio
• oversample() : packstat
• overwrite() : out
• overwrite_filter_scorefxn() : basic::options::OptionKeys::fast_loops , fast_loops
• owning_ptr_acquire() : utility::pointer
• owning_ptr_release() : utility::pointer