Here is a list of all namespace members with links to the namespace documentation for each member:

- o -

• O : core::chemical::element , protocols::comparative_modeling::features , protocols::sic_dock::scores
• O2H : core::chemical::rna
• O2PRIME : core::chemical::rna
• O2PRIME_PACK : protocols::stepwise::screener
• o2prime_trials() : protocols::stepwise::modeler::rna
• O2PrimePackerCOP : protocols::stepwise::modeler::rna::o2prime
• O2PrimePackerOP : protocols::stepwise::modeler::rna::o2prime
• O2PrimeScreenerCOP : protocols::stepwise::screener
• O2PrimeScreenerOP : protocols::stepwise::screener
• O_p_sp2 : core::chemical::orbitals
• O_p_sp2_bb : core::chemical::orbitals
• O_p_sp3 : core::chemical::orbitals
• O_pi_sp2 : core::chemical::orbitals
• O_pi_sp2_bb : core::chemical::orbitals
• ObserverCacheAP : core::pose::datacache
• ObserverCacheCAP : core::pose::datacache
• ObserverCacheCOP : core::pose::datacache
• ObserverCacheOP : core::pose::datacache
• OBSLTE : core::io::pdb
• Obsolet_NamedAtomPairConstraintCOP : core::scoring::constraints
• Obsolet_NamedAtomPairConstraintOP : core::scoring::constraints
• occ_sol_exact : core::scoring
• occ_sol_fitted : core::scoring
• occ_sol_fitted_onebody : core::scoring
• OccFitParam : core::scoring::geometric_solvation
• OccFitParam_amp : core::scoring::geometric_solvation
• OccFitParam_cos_angle_mu : core::scoring::geometric_solvation
• OccFitParam_dist_mu : core::scoring::geometric_solvation
• OccFitParam_max_sq_dist : core::scoring::geometric_solvation
• OccFitParam_min_cos_angle : core::scoring::geometric_solvation
• OccFitParam_num_params : core::scoring::geometric_solvation
• OccFitParam_twice_cos_angle_sigma_sq : core::scoring::geometric_solvation
• OccFitParam_twice_dist_sigma_sq : core::scoring::geometric_solvation
• OccludedHbondSolEnergy_onebodyCreator_registrator : core::init
• OccludedHbondSolEnergyCreator_registrator : core::init
• OccupiedSpaceHashCOP : protocols::match
• OccupiedSpaceHashOP : protocols::match
• OCTOSE : core::chemical
• OCTREE : core::conformation
• off_rotamer_pack() : core::pack
• off_rotamer_pack_optimize() : core::pack
• off_rotamer_pack_setup() : core::pack
• off_rotamer_pack_update_pose() : core::pack
• ok_annotations : core::io::rna
• OL_features : protocols::rotamer_recovery
• OL_full : protocols::rotamer_recovery
• OL_none : protocols::rotamer_recovery
• OligomericAverageDegreeFilterCOP : protocols::matdes
• OligomericAverageDegreeFilterOP : protocols::matdes
• omega : core::scoring
• OMEGA : core::scoring
• omega2_dihedral : core::id
• omega3_dihedral : core::id
• omega_dihedral : core::id
• omega_ref : core::scoring
• omega_torsion() : core::id
• omega_torsion_beta_aa() : core::id
• OmegaPerturberCOP : protocols::kinematic_closure::perturbers
• OmegaPerturberOP : protocols::kinematic_closure::perturbers
• OmegaTetherCOP : core::scoring
• OmegaTetherEnergyCOP : core::scoring::methods
• OmegaTetherEnergyCreator_registrator : core::init
• OmegaTetherEnergyOP : core::scoring::methods
• OmegaTetherOP : core::scoring
• OMICRON_ATOM : core::chemical
• on_pose_accept() : protocols::medal
• ONE : core::pack::dunbrack
• one_group : protocols::toolbox::pose_metric_calculators
• ONE_TORSION : protocols::stepwise::sampler
• ONE_VALUE : protocols::stepwise::sampler
• ONE_VALUE_COMB : protocols::stepwise::sampler
• OneBodyEnergyCOP : core::scoring::methods
• OneBodyEnergyOP : core::scoring::methods
• oneletter2aa() : core::chemical
• oneletter_code_from_aa() : core::chemical
• oneletter_code_specifies_aa() : core::chemical
• onError() : core::pack::task
• OneToAllEnergyContainerOP : core::scoring
• OneToAllNeighborIteratorOP : core::scoring
• OnTheFlyInteractionGraphCOP : core::pack::interaction_graph
• OnTheFlyInteractionGraphOP : core::pack::interaction_graph
• OOP_POST : core::chemical
• OOP_PRE : core::chemical
• OopCreatorMoverCOP : protocols::ncbb::oop
• OopCreatorMoverCreatorCOP : protocols::ncbb::oop
• OopCreatorMoverCreatorOP : protocols::ncbb::oop
• OopCreatorMoverOP : protocols::ncbb::oop
• OopDockDesignProtocolCOP : protocols::ncbb::oop
• OopDockDesignProtocolCreatorCOP : protocols::ncbb::oop
• OopDockDesignProtocolCreatorOP : protocols::ncbb::oop
• OopDockDesignProtocolOP : protocols::ncbb::oop
• OopDPuckMinusMoverCOP : protocols::simple_moves::oop
• OopDPuckMinusMoverOP : protocols::simple_moves::oop
• OopDPuckPlusMoverCOP : protocols::simple_moves::oop
• OopDPuckPlusMoverOP : protocols::simple_moves::oop
• OopMoverCOP : protocols::simple_moves::oop
• OopMoverOP : protocols::simple_moves::oop
• OopPatcherCOP : protocols::simple_moves::oop
• OopPatcherOP : protocols::simple_moves::oop
• OopPuckMinusMoverCOP : protocols::simple_moves::oop
• OopPuckMinusMoverOP : protocols::simple_moves::oop
• OopPuckPlusMoverCOP : protocols::simple_moves::oop
• OopPuckPlusMoverOP : protocols::simple_moves::oop
• OopRandomPuckMoverCOP : protocols::simple_moves::oop
• OopRandomPuckMoverOP : protocols::simple_moves::oop
• OopRandomSmallMoverCOP : protocols::simple_moves::oop
• OopRandomSmallMoverOP : protocols::simple_moves::oop
• open_stream() : protocols::noesy_assign
• OperateOnCertainResiduesCOP : core::pack::task::operation
• OperateOnCertainResiduesCreator_registrator : core::init
• OperateOnCertainResiduesOP : core::pack::task::operation
• OperateOnResidueSubsetCOP : core::pack::task::operation
• OperateOnResidueSubsetCreator_registrator : core::init
• OperateOnResidueSubsetOP : core::pack::task::operation
• Operation : protocols::simple_filters
• operator!=() : core::chemical , core::conformation::symmetry , core::kinematics , core::pose::full_model_info , core::scoring::hbonds , core::scoring::methods , protocols::jd2
• operator&() : protocols::loop_modeling
• operator*() : core::kinematics
• operator++() : core::chemical , core::scoring::carbohydrates
• operator<() : core::chemical , core::kinematics , core::pose::rna , core::scoring::etable , core::sequence
• 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::indexed_structure_store , core::io , core::io::pdb , core::kinematics , core::optimization , core::pack::interaction_graph , core::pack::rotamer_set , core::pack::task , core::pose::full_model_info , core::pose , core::pose::rna , core::scoring::constraints , core::scoring::dssp , core::scoring::elec , 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::abinitio , protocols::antibody , protocols::canonical_sampling , protocols::carbohydrates , protocols::denovo_design::components , protocols::denovo_design::connection , protocols::denovo_design::task_operations , protocols::dna , protocols::docking , protocols::environment::claims , protocols::farna::movers , protocols::farna , protocols::features::helixAssembly , protocols::fldsgn::topology , protocols::frag_picker , protocols::frags , protocols::genetic_algorithm , protocols::hotspot_hashing , protocols::jd2::archive , protocols::jd2 , protocols::jd3 , protocols::jumping , protocols::ligand_docking::ligand_options , protocols::loops::loop_closure::ccd , protocols::loops::loop_mover::perturb , protocols::loops::loop_mover::refine , protocols::loops , protocols::match::output , protocols::motifs , protocols::moves , protocols::noesy_assign , protocols::optimize_weights , protocols::pmut_scan , protocols::rigid , 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 , 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==() : boost::tuples , core::chemical , core::conformation::symmetry , core::kinematics , core::pose::full_model_info , core::pose::rna , core::scoring::etable , core::scoring::hbonds , core::scoring::methods , core::scoring , core::scoring::rna , protocols::jd2 , protocols::make_rot_lib , protocols::stepwise::monte_carlo::mover
• 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
• OperatorCOP : protocols::simple_filters
• OperatorOP : protocols::simple_filters
• operator|() : protocols::loop_modeling , protocols::moves
• oprod() : protocols::toolbox
• OptCysHGAP : core::pack::task::operation
• OptCysHGCAP : core::pack::task::operation
• OptCysHGCOP : core::pack::task::operation
• OptCysHGCreator_registrator : core::init
• OptCysHGOP : core::pack::task::operation
• OptEDataOP : protocols::optimize_weights
• OptEMultifuncAP : protocols::optimize_weights
• OptEMultifuncCAP : protocols::optimize_weights
• OptEMultifuncCOP : protocols::optimize_weights
• OptEMultifuncMPIMessages : protocols::optimize_weights
• OptEMultifuncOP : protocols::optimize_weights
• OptEPositionDataOP : protocols::optimize_weights
• OptEPositionDataOPs : protocols::optimize_weights
• OptEPositionDataType : protocols::optimize_weights
• OptEVariableExpressionCOP : protocols::optimize_weights
• OptEVariableExpressionOP : protocols::optimize_weights
• OptHAP : core::pack::task::operation
• OptHCAP : core::pack::task::operation
• OptHCOP : core::pack::task::operation
• OptHCreator_registrator : core::init
• OptHOP : core::pack::task::operation
• 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
• OptimizeMembranePositionMoverCOP : protocols::membrane
• OptimizeMembranePositionMoverOP : protocols::membrane
• OptimizeProteinEmbeddingMoverCOP : protocols::membrane
• OptimizeProteinEmbeddingMoverOP : protocols::membrane
• option_vdw_rep_screen_info_user() : protocols::stepwise::modeler::rna::checker
• options_registered_ : protocols::evaluation
• OR : protocols::filters , protocols::toolbox::task_operations
• orbital_type_enum : core::chemical::orbitals
• OrbitalBond : core::chemical
• OrbitalBondOrder : core::chemical
• OrbitalCOP : core::chemical
• OrbitalCOPs : core::chemical
• OrbitalIndices : core::chemical
• OrbitalOP : core::chemical
• OrbitalOPs : core::chemical
• orbitals_hpol_bb : core::scoring
• OrbitalsFeaturesCOP : protocols::features
• OrbitalsFeaturesOP : protocols::features
• OrbitalsLookupCOP : core::scoring::orbitals
• OrbitalsLookupOP : core::scoring::orbitals
• OrbitalsScoreCreator_registrator : core::init
• OrbitalsScoreOP : core::scoring::orbitals
• OrbitalTypeSetAP : core::chemical::orbitals
• OrbitalTypeSetCAP : core::chemical::orbitals
• OrbitalTypeSetCOP : core::chemical::orbitals
• OrbitalTypeSetOP : core::chemical::orbitals
• order() : protocols::forge::methods
• ORDERED_SEQUENTIAL : core::conformation::symmetry
• OrderedFragSetCOP : core::fragment
• OrderedFragSetOP : core::fragment
• OrderedSequentialSymmetrySliderCOP : protocols::simple_moves::symmetry
• OrderedSequentialSymmetrySliderOP : protocols::simple_moves::symmetry
• orient_residue_for_ideal_bond() : core::conformation
• original_pose_residue_is_in_residue_map() : protocols::generalized_kinematic_closure
• OriginalBackboneBuildPointCOP : protocols::match::upstream
• OriginalBackboneBuildPointOP : protocols::match::upstream
• ORIGX1 : core::io::pdb
• ORIGX2 : core::io::pdb
• ORIGX3 : core::io::pdb
• ORNOT : protocols::filters , protocols::toolbox::task_operations
• OrResidueSelectorCOP : core::select::residue_selector
• OrResidueSelectorOP : core::select::residue_selector
• ORTHORHOMBIC : protocols::cryst
• Os : core::chemical::element
• oshi : core::scoring::rna::chemical_shift
• OTFFlexbbInteractionGraphCOP : protocols::flexpack::interaction_graph
• OTFFlexbbInteractionGraphOP : protocols::flexpack::interaction_graph
• other_pose : core::scoring
• OtherContextScoreFunctionCOP : protocols::flexpack
• OtherContextScoreFunctionOP : protocols::flexpack
• OtherPoseEnergyCOP : core::scoring::methods
• OtherPoseEnergyCreator_registrator : core::init
• OtherPoseEnergyOP : core::scoring::methods
• OutEdgeIter : core::chemical
• OutEdgeIterPair : core::chemical
• output_bool_list() : protocols::stepwise::legacy::modeler::rna
• output_boolean() : core::pose::rna , protocols::stepwise::modeler
• output_copy_dofs() : protocols::stepwise::modeler::rna
• output_data() : protocols::stepwise::modeler::rna
• output_error_message() : protocols::scoring::methods::pcs2
• output_fold_tree_info() : protocols::stepwise::legacy::modeler::rna
• output_interaction_graph_memory_usage : core::graph
• output_intermediate_pose() : protocols::jd2
• output_is_prepend_map() : protocols::stepwise::legacy::modeler::rna
• output_movemap() : protocols::stepwise::modeler
• 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_residue_struct() : protocols::stepwise::modeler::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_title_text() : protocols::stepwise::modeler::rna
• output_to_silent_file() : protocols::stepwise::monte_carlo
• OutputLevel : protocols::rotamer_recovery
• OutputWriterCOP : protocols::match::output
• OutputWriterOP : protocols::match::output
• overlap() : core::scoring::packstat
• overlap_chainbreak : core::scoring , protocols::forge::methods
• OXETOSE : core::chemical
• OXIROSE : core::chemical
• OXY : protocols::match