- o -

• o1_ : core::scoring::func::CircularSigmoidalFunc
• o2_ : core::scoring::func::CircularSigmoidalFunc
• o2h_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• o2h_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• o2p_index_within_special_backbone_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• o2prime_index_ : core::chemical::rna::RNA_ResidueType
• o2prime_index_within_special_backbone_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• o3prime_c3prime_c2prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• o3prime_c3prime_c2prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• o3prime_index_ : core::chemical::rna::RNA_ResidueType
• o4prime_c1prime_bond_length_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_bond_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_bond_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_c2prime_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_dist_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_first_base_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_first_base_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_n1_9_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_n1_9_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_c1prime_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• o4prime_index_ : core::chemical::rna::RNA_ResidueType
• o5prime_index_ : core::chemical::rna::RNA_ResidueType
• O_ : core::scoring::BB_Pos
• O_index_ : core::scoring::BB_Pos
• obey_ENDMDL_ : core::io::pdb::PDB_DReaderOptions
• observed_sufficient_hpatch_E_to_predict_min_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• observed_sufficient_surface_E_to_predict_min_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• observer_cache_ : core::pose::Pose
• obsolete_ : core::pose::PDBInfo
• occ : core::scoring::packstat::SimplePDB_Atom
• occ_hbond_sol_database_ : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::ScoringManager
• occ_radius_scaling_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occluded_sites_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occupancy : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord
• occurrence_data_ : core::sequence::SequenceProfile
• offset_ : core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::KarplusFunc , core::scoring::PeptideBondedEnergyContainer
• offsets_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• ofrac : core::scoring::APBSConfig
• omega_ : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::scoring::ScoringManager
• omega_mu_ : core::scoring::Rama2BOffset
• omega_mus_all_ : core::scoring::OmegaTether
• omega_mus_all_splines_ : core::scoring::OmegaTether
• omega_sig_ : core::scoring::Rama2BOffset
• omega_sigmas_all_ : core::scoring::OmegaTether
• omega_sigmas_all_splines_ : core::scoring::OmegaTether
• one_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode
• one_letter_sequence_ : core::sequence::AnnotatedSequence
• onebody_energies_ : core::scoring::Energies
• onebody_enmeths_ : core::scoring::MinimizationNode
• op1_atom_index_ : core::chemical::rna::RNA_ResidueType
• op2_atom_index_ : core::chemical::rna::RNA_ResidueType
• op_ : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset
• operate_on_ex1_ : core::pack::task::ResidueLevelTask_
• operate_on_ex2_ : core::pack::task::ResidueLevelTask_
• operate_on_ex3_ : core::pack::task::ResidueLevelTask_
• operate_on_ex4_ : core::pack::task::ResidueLevelTask_
• operating_on_pos1_ : core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• operations_ : core::chemical::PatchCase , core::pack::task::TaskFactory
• optimize_H_ : core::pack::task::PackerTask_
• optimize_H_mode_ : core::pack::task::ResidueLevelTask_
• options_ : core::optimization::Minimizer , core::optimization::NelderMeadSimplex , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::HBondSet
• options_registered_ : core::scoring::FACTSPotential
• orbital_e_neg_pos_ : core::chemical::gasteiger::GasteigerAtomTypeData
• orbital_name_ : core::chemical::orbitals::OrbitalType
• orbital_set_tag_ : core::chemical::ResidueLoaderOptions
• orbital_type_2_enum_ : core::chemical::orbitals::OrbitalTypeMapper , core::scoring::orbitals::OrbitalsStatistics
• orbital_type_enum_ : core::chemical::orbitals::OrbitalType
• orbital_type_index_ : core::chemical::Orbital , core::chemical::orbitals::OrbitalTypeSet
• orbital_type_name_ : core::chemical::orbitals::OrbitalType
• orbital_type_sets_ : core::chemical::ChemicalManager
• orbital_types_ : core::chemical::ResidueType , core::chemical::ResidueTypeSet
• orbitals_ : core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueType , core::conformation::Residue
• orbitals_index_ : core::chemical::ResidueType
• orbitals_lookup_table_ : core::scoring::ScoringManager
• Orbtype_ : core::chemical::orbitals::AssignOrbitals
• order_ : core::chemical::Bond , core::fragment::picking_old::vall::VallResidue
• order_by_energy_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• ordered_atoms_ : core::chemical::ResidueType
• orientation : core::scoring::rna::Base_pair , core::scoring::rna::Base_stack
• orientation_ : core::scoring::dssp::Pairing
• orientation_dep_rna_ch_o_bonds_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• orientation_vectors_ : core::scoring::methods::LK_hack
• orig : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• origin : core::scoring::electron_density::ElectronDensity
• original_residue_type_ : core::pack::task::ResidueLevelTask_
• original_rotamer_id_ : core::pack::scmin::SidechainStateAssignment
• other_distances_ : core::scoring::func::GaussianChainFunc
• other_pose_list_ : core::pose::full_model_info::FullModelInfo
• outer_ : core::fragment::OrderedFragSetIterator_
• outer_end_ : core::fragment::OrderedFragSetIterator_
• outeriterations_ : core::pack::annealer::SimAnnealerBase
• outeriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• outlier : core::pose::rna::RNA_SuiteName
• outnml : core::scoring::sc::_DOT
• output_subunit_ : core::conformation::symmetry::SymmData
• OUTWARDS : core::scoring::dssp::Pairing
• ownbuf_ : core::io::serialization::BUFFER
• owner_ : core::graph::Edge , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::graph::Node , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::Energies