Here is a list of all class members with links to the classes they belong to:

- o -

• O() : core::scoring::BB_Pos
• 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_ : core::chemical::rna::RNA_ResidueType
• o2prime_index_within_special_backbone_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• o3prime_atom_index() : core::chemical::rna::RNA_ResidueType
• 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_atom_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_atom_index() : core::chemical::rna::RNA_ResidueType
• o5prime_index_ : core::chemical::rna::RNA_ResidueType
• O_ : core::scoring::BB_Pos
• O_index_ : core::scoring::BB_Pos
• O_p_sp2 : core::scoring::orbitals::OrbitalsStatistics
• O_p_sp3 : core::scoring::orbitals::OrbitalsStatistics
• O_pi_sp2 : core::scoring::orbitals::OrbitalsStatistics
• obey_ENDMDL() : core::io::pdb::PDB_DReaderOptions
• 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
• observer_cache_ : core::pose::Pose
• ObserverCache() : core::pose::datacache::ObserverCache , core::pose::Pose
• ObserverCacheOP : core::pose::Pose
• ObserverOPs : core::pose::datacache::ObserverCache
• Obsolet_NamedAtomPairConstraint() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• obsolete() : core::pose::PDBInfo
• obsolete_ : core::pose::PDBInfo
• occ : core::scoring::packstat::SimplePDB_Atom
• occ_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• 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
• occ_shells_ : core::scoring::rna::data::RNA_DMS_Potential
• occ_values_ : core::scoring::rna::data::RNA_DMS_Potential
• occluded_sites_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• occluded_water_hbond_penalty() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• OccludedHbondSolEnergy() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• OccludedHbondSolEnergy_onebody() : core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• occupancy : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord , core::pose::PDBInfo
• occurrence_data() : core::sequence::SequenceProfile
• occurrence_data_ : core::sequence::SequenceProfile
• Octree2D() : core::scoring::packstat::Octree2D
• offset() : core::io::rna::RDAT
• offset_ : core::io::rna::RDAT , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::KarplusFunc , core::scoring::PeptideBondedEnergyContainer , core::scoring::rna::RNA_SuitePotential
• OffsetPeriodicBoundFunc() : core::scoring::constraints::OffsetPeriodicBoundFunc
• offsets_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• ofrac : core::scoring::APBSConfig
• old_eval_atom_derivative() : core::scoring::disulfides::FullatomDisulfideEnergy
• old_eval_dof_derivative() : core::scoring::methods::OmegaTetherEnergy
• omega() : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose
• 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
• OmegaTether() : core::scoring::OmegaTether
• OmegaTetherEnergy() : core::scoring::methods::OmegaTetherEnergy
• omg() : core::scoring::motif::Xfres
• omg_ : core::scoring::motif::Xfres
• OMG_BINRANGE : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• on_conf_xyz_change() : core::pose::Pose
• on_connection_change() : core::pose::PDBInfo , core::scoring::constraints::ConstraintSet
• on_identity_change() : core::pose::PDBInfo
• on_length_change() : core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , core::pose::PDBInfo , core::scoring::constraints::ConstraintSet
• on_pose_conf_change() : core::pose::metrics::PoseMetricContainer
• on_pose_destruction_change() : core::pose::metrics::PoseMetricContainer
• on_pose_energy_change() : core::pose::metrics::PoseMetricContainer
• One : core::chemical::gasteiger::GasteigerAtomTypeData
• 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_body_energy() : core::pack::interaction_graph::SimpleNode
• one_letter() : core::sequence::AnnotatedSequence
• one_letter_sequence() : core::io::silent::SilentStruct , core::sequence::AnnotatedSequence
• one_letter_sequence_ : core::sequence::AnnotatedSequence
• onebody_energies() : core::scoring::Energies
• onebody_energies_ : core::scoring::Energies
• onebody_enmeths_ : core::scoring::MinimizationNode
• OneBodyEnergies : core::scoring::MinimizationNode
• OneBodyEnergiesIterator : core::scoring::MinimizationNode
• OneBodyEnergy() : core::scoring::methods::OneBodyEnergy
• OneGaussianScattering() : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering
• OneToAllEnergyContainer() : core::scoring::OneToAllEnergyContainer
• OneToAllNeighborConstIterator() : core::scoring::OneToAllNeighborConstIterator
• OneToAllNeighborIterator() : core::scoring::OneToAllNeighborIterator
• OnTheFlyEdge() : core::pack::interaction_graph::OnTheFlyEdge
• OnTheFlyInteractionGraph() : core::pack::interaction_graph::OnTheFlyInteractionGraph
• OnTheFlyNode() : core::pack::interaction_graph::OnTheFlyNode
• op() : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset
• op1_atom_index() : core::chemical::rna::RNA_ResidueType
• op1_atom_index_ : core::chemical::rna::RNA_ResidueType
• op2_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 , core::pack::task::ResidueLevelTask_
• operate_on_ex1_ : core::pack::task::ResidueLevelTask_
• operate_on_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex2_ : core::pack::task::ResidueLevelTask_
• operate_on_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex3_ : core::pack::task::ResidueLevelTask_
• operate_on_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex4_ : core::pack::task::ResidueLevelTask_
• OperateOnCertainResidues() : core::pack::task::operation::OperateOnCertainResidues
• OperateOnResidueSubset() : core::pack::task::operation::OperateOnResidueSubset
• operating_on_pos1_ : core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• OperationList : core::pack::task::TaskFactory
• operations_ : core::chemical::PatchCase , core::pack::task::TaskFactory
• operator!= : core::chemical::ResConnID , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::environment::LocalPosition , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::AtomID , core::id::AtomID_Map< T > , core::id::DOF_ID , core::id::DOF_ID_Map< T > , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedAtomID_Map< T > , core::id::TorsionID , core::id::TorsionID_Range , core::io::pdb::ResidueInformation , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots , core::pose::full_model_info::FullModelParameters , core::scoring::constraints::Constraint , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , 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::EMapVector , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ScoreFunctionInfo
• operator()() : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::CopyEdge< Graph1, Graph2 > , core::chemical::CopyVertex< Graph1, Graph2 > , core::chemical::ElectronConfiguration , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::PolarHydrogenFilter , core::chemical::RealFilter , core::chemical::RerootEdgeSorter , core::conformation::DefaultCubeHash , core::conformation::ExactResidueMatcher , core::conformation::ResidueMatcher , core::conformation::WatsonCrickResidueMatcher , core::environment::LengthChecker , core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::import_pose::atom_tree_diffs::ScoreLessThanComparator , core::io::pdb::GeometricRenameIsomorphismCallback , core::io::pdb::GeometricRenameVerticiesEquivalent , core::optimization::ArmijoLineMinimization , core::optimization::AtomTreeMultifunc , core::optimization::BrentLineMinimization , core::optimization::CartesianMultifunc , core::optimization::ConvergenceTest , core::optimization::DFPMinConvergedAbsolute , core::optimization::DFPMinConvergedFractional , core::optimization::func_1d , core::optimization::LineMinimizationAlgorithm , core::optimization::Multifunc , core::optimization::SingleResidueMultifunc , core::optimization::sort_pred , core::optimization::StrongWolfeLineMinimization , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::rotamer_set::RotamerOperation , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::pack::task::operation::NoResFilter , core::pack::task::operation::ResFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResidueTypeFilter , core::scoring::AtomVDW , core::scoring::DockingScoreFunction , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::ExcludedResPredicate , core::scoring::func::ConformationXYZ , core::scoring::func::FourPointsFunc , core::scoring::func::ResiduePairXYZ , core::scoring::func::ResidueXYZ , core::scoring::func::XYZ_Func , core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::IsProteinCAPredicate , core::scoring::MinScoreScoreFunction , core::scoring::motif::MyHash , core::scoring::motif::MyPred , core::scoring::motif::RMSandEnergyCMP , core::scoring::packstat::Array2D , core::scoring::packstat::HTL_EventX , core::scoring::packstat::OrderCavBallOnR , core::scoring::packstat::OrderCavBallOnRmAnb , core::scoring::packstat::OrderCavBallOnRmE , core::scoring::packstat::OrderCavBallOnX , core::scoring::packstat::OrderCBC , core::scoring::packstat::OrderSphereOnID , core::scoring::packstat::OrderSphereOnX , core::scoring::Predicate , core::scoring::ResRangePredicate , core::scoring::saxs::DistanceHistogram , core::scoring::sc::CloserToAtom , core::scoring::ScoreFunction , core::scoring::SelectedResPredicate , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::vdwaals::VDWTrieCountPair1B , core::sequence::DP_Matrix , core::sequence::SequenceAlignmentHasher
• operator*() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::scoring::EMapVector
• operator*=() : core::scoring::EMapVector
• operator+() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_
• operator++() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , 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::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• operator+=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector
• operator--() : core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• operator-=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector
• operator->() : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• operator< : core::chemical::ResConnID , core::chemical::sdf::BondData , core::environment::LocalPosition , core::fragment::FragID , core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::AtomID , core::id::DOF_ID , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::kinematics::Edge , core::optimization::DOF_Node , core::pose::PDBPoseMap::ResidueKey , core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing , core::scoring::elec::ElecAtom , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotif , core::scoring::packstat::CavityBall , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , core::sequence::Sequence , core::sequence::SequenceAlignment
• operator<< : core::chemical::AtomType , core::chemical::Bond , core::chemical::Orbital , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmetryInfo , core::fragment::FragSet , core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::AtomID , core::id::DOF_ID , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::id::TorsionID_Range , core::indexed_structure_store::FragmentSpecification , core::io::pdb::AtomInformation , core::io::pdb::Field , core::io::pdb::FileData , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::RT , core::pack::task::PackerTask , core::pose::CrystInfo , core::pose::full_model_info::FullModelParameters , core::pose::RemarkInfo , core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::Energies , core::scoring::etable::EtableOptions , core::scoring::func::ConstantFunc , core::scoring::func::EtableFunc , core::scoring::func::Func , core::scoring::func::GaussianFunc , core::scoring::func::MixtureFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::Hairpin , core::scoring::Hairpins , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondSet , core::scoring::Helices , core::scoring::loop_graph::Loop , core::scoring::loop_graph::LoopCycle , core::scoring::methods::FreeDOF_Options , core::scoring::mm::MMBondAngleResidueTypeParam , core::scoring::motif::MotifHash , core::scoring::motif::MotifHits , core::scoring::motif::ResPairMotif , core::scoring::motif::ResPairMotifQuery , core::scoring::motif::RPM_FilterStats , core::scoring::motif::XformScore , core::scoring::motif::Xfres , core::scoring::packing::HolesParams , core::scoring::packstat::SimplePDB , core::scoring::packstat::SimplePDB_Atom , core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::Strands , core::scoring::vdwaals::VDWAtom , core::sequence::ChemicalShiftSequence , core::sequence::DP_Matrix , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile
• operator<=() : core::scoring::sc::Atom
• operator=() : core::chemical::Atom , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::orbitals::OrbitalTypeMapper , core::chemical::ResConnID , core::chemical::ResidueProperties , core::chemical::ResidueTypeSet , core::chemical::RingConformerSet , core::conformation::Conformation , core::conformation::membrane::LipidAccInfo , core::conformation::membrane::MembraneInfo , core::conformation::membrane::Span , core::conformation::membrane::SpanningTopology , core::conformation::PseudoBond , core::conformation::Residue , core::conformation::signals::ConnectionEvent , core::conformation::signals::GeneralEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::conformation::signals::XYZEvent , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmetricConformation , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::IndependentBBTorsionSRFD , core::fragment::OrderedFragSetIterator_ , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallResidue , core::graph::Array0< T > , core::graph::Edge , core::graph::EdgeList , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::graph::Graph , core::graph::Node , core::graph::UpperEdgeGraph< V, E > , core::id::SequenceMapping , core::import_pose::PDBSilentStruct , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentStruct , core::io::silent::SilentStructFactory , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::ResidueCoordinateChangeList , core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::Multifunc , core::pack::annealer::MultiCoolAnnealer , core::pack::dunbrack::RotamerLibrary , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FirstClassEdge< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::pack::scmin::SidechainStateAssignment , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::TaskFactory , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , core::pose::metrics::CalculatorFactory , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , core::pose::PDBPoseMap , core::pose::Pose , core::pose::rna::RNA_SuiteName , core::pose::signals::ConformationEvent , core::pose::signals::DestructionEvent , core::pose::signals::EnergyEvent , core::pose::signals::GeneralEvent , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::Constraints , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::ContextGraph , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DipolarCoupling , 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::DockingScoreFunction , core::scoring::EMapVector , core::scoring::Energies , core::scoring::EnergyGraph , core::scoring::etable::EtableOptions , core::scoring::Hairpin , core::scoring::Hairpins , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBondOptions , core::scoring::Helices , core::scoring::loop_graph::Loop , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::LinearChainbreakEnergy , core::scoring::MinimizationGraph , core::scoring::MinScoreScoreFunction , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidualDipolarCoupling , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData , core::scoring::rna::data::RNA_DataInfo , core::scoring::ScoreFunction , core::scoring::ScoreFunctionInfo , core::scoring::SecondaryStructureWeights , core::scoring::solid_surface::SurfaceEnergies , core::scoring::Strands , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , core::sequence::AnnotatedSequence , core::sequence::Cell , core::sequence::ChemicalShiftSequence , core::sequence::CompositeSequence , core::sequence::DerivedSequenceMapping , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceCoupling , core::sequence::SequenceFactory , core::sequence::SequenceProfile , core::util::Line
• operator==() : core::chemical::Atom , core::chemical::ResConnID , core::chemical::sdf::BondData , core::conformation::PseudoBond , core::conformation::symmetry::SymDof , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymSlideInfo , core::conformation::symmetry::VirtualCoordinate , core::environment::LocalPosition , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::AtomID , core::id::AtomID_Map< T > , core::id::BondID , core::id::DOF_ID , core::id::DOF_ID_Map< T > , core::id::DOF_ID_Range , core::id::JumpID , core::id::NamedAtomID , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::id::TorsionID , core::id::TorsionID_Range , core::io::pdb::ResidueInformation , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::EnergyNames , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBDepScoreInterpData< N > , core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::pose::full_model_info::FullModelParameters , core::pose::rna::BasePair , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , 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::dssp::Pairing , core::scoring::dssp::StrandPairing , core::scoring::elec::ElecAtom , core::scoring::EMapVector , core::scoring::etable::EtableOptions , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondSet , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::loop_graph::Loop , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::FreeDOF_Options , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotif , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::sc::Atom , core::scoring::ScoreFunctionInfo , core::scoring::SecondaryStructureWeights , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , core::sequence::Sequence , core::sequence::SequenceAlignment
• operator>> : core::conformation::symmetry::SymmetryInfo , core::id::NamedAtomID , core::id::NamedStubID , core::kinematics::Edge , core::kinematics::FoldTree , core::kinematics::Jump , core::kinematics::RT , core::pose::full_model_info::FullModelParameters , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::packstat::SimplePDB , core::scoring::packstat::SimplePDB_Atom , core::sequence::Sequence , core::sequence::SequenceAlignment
• operator[]() : core::chemical::AtomTypeSet , core::chemical::ElementSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueSelector , core::chemical::ResidueSelectorSingle , core::chemical::Selector_AA , core::chemical::Selector_CMDFLAG , core::chemical::Selector_MATCH_VARIANTS , core::chemical::Selector_NAME1 , core::chemical::Selector_NAME3 , core::chemical::Selector_NO_VARIANTS , core::chemical::Selector_PROPERTY , core::chemical::Selector_UPPER_POSITION , core::chemical::Selector_VARIANT_TYPE , core::conformation::UltraLightResidue , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::graph::Array0< T > , core::graph::ArrayPoolElement< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::io::silent::SilentFileData , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::rotamer_set::RotamerCouplings , core::pack::rotamer_set::WaterPackingInfo , core::scoring::dna::BasePartner , core::scoring::EMapVector , core::scoring::EnergyEdge , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::methods::LKB_ResiduesInfo , core::scoring::ScoreFunction , core::sequence::Sequence
• oprev_cprev_n_h_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• oprev_cprev_n_h_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• OptCysHG() : core::pack::task::operation::OptCysHG
• OptH() : core::pack::task::operation::OptH
• optimize_h() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• optimize_H_ : core::pack::task::PackerTask_
• optimize_H_mode_ : core::pack::task::ResidueLevelTask_
• optimizeSolventMask() : core::scoring::cryst::PhenixInterface
• optimizeSolvParams() : core::scoring::cryst::PhenixInterface
• optimizeSolvParamsAndMask() : core::scoring::cryst::PhenixInterface
• options_ : core::optimization::Minimizer , core::optimization::NelderMeadSimplex , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::HBondSet , core::scoring::methods::FreeDOF_Energy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy
• options_registered_ : core::scoring::FACTSPotential
• options_type() : core::chemical::ResidueLoaderOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator , core::import_pose::ImportPoseOptionsCreator , core::io::silent::SilentFileOptionsCreator , core::scoring::electron_density::ElectronDensityOptionsCreator , core::scoring::fiber_diffraction::FiberDiffractionOptionsCreator
• or_adducts() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_double_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex1aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex2aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex3_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_ex4_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_exdna_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_fix_his_tautomer() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_flip_HNQ() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_include_current() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_include_virtual_side_chain() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_linmem_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_multi_cool_annealer() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_operate_on_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_operate_on_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_optimize_h() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• or_optimize_h_mode() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• or_preserve_c_beta() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• orb_orb_rules() : core::scoring::orbitals::OrbitalsScore
• OrbHdist_cosAOH_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbHdist_cosDHO_energy() : core::scoring::orbitals::OrbitalsLookup
• Orbital() : core::chemical::Orbital
• orbital() : core::chemical::ResidueType
• orbital_e_neg_pos_ : core::chemical::gasteiger::GasteigerAtomTypeData
• orbital_enum() : core::chemical::orbitals::OrbitalType
• orbital_icoor_data() : core::chemical::ResidueType
• orbital_index() : core::chemical::ResidueType
• orbital_name() : core::chemical::orbitals::OrbitalType , core::conformation::Residue
• orbital_name_ : core::chemical::orbitals::OrbitalType
• orbital_set_tag() : core::chemical::ResidueLoaderOptions
• orbital_set_tag_ : core::chemical::ResidueLoaderOptions
• orbital_type() : core::chemical::ResidueType , core::conformation::Residue
• 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 , core::conformation::Residue
• orbital_type_index_ : core::chemical::Orbital , core::chemical::orbitals::OrbitalTypeSet
• orbital_type_name : core::scoring::orbitals::OrbitalsStatistics
• orbital_type_name_ : core::chemical::orbitals::OrbitalType
• orbital_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueTypeSet
• orbital_type_sets_ : core::chemical::ChemicalManager
• orbital_types_ : core::chemical::ResidueType , core::chemical::ResidueTypeSet
• orbital_xyz() : core::conformation::Residue
• orbitals_ : core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueType , core::conformation::Residue
• orbitals_index_ : core::chemical::ResidueType
• orbitals_lookup_table_ : core::scoring::ScoringManager
• OrbitalsLookup() : core::scoring::orbitals::OrbitalsLookup
• OrbitalsScore() : core::scoring::orbitals::OrbitalsScore
• OrbitalsStatistics() : core::scoring::orbitals::OrbitalsStatistics
• OrbitalType() : core::chemical::orbitals::OrbitalType
• OrbitalTypeMapper() : core::chemical::orbitals::OrbitalTypeMapper
• OrbitalTypeSet() : core::chemical::orbitals::OrbitalTypeSet
• OrbitalTypeSets : core::chemical::ChemicalManager
• OrbitalXYZCoords() : core::conformation::orbitals::OrbitalXYZCoords
• OrbOrbDist_cosAOD_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbOrbDist_cosDOA_energy() : core::scoring::orbitals::OrbitalsLookup
• Orbtype_ : core::chemical::orbitals::AssignOrbitals
• order() : core::chemical::Bond
• order_ : core::chemical::Bond , core::fragment::picking_old::vall::VallResidue
• order_atoms() : core::chemical::ResidueType
• order_by_energy() : core::io::silent::SilentFileData
• order_by_energy_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• order_vector() : core::fragment::picking_old::vall::VallResidue
• ordered_atoms_ : core::chemical::ResidueType
• OrderedFragSet() : core::fragment::OrderedFragSet , core::fragment::OrderedFragSetIterator_
• OrderedFragSetIterator_() : core::fragment::OrderedFragSetIterator_
• orient_onto_residue() : core::conformation::Residue
• orient_onto_residue_peptoid() : core::conformation::Residue
• orient_rotamer_set_to_symmetric_partner() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• orientation : core::pose::rna::BasePair , core::pose::rna::BaseStack
• Orientation() : core::scoring::dssp::Pairing
• 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
• orig_rotamer_id_for_moltenres() : core::pack::scmin::SidechainStateAssignment
• origin : core::scoring::electron_density::ElectronDensity
• original_layer_lines_I : core::scoring::fiber_diffraction::FiberDiffraction
• original_layer_lines_R : core::scoring::fiber_diffraction::FiberDiffraction
• original_residue_type_ : core::pack::task::ResidueLevelTask_
• original_rotamer_id_ : core::pack::scmin::SidechainStateAssignment
• OrResidueSelector() : core::pack::task::residue_selector::OrResidueSelector
• ortho_check() : core::kinematics::Jump , core::kinematics::RT
• Other : core::chemical::gasteiger::GasteigerAtomTypeData
• other_atom() : core::id::BondID
• OTHER_DETAILS : core::io::pdb::HeaderInformation
• other_distances_ : core::scoring::func::GaussianChainFunc
• other_neighbor_atom_indices() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• other_neighbor_id() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• other_pose_list() : core::pose::full_model_info::FullModelInfo
• other_pose_list_ : core::pose::full_model_info::FullModelInfo
• other_struct_list() : core::io::silent::SilentStruct
• other_struct_list_ : core::io::silent::SilentStruct
• OtherPoseEnergy() : core::scoring::methods::OtherPoseEnergy
• out_of_bounds() : core::scoring::PoissonBoltzmannPotential
• outer_ : core::fragment::OrderedFragSetIterator_
• outer_end_ : core::fragment::OrderedFragSetIterator_
• outeriterations_ : core::pack::annealer::SimAnnealerBase
• outeriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• OuterIterator : core::fragment::OrderedFragSetIterator_
• outnml : core::scoring::sc::_DOT
• output_connectivity() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• output_data() : core::io::rna::RDAT
• output_dimacs() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• output_etable() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• output_local_prediction() : core::scoring::methods::ProQ_Energy
• output_pdb() : core::scoring::packing::PoseBalls
• output_rdat_header() : core::io::rna::RDAT
• output_rdat_to_file() : core::io::rna::RDAT
• output_residue() : core::chemical::sdf::MolWriter
• output_sqc_file() : core::io::sequence_comparation::DesignContrast
• output_subunit_ : core::conformation::symmetry::SymmData
• OUTWARDS : core::scoring::dssp::Pairing
• overlap() : core::scoring::packstat::Circle
• overlap1() : core::scoring::motif::ResPairMotifQuery
• overlap1_ : core::scoring::motif::ResPairMotifQuery
• overlap2() : core::scoring::motif::ResPairMotifQuery
• overlap2_ : core::scoring::motif::ResPairMotifQuery
• overlap_exposed() : core::pack::interaction_graph::InvRotamerDots
• overlapping_with_region() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet
• overlaps() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::RotamerDots
• ownbuf_ : core::io::serialization::BUFFER
• owner() : core::scoring::Energies
• 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
• oxygen_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential