- o -

• O() : core::scoring::BB_Pos
• o2prime_index() : core::chemical::rna::RNA_ResidueType
• o3prime_atom_index() : core::chemical::rna::RNA_ResidueType
• o4prime_atom_index() : core::chemical::rna::RNA_ResidueType
• o5prime_atom_index() : core::chemical::rna::RNA_ResidueType
• obey_ENDMDL() : core::io::pdb::PDB_DReaderOptions
• observer_cache() : core::pose::Pose
• ObserverCache() : core::pose::datacache::ObserverCache
• Obsolet_NamedAtomPairConstraint() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• obsolete() : core::pose::PDBInfo
• 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::pose::PDBInfo
• occurrence_data() : core::sequence::SequenceProfile
• Octree2D() : core::scoring::packstat::Octree2D
• OffsetPeriodicBoundFunc() : core::scoring::constraints::OffsetPeriodicBoundFunc
• 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
• OmegaTether() : core::scoring::OmegaTether
• OmegaTetherEnergy() : core::scoring::methods::OmegaTetherEnergy
• 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_body_energy() : core::pack::interaction_graph::SimpleNode
• one_letter() : core::sequence::AnnotatedSequence
• one_letter_sequence() : core::io::silent::SilentStruct , core::sequence::AnnotatedSequence
• onebody_energies() : core::scoring::Energies
• OneBodyEnergy() : core::scoring::methods::OneBodyEnergy
• OneGaussianScattering() : core::scoring::electron_density::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
• op2_atom_index() : core::chemical::rna::RNA_ResidueType
• operate_on_ex1() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• operate_on_ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• OperateOnCertainResidues() : core::pack::task::operation::OperateOnCertainResidues
• OperateOnResidueSubset() : core::pack::task::operation::OperateOnResidueSubset
• operator!=() : 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::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::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots , 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::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• operator()() : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::ElectronConfiguration , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::PolarHydrogenFilter , core::chemical::RealFilter , core::conformation::DefaultCubeHash , core::conformation::ExactResidueMatcher , core::conformation::ResidueMatcher , core::conformation::WatsonCrickResidueMatcher , core::environment::LengthChecker , core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext > , 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::import_pose::atom_tree_diffs::ScoreLessThanComparator , 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::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , 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::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::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::sdf::BondData , core::environment::LocalPosition , core::fragment::FragID , core::fragment::picking_old::concepts::Bookmark< PageConstIterator > , core::fragment::picking_old::vall::scores::VallFragmentScore , core::pose::PDBPoseMap::ResidueKey , 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::packstat::CavityBall , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , core::sequence::Sequence
• operator<<() : core::coarse::Rule::BeadAdder
• operator<=() : core::scoring::sc::Atom
• operator=() : core::chemical::Atom , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::orbitals::OrbitalTypeMapper , core::chemical::ResConnID , core::chemical::ResidueTypeSet , core::chemical::RingConformerSet , core::coarse::Translator , core::conformation::Conformation , 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::conformation::symmetry::VirtualCoordinates , 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::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::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::sdf::BondData , core::coarse::Translator::BeadAtom , core::conformation::PseudoBond , core::environment::LocalPosition , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::SequenceMapping , 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::pack::task::operation::ResiduePDBIndexIs::ChainPos , 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::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::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::sc::Atom , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::vdwaals::VDWAtom , 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::coarse::RuleSet , 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::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
• OptCysHG() : core::pack::task::operation::OptCysHG
• OptH() : core::pack::task::operation::OptH
• optimize_h() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• optimizeSolventMask() : core::scoring::cryst::PhenixInterface
• optimizeSolvParams() : core::scoring::cryst::PhenixInterface
• optimizeSolvParamsAndMask() : core::scoring::cryst::PhenixInterface
• options_type() : core::chemical::ResidueLoaderOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator , core::import_pose::ImportPoseOptionsCreator , core::io::silent::SilentFileOptionsCreator , core::membrane::io::EmbedDefOptionsCreator , core::membrane::io::EmbedSearchParamsOptionsCreator , core::membrane::io::LipoFileOptionsCreator , core::membrane::io::SpanFileOptionsCreator , core::scoring::electron_density::ElectronDensityOptionsCreator
• 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_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_set_tag() : core::chemical::ResidueLoaderOptions
• orbital_type() : core::chemical::ResidueType , core::conformation::Residue
• orbital_type_index() : core::chemical::Orbital , core::chemical::orbitals::OrbitalTypeSet , core::conformation::Residue
• orbital_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueTypeSet
• orbital_xyz() : core::conformation::Residue
• 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
• OrbitalXYZCoords() : core::conformation::orbitals::OrbitalXYZCoords
• OrbOrbDist_cosAOD_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbOrbDist_cosDOA_energy() : core::scoring::orbitals::OrbitalsLookup
• order() : core::chemical::Bond
• order_atoms() : core::chemical::ResidueType
• order_by_energy() : core::io::silent::SilentFileData
• order_vector() : core::fragment::picking_old::vall::VallResidue
• OrderedFragSet() : core::fragment::OrderedFragSet
• OrderedFragSetIterator_() : core::fragment::OrderedFragSetIterator_
• orient_onto_residue() : core::conformation::Residue
• orient_rotamer_set_to_symmetric_partner() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• Orientation() : core::scoring::dssp::Pairing
• orig_rotamer_id_for_moltenres() : core::pack::scmin::SidechainStateAssignment
• OrResidueSelector() : core::pack::task::residue_selector::OrResidueSelector
• ortho_check() : core::kinematics::Jump , core::kinematics::RT
• other_atom() : core::id::BondID
• 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
• OtherPoseEnergy() : core::scoring::methods::OtherPoseEnergy
• out_of_bounds() : core::scoring::PoissonBoltzmannPotential
• Output_boolean() : core::scoring::rna::RNA_TorsionPotential
• output_connectivity() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• 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_residue() : core::chemical::sdf::MolWriter
• output_sqc_file() : core::io::sequence_comparation::DesignContrast
• overlap() : core::scoring::packstat::Circle
• overlap_exposed() : core::pack::interaction_graph::InvRotamerDots
• overlaps() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::RotamerDots
• owner() : core::scoring::Energies