- o -

• O() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• o1p_atom_index() : core::chemical::rna::RNA_ResidueType
• O2M_MutateMover() : protocols::simple_moves::O2M_MutateMover
• o2p_atom_index() : core::chemical::rna::RNA_ResidueType
• o2star_index() : core::chemical::rna::RNA_ResidueType
• o2star_trials() : protocols::rna::RNA_Minimizer
• o3star_atom_index() : core::chemical::rna::RNA_ResidueType
• o4star_atom_index() : core::chemical::rna::RNA_ResidueType
• o5star_atom_index() : core::chemical::rna::RNA_ResidueType
• O_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• O_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• oatom1_oatom2_distance() : protocols::toolbox::match_enzdes_util::LigandConformer
• oatom1_oatom2_oatom3_angle() : protocols::toolbox::match_enzdes_util::LigandConformer
• oatom2_oatom3_distance() : protocols::toolbox::match_enzdes_util::LigandConformer
• obey_ENDMDL() : core::io::pdb::PDB_DReaderOptions
• objective_function() : protocols::loophash::MPI_LoopHashRefine
• observe_after_metropolis() : protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver
• observer_cache() : core::pose::Pose
• ObserverCache() : core::pose::datacache::ObserverCache
• observers() : protocols::canonical_sampling::MetropolisHastingsMover
• Obsolet_NamedAtomPairConstraint() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• obsolete() : core::pose::PDBInfo
• obtain_new_job() : protocols::jd2::JobDistributor
• obtain_templates_names() : protocols::antibody2::Ab_TemplateInfo
• occ_space() : protocols::match::downstream::DownstreamBuilder
• occ_space_bounding_box() : protocols::match::MatcherTask
• occ_space_hash() : protocols::match::Matcher
• occ_space_set() : protocols::match::downstream::DownstreamBuilder
• occluded_water_hbond_penalty() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• OccludedHbondSolEnergy() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• OccludedHbondSolEnergy_onebody() : core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• occupancy() : core::pose::PDBInfo
• occupied() : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• OccupiedSpaceHash() : protocols::match::OccupiedSpaceHash
• Octree2D() : core::scoring::packstat::Octree2D
• offset() : protocols::inputter::Inputter , protocols::simple_filters::Sigmoid , protocols::topology_broker::SequenceClaim , protocols::topology_broker::SequenceClaimer
• OffsetPeriodicBoundFunc() : core::scoring::constraints::OffsetPeriodicBoundFunc
• old_eval_atom_derivative() : core::scoring::disulfides::FullatomDisulfideEnergy
• old_eval_dof_derivative() : core::scoring::methods::OmegaTetherEnergy
• old_seqpos() : protocols::forge::remodel::ResidueVicinityInfo
• omega() : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::protein_interface_design::movers::BBDofs , protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet
• OmegaTether() : core::scoring::OmegaTether
• OmegaTetherEnergy() : core::scoring::methods::OmegaTetherEnergy
• on_conf_change() : protocols::boinc::BoincCurrentPoseObserver
• on_conf_xyz_change() : core::pose::Pose
• on_connection_change() : core::pose::PDBInfo , core::scoring::constraints::ConstraintSet , protocols::viewer::ConformationViewer
• on_energy_change() : protocols::viewer::SilentObserver
• on_identity_change() : core::pose::PDBInfo
• on_length_change() : core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , core::pose::PDBInfo , core::scoring::constraints::ConstraintSet , protocols::forge::build::BuildInstruction , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• on_new_fragments() : protocols::simple_moves::FragmentMover , protocols::simple_moves::ClassicFragmentMover
• on_pose_conf_change() : core::pose::metrics::PoseMetricContainer
• on_pose_destruction_change() : core::pose::metrics::PoseMetricContainer
• on_pose_energy_change() : core::pose::metrics::PoseMetricContainer
• on_residue_append() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• on_residue_delete() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• on_residue_prepend() : protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert
• on_xyz_change() : protocols::viewer::ConformationViewer
• one_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• one_body_energy() : core::pack::interaction_graph::SimpleNode
• one_letter() : core::sequence::AnnotatedSequence
• one_letter_sequence() : core::io::silent::SilentStruct , core::sequence::AnnotatedSequence
• one_random_loop() : protocols::loops::Loops
• onebody_energies() : core::scoring::Energies , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• OneBodyEnergy() : core::scoring::methods::OneBodyEnergy
• OneGaussianScattering() : core::scoring::electron_density::OneGaussianScattering
• OneToAllEnergyContainer() : core::scoring::OneToAllEnergyContainer
• OneToAllNeighborConstIterator() : core::scoring::OneToAllNeighborConstIterator
• OneToAllNeighborIterator() : core::scoring::OneToAllNeighborIterator
• only_enumerate_non_match_redundant_ligand_rotamers() : protocols::match::MatcherTask
• OnTheFlyEdge() : core::pack::interaction_graph::OnTheFlyEdge
• OnTheFlyInteractionGraph() : core::pack::interaction_graph::OnTheFlyInteractionGraph
• OnTheFlyNode() : core::pack::interaction_graph::OnTheFlyNode
• OopDPuckMinusMover() : protocols::simple_moves::oop::OopDPuckMinusMover
• OopDPuckPlusMover() : protocols::simple_moves::oop::OopDPuckPlusMover
• OopMover() : protocols::simple_moves::oop::OopMover
• OopPatcher() : protocols::simple_moves::oop::OopPatcher
• OopPuckMinusMover() : protocols::simple_moves::oop::OopPuckMinusMover
• OopPuckPlusMover() : protocols::simple_moves::oop::OopPuckPlusMover
• OopRandomPuckMover() : protocols::simple_moves::oop::OopRandomPuckMover
• OopRandomSmallMover() : protocols::simple_moves::oop::OopRandomSmallMover
• op() : core::pack::task::operation::OperateOnCertainResidues
• OP_const_iterator() : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• open_channel() : protocols::jd2::MpiFileBuffer
• opening() : protocols::dna::DNABasepair
• 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
• operation() : protocols::simple_filters::Operator
• Operator() : protocols::simple_filters::Operator
• operator!=() : core::conformation::symmetry::SymmetryInfo , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::io::pdb::ResidueInformation , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots , core::scoring::constraints::Constraint , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::EMapVector , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , protocols::abinitio::PairingStatEntry , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator()() : core::optimization::Multifunc , core::optimization::SingleResidueMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::rotamer_set::RotamerOperation , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pack::task::operation::ResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AllResFilter , core::pack::task::operation::NoResFilter , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::scoring::AtomVDW , core::scoring::constraints::FourPointsFunc , core::scoring::constraints::XYZ_Func , core::scoring::constraints::ResidueXYZ , core::scoring::constraints::ResiduePairXYZ , core::scoring::constraints::ConformationXYZ , 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::geometric_solvation::DatabaseOccSolEne , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::MinScoreScoreFunction , core::scoring::packstat::OrderSphereOnX , core::scoring::packstat::OrderSphereOnID , core::scoring::packstat::OrderCavBallOnX , core::scoring::packstat::OrderCavBallOnRmE , core::scoring::packstat::OrderCavBallOnR , core::scoring::packstat::OrderCavBallOnRmAnb , core::scoring::packstat::OrderCBC , core::scoring::packstat::HTL_EventX , core::scoring::packstat::Array2D , core::scoring::Predicate , core::scoring::IsProteinCAPredicate , core::scoring::ResRangePredicate , core::scoring::SelectedResPredicate , core::scoring::ExcludedResPredicate , core::scoring::saxs::DistanceHistogram , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction , core::sequence::DP_Matrix , core::sequence::SequenceAlignmentHasher , protocols::abinitio::AllResiduesChanged , protocols::abinitio::hConvergenceCheck , protocols::abinitio::AllResiduesChanged , protocols::abinitio::_MergableEntries , protocols::abinitio::_HashEntry , protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck , protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::dna::ResTypeSequence_lt , protocols::dna::PDBOutput , protocols::dna::RotamerDNAHBondFilter , protocols::features::DatabaseFilter , protocols::features::TopCountOfEachInput , protocols::features::TopCountOfAllInputs , protocols::features::TopPercentOfEachInput , protocols::features::TopPercentOfAllInputs , protocols::forge::build::RelativeSequencePosition , protocols::forge::build::CountFromLeft , protocols::frag_picker::CompareQueryPosition , protocols::frag_picker::CompareTotalScore , protocols::frag_picker::CompareByScoreCombination , protocols::frag_picker::CompareScoreComponent , protocols::frag_picker::FragmentComparatorBase , protocols::frag_picker::quota::quota_limits_sorter_biggest_first , protocols::frag_picker::quota::quota_limits_sorter_smallest_first , protocols::frag_picker::quota::missing_fraction_sorter_biggest_first , protocols::genetic_algorithm::Vec1Hash , protocols::genetic_algorithm::EntityElementsEqual , protocols::hybridization::AllResiduesChanged , protocols::hybridization::hConvergenceCheck , protocols::jd2::archive::SortPredicate , protocols::jd2::CompareTags , protocols::loophash::LoopHashMap::by_index , protocols::loops::RationalLoopComparator , protocols::loops::Loop_lt , protocols::match::downstream::hash_upstream_hit , protocols::match::downstream::us_secmatch_hit_compare , protocols::match::match_lite_equals , protocols::match::match_lite_hasher , protocols::moves::mc_convergence_checks::ConvergenceCheck , protocols::moves::MonteCarloExceptionConverge , protocols::moves::PoseCondition , protocols::noesy_assign::FoldResonance , protocols::noesy_assign::PeakCalibrator , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMin , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMinBy , protocols::pack_daemon::PowExpression , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::EntityHistoryLT , protocols::pockets::FingerprintMultifunc , protocols::qsar::qsarOptFunc , protocols::rbsegment_relax::RB_lt , protocols::sasa_scores::Poly , protocols::sasa_scores::PPoly , protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , protocols::swa::rna::compare_base_bin , protocols::swa::rna::compare_int_pair , protocols::swa::rna::compare_test , protocols::toolbox::SF_Replica , protocols::toolbox::task_operations::ProteinCore , protocols::wum::sort_SilentStructOPs , protocols::wum::find_SilentStructOPs , core::conformation::DefaultCubeHash , core::conformation::ResidueMatcher , core::conformation::WatsonCrickResidueMatcher , core::conformation::ExactResidueMatcher , 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::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::func_1d , core::optimization::LineMinimizationAlgorithm , core::optimization::BrentLineMinimization , core::optimization::ArmijoLineMinimization , core::optimization::StrongWolfeLineMinimization , core::optimization::ConvergenceTest , core::optimization::DFPMinConvergedFractional , core::optimization::DFPMinConvergedAbsolute
• operator*() : core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::scoring::EMapVector , protocols::sic_dock::Rose , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator*=() : core::scoring::EMapVector
• operator+() : core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , protocols::sic_dock::Rose
• operator++() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , protocols::match::VoxelSetIterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator+=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector , protocols::match::MatcherOutputStats
• operator-() : protocols::sic_dock::Rose
• operator--() : core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator-=() : core::pack::interaction_graph::DotSphere , core::scoring::EMapVector
• operator->() : core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• operator<() : core::chemical::sdf::BondData , 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::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::hackelec::ElecAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::packstat::CavityBall , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::sequence::Sequence , protocols::dna::Reversion , protocols::forge::build::Interval , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::Entity , protocols::hotspot_hashing::HotspotStub , protocols::ligand_docking::Ligand_info , protocols::loops::Loop , protocols::match::upstream_hit , protocols::match::downstream_hit , protocols::multistate_design::PosType
• operator<<() : core::coarse::Rule::BeadAdder , protocols::evaluation::MetaPoseEvaluator
• operator<=() : core::scoring::sc::Atom
• operator=() : 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::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::EdgeListIterator , core::graph::EdgeListConstIterator , core::graph::EdgeList , core::graph::Node , core::graph::Edge , core::graph::Graph , core::graph::UpperEdgeGraph< V, E > , core::id::SequenceMapping , core::import_pose::PDBSilentStruct , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_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::FirstClassNode< V, E, G > , core::pack::interaction_graph::FirstClassEdge< V, E, G > , protocols::viewer::SilentObserver , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , protocols::swa::protein::MainChainTorsionSet , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERNode , protocols::simple_moves::DOFHistogramRecorder , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase , protocols::scoring::methods::pcs2::PcsDataCenterManager , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , protocols::scoring::methods::pcs::PCS_tensor , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots , protocols::scoring::InterchainPotential , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::SurfaceNode< V, E, G > , protocols::qsar::scoring_grid::GridManager , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< 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::ResidueAtomTreeCollectionMomento , core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::SidechainStateAssignment , protocols::motifs::MotifSearch , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , protocols::match::Matcher , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::TaskFactory , protocols::loops::GuardedLoopsFromFile , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , core::pose::datacache::CacheableObserver , core::pose::datacache::ObserverCache , core::pose::metrics::CalculatorFactory , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , core::pose::PDBPoseMap , core::pose::Pose , core::pose::signals::ConformationEvent , protocols::jd2::JobOutputterFactory , core::pose::signals::DestructionEvent , core::pose::signals::EnergyEvent , core::pose::signals::GeneralEvent , protocols::genetic_algorithm::Entity , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::Constraints , core::scoring::ContextGraph , protocols::forge::build::SegmentSwap , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DipolarCoupling , protocols::forge::build::Interval , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , protocols::forge::build::BuildManager , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::DockingScoreFunction , core::scoring::Energies , core::scoring::EnergyGraph , core::scoring::EMapVector , protocols::filters::FilterFactory , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBondOptions , core::scoring::ResidueNeighborIterator , protocols::docking::DockSetupMover , core::scoring::ResidueNeighborConstIterator , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::LinearChainbreakEnergy , protocols::canonical_sampling::TrajectoryRecorder , core::scoring::ResSingleMinimizationData , core::scoring::ResPairMinimizationData , core::scoring::MinimizationGraph , core::scoring::MinScoreScoreFunction , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , protocols::antibody2::SnugDock , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::ResidualDipolarCoupling , core::scoring::rna::Gaussian_parameter , protocols::anchored_design::Anchor , core::scoring::rna::RNA_DataInfo , core::scoring::ScoreFunction , core::scoring::ScoreFunctionInfo , core::sequence::SequenceProfile , core::scoring::SecondaryStructureWeights , core::scoring::solid_surface::SurfaceEnergies , core::scoring::Strands , core::scoring::Helices , core::scoring::Hairpin , core::scoring::Hairpins , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , core::sequence::AnnotatedSequence , core::sequence::ChemicalShiftSequence , core::sequence::CompositeSequence , core::sequence::DerivedSequenceMapping , core::sequence::Cell , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceCoupling , core::sequence::SequenceFactory , core::util::Line , protocols::abinitio::ClassicAbinitio , protocols::analysis::LoopAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::SnugDockProtocol , protocols::boinc::BoincCurrentPoseObserver , protocols::branch_angle::BranchAngleOptimizer , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::comparative_modeling::LoopRelaxMover , protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::floppy_tail::FloppyTailMover , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::WorkingRemodelSet , protocols::frag_picker::VallResidue , protocols::genetic_algorithm::EntityElement , protocols::hotspot_hashing::HotspotStub , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputter , protocols::jd2::parser::DataLoaderFactory , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::LoopMoverFactory , protocols::loops::Loops , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::DownstreamAlgorithm , protocols::match::MatcherTask , protocols::match::upstream::BuildSet , protocols::motifs::LigandMotifSearch , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::multistate_design::PosType , protocols::noesy_assign::ResonanceList , protocols::nonlocal::Chunk , protocols::pack_daemon::EntityCorrespondence , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::VLB , protocols::qsar::scoring_grid::GridFactory , protocols::rna::TorsionSet , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIteratorCA , protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::scoring::methods::pcs2::PcsInputCenter , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs2::PcsTensor , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::MinimalRotamer , protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet , protocols::toolbox::AllowInsert , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP > , protocols::toolbox::pose_metric_calculators::MetricValueGetter , protocols::toolbox::DummyClass , protocols::toolbox::SF_Replica , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::topology_broker::TopologyBroker , protocols::viewer::ConformationViewer , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::orbitals::OrbitalTypeMapper , core::chemical::ResConnID , core::chemical::ResidueTypeSet , 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
• operator==() : core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::constraints::ResidueTypeConstraint , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::constraints::Constraint , core::io::silent::EnergyNames , core::scoring::constraints::AmbiguousConstraint , core::fragment::FrameIteratorWorker_ , core::conformation::symmetry::SymmetryInfo , core::chemical::sdf::BondData , core::coarse::Translator::BeadAtom , core::conformation::PseudoBond , core::fragment::FragID , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::graph::EdgeListIterator , core::graph::EdgeListConstIterator , core::id::SequenceMapping , core::io::pdb::ResidueInformation , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing , 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::hackelec::ElecAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::sc::Atom , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::sequence::Sequence , protocols::abinitio::PairingStatEntry , protocols::fldsgn::topology::HSSTriplet , protocols::forge::build::Interval , protocols::genetic_algorithm::Entity , protocols::jumping::DisulfPairing , protocols::ligand_docking::MinimizeLigand , protocols::loophash::BackboneSegment , protocols::loops::Loop , protocols::loops::Loops , protocols::match::upstream_hit , protocols::match::downstream_hit , protocols::multistate_design::PosType , protocols::noesy_assign::CrossPeakInfo , protocols::pmut_scan::MutationData , protocols::pmut_scan::Mutant , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP > , protocols::noesy_assign::PeakAssignment , protocols::ligand_docking::ResidueTorsionRestraints , protocols::genetic_algorithm::EntityElement , core::sequence::SequenceAlignment
• operator[]() : core::pack::rotamer_set::WaterPackingInfo , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::rotamer_set::WaterPackingInfo , core::scoring::methods::LKB_ResiduesInfo , core::id::DOF_ID_Map< T > , protocols::frags::TorsionFragmentLibrary , core::id::AtomID_Map< T > , protocols::frags::TorsionFragmentLibrary , protocols::noesy_assign::ResonanceList , core::fragment::picking_old::vall::VallSection , protocols::rbsegment_relax::RBSegment , core::chemical::ResidueSelector , core::chemical::Selector_NO_VARIANTS , core::chemical::Selector_VARIANT_TYPE , core::chemical::Selector_PROPERTY , core::chemical::Selector_AA , protocols::optimize_weights::PNatRotOptERotamerData , core::graph::ArrayPoolElement< T > , core::chemical::CSDAtomTypeSet , core::id::AtomID_Map< T > , protocols::protein_interface_design::movers::ResidueBBDofs , protocols::noesy_assign::ResonanceList , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::moves::DataMap , protocols::ligand_docking::DistributionMap , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::dna::DnaChains , core::scoring::EnergyEdge , protocols::canonical_sampling::MultiTemperatureTrialCounter , core::scoring::ScoreFunction , core::scoring::EMapVector , core::scoring::dna::BasePartner , core::id::AtomID_Map< T > , core::pack::rotamer_set::RotamerCouplings , protocols::optimize_weights::SingleStructureData , core::id::SequenceMapping , core::id::DOF_ID_Map< T > , core::scoring::dna::BasePartner , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::cluster::Cluster , protocols::coarse_rna::SourcePositions , core::chemical::Selector_NAME1 , protocols::loops::LoopsFileData , core::graph::ArrayPoolElement< T > , core::chemical::AtomTypeSet , core::graph::Array0< T > , core::chemical::orbitals::OrbitalTypeSet , core::chemical::ResidueSelectorSingle , core::chemical::Selector_NAME3 , core::coarse::RuleSet , core::graph::Array0< T > , core::fragment::picking_old::vall::VallLibrary , core::chemical::Selector_MATCH_VARIANTS , core::graph::Array0< T > , core::graph::ArrayPoolElement< T > , core::chemical::Selector_CMDFLAG , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::chemical::MMAtomTypeSet , core::io::silent::SilentFileData , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::rotamer_set::RotamerCouplings , core::chemical::AtomTypeSet , core::chemical::ElementSet , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::EMapVector , core::id::SequenceMapping , core::sequence::Sequence , protocols::abinitio::StructureStore , protocols::cluster::Cluster , protocols::dna::DnaChains , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::loops::Loops , protocols::noesy_assign::MethylNameLibrary , core::id::DOF_ID_Map< T > , protocols::optimize_weights::PNatAAOptERotamerData , protocols::rbsegment_relax::RBSegment
• oprod() : protocols::evaluation::PCA
• OptCysHG() : core::pack::task::operation::OptCysHG
• optE_type_from_name() : protocols::optimize_weights::OptEPositionDataFactory
• optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• opte_weight_mixing_factor() : protocols::optimize_weights::IterativeOptEDriver
• OptEData() : protocols::optimize_weights::OptEData
• OptEMultifunc() : protocols::optimize_weights::OptEMultifunc
• OptEPositionData() : protocols::optimize_weights::OptEPositionData
• OptEVariableExpression() : protocols::optimize_weights::OptEVariableExpression
• OptH() : core::pack::task::operation::OptH
• optimize_angles() : protocols::branch_angle::BranchAngleOptimizer
• optimize_branch_angles() : protocols::backrub::BackrubMover
• optimize_cov_bond() : protocols::ub_e2c::ubi_e2c_modeler
• optimize_foldtree() : protocols::simple_moves::DesignRepackMover
• optimize_h() : core::pack::task::ResidueLevelTask_ , core::pack::task::ResidueLevelTask
• optimize_kurtosis() : protocols::toolbox::InteratomicVarianceMatrix
• optimize_orientation3() : protocols::ligand_docking::LigandDockProtocol
• optimize_weights() : protocols::optimize_weights::IterativeOptEDriver
• options_type() : core::chemical::ResidueLoaderOptionsCreator , protocols::loops::LoopsFileOptionsCreator , core::import_pose::ImportPoseOptionsCreator , core::io::silent::SilentFileOptionsCreator , core::scoring::electron_density::ElectronDensityOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator
• or_adducts() : core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_ , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask
• or_by_box_liberal() : protocols::match::Bool3DGrid
• or_by_sphere() : protocols::match::BumpGrid
• or_by_sphere_conservative() : protocols::match::Bool3DGrid
• or_by_sphere_liberal() : protocols::match::Bool3DGrid
• or_by_spheres_conservative() : protocols::match::Bool3DGrid
• 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::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask_
• or_include_current() : core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_ , core::pack::task::PackerTask , 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::ResidueLevelTask_ , core::pack::task::ResidueLevelTask , core::pack::task::PackerTask
• or_with() : protocols::match::BumpGrid , protocols::match::Bool3DGrid
• or_within_radius_of_backbone() : protocols::match::downstream::ActiveSiteGrid
• or_within_radius_of_residue() : protocols::match::downstream::ActiveSiteGrid
• or_within_radius_of_sidechain() : protocols::match::downstream::ActiveSiteGrid
• orb_orb_rules() : core::scoring::orbitals::OrbitalsScore
• OrbHdist_cosAOH_energy() : core::scoring::orbitals::OrbitalsLookup
• OrbHdist_cosDHO_energy() : core::scoring::orbitals::OrbitalsLookup
• orbital() : core::chemical::ResidueType
• Orbital() : core::chemical::Orbital
• orbital() : core::chemical::ResidueType
• Orbital() : core::chemical::Orbital
• 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::conformation::Residue , core::chemical::ResidueType
• orbital_type_index() : core::chemical::orbitals::OrbitalTypeSet , core::chemical::Orbital , core::conformation::Residue , core::chemical::orbitals::OrbitalTypeSet , core::chemical::Orbital
• orbital_type_set() : core::chemical::ChemicalManager
• orbital_xyz() : core::conformation::Residue
• OrbitalsFeatures() : protocols::features::OrbitalsFeatures
• OrbitalsFeaturesCreator() : protocols::features::OrbitalsFeaturesCreator
• 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_by_energy() : core::io::silent::SilentFileData
• order_parameter() : protocols::toolbox::InteratomicVarianceMatrix
• order_strand() : protocols::fldsgn::topology::Sheet
• order_strands() : protocols::fldsgn::topology::Sheet
• order_vector() : protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue
• ordered_constrained_positions() : protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzConstraintIO
• OrderedFragSet() : core::fragment::OrderedFragSet
• OrderedFragSetIterator_() : core::fragment::OrderedFragSetIterator_
• OrderedSequentialSymmetrySlider() : protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider
• orient() : protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::SS_Base
• orient_onto_residue() : core::conformation::Residue
• orient_rotamer_set_to_symmetric_partner() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• orient_strand() : protocols::fldsgn::topology::Sheet
• orient_strands() : protocols::fldsgn::topology::Sheet
• Orientation() : core::scoring::dssp::Pairing
• orig_rotamer_id_for_moltenres() : core::pack::scmin::SidechainStateAssignment
• origin() : protocols::pockets::FingerprintBase
• original2modified() : protocols::forge::build::BuildManager
• original2modified_interval_endpoints() : protocols::forge::build::BuildManager
• original2modified_intervals() : protocols::forge::build::BuildManager
• original_deleted_positions() : protocols::forge::build::GrowRight , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::SegmentInsert , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction
• original_fixed_positions() : protocols::forge::build::SegmentInsert , protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentSwap , protocols::forge::build::ConnectRight , protocols::forge::build::GrowRight , protocols::forge::build::SegmentRebuild , protocols::forge::build::RelativeConnectRight , protocols::forge::build::Bridge , protocols::forge::build::GrowLeft
• original_i2p_deleted() : protocols::forge::build::BuildManager
• original_i2p_kept() : protocols::forge::build::BuildManager
• original_insertion_point() : protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::OriginalBackboneBuildPoint
• original_interval() : protocols::forge::build::BuildInstruction
• original_interval_valid() : protocols::forge::build::GrowRight , protocols::forge::build::ConnectRight , protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentSwap , protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild
• original_intervals_containing_deleted_positions() : protocols::forge::build::BuildManager
• original_intervals_containing_kept_positions() : protocols::forge::build::BuildManager
• original_kept_positions() : protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentRebuild , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentSwap , protocols::forge::build::GrowLeft , protocols::forge::build::BuildManager , protocols::forge::build::SegmentInsert , protocols::forge::build::Bridge , protocols::forge::build::GrowRight
• original_mutable_positions() : protocols::forge::build::GrowLeft , protocols::forge::build::SegmentSwap , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::Bridge , protocols::forge::build::SegmentRebuild , protocols::forge::build::ConnectRight , protocols::forge::build::BuildInstruction
• original_resid() : protocols::match::upstream::OriginalBackboneBuildPoint
• original_sequence() : protocols::forge::components::VarLengthBuild
• original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• OriginalBackboneBuildPoint() : protocols::match::upstream::OriginalBackboneBuildPoint
• ortho_check() : core::kinematics::RT , core::kinematics::Jump
• otfedge_note_substitution_accepted() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• OTFFlexbbEdge() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• OTFFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• OTFFlexbbNode() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• other_atom() : core::id::BondID
• other_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• other_neighbor_atom_indices() : core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer
• other_neighbor_id() : core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• other_pose() : protocols::jd2::PDBJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::SilentFileJobOutputter
• OtherContextScoreFunction() : protocols::flexpack::OtherContextScoreFunction
• out_of_bounds() : core::scoring::PoissonBoltzmannPotential
• outbound() : protocols::wum::WorkUnitManager
• outer_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• output() : protocols::comparative_modeling::AlignmentCluster
• output_alternative_states() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• output_atom_bin() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• Output_boolean() : core::scoring::rna::RNA_TorsionPotential
• output_buried_unsatisfied_hbonds() : protocols::dna::PDBOutput
• output_centroid_silent_struct() : protocols::swa::StepWiseScreener , protocols::swa::protein::StepWiseProteinScreener
• output_chainTORS() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser , protocols::swa::protein::StepWiseProteinLoopBridger
• output_connectivity() : core::pack::interaction_graph::InteractionGraphBase , core::graph::Graph
• output_count() : protocols::canonical_sampling::SidechainMetropolisHastingsMover
• output_debug_structure() : protocols::abinitio::Protocol , protocols::relax::RelaxProtocolBase , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• output_design_tags() : protocols::dna::PDBOutput
• output_diagnosis() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat
• output_dimacs() : core::pack::interaction_graph::InteractionGraphBase , core::graph::Graph
• output_empty_minimizer_silent_file() : protocols::swa::rna::StepWiseRNA_Minimizer
• output_etable() : core::scoring::etable::MembEtable , core::scoring::etable::Etable
• output_extra_RMSDs() : protocols::swa::rna::StepWiseRNA_JobParameters
• output_file_name() : protocols::match::MatcherTask , protocols::canonical_sampling::MetropolisHastingsMover , protocols::match::MatcherTask , protocols::jobdist::BasicJob
• output_forward_backward_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• output_fragments() : protocols::frag_picker::FragmentPicker
• output_hbond_info() : protocols::dna::PDBOutput
• output_histogram() : protocols::swa::RigidBodySampler
• output_hit() : protocols::match::output::WriteUpstreamHitKinemage
• output_id() : protocols::fldsgn::filters::HSSTripletFilter
• output_info() : protocols::dna::PDBOutput
• output_lores_silent_file() : protocols::rna::RNA_DeNovoProtocol
• output_matchres_only() : protocols::match::MatcherTask
• output_name() : protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::JobOutputter , protocols::canonical_sampling::MetropolisHastingsMover , protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::ScoreOnlyJobOutputter
• output_only_cluster_transitions() : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• output_pdb() : core::scoring::packing::PoseBalls , protocols::dna::PDBOutput
• output_pose() : protocols::protein_interface_design::movers::MapHotspot
• output_pose_data_list() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• output_pose_data_wrapper() : protocols::swa::rna::StepWiseRNA_Minimizer
• output_repacked_poses() : protocols::simple_moves::SetReturningPackRotamersMover
• output_residue() : core::chemical::sdf::MolWriter
• output_residue_pair_energies() : protocols::simple_filters::ScoreCutoffFilter
• output_results() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::swa::RigidBodySampler , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• output_score_info() : protocols::dna::PDBOutput
• output_silent() : protocols::frag_picker::FragmentCandidate
• output_silent_file() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer , protocols::swa::RigidBodySampler
• output_silent_struct() : protocols::rna::RNA_DeNovoProtocol
• output_sqc_file() : core::io::sequence_comparation::DesignContrast
• output_statistics() : protocols::backrub::BackrubSidechainMover
• output_string_real_pairs_begin() : protocols::jd2::Job
• output_string_real_pairs_end() : protocols::jd2::Job
• output_string_string_pairs_begin() : protocols::jd2::Job
• output_string_string_pairs_end() : protocols::jd2::Job
• output_strings_begin() : protocols::jd2::Job
• output_strings_end() : protocols::jd2::Job
• output_tag() : protocols::jobdist::BasicJob
• output_to_silent_file() : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• output_type() : protocols::fldsgn::filters::HSSTripletFilter
• output_upstream_coordinates() : protocols::match::output::WriteUpstreamHitKinemage
• output_weighted_unfolded_energies() : protocols::optimize_weights::IterativeOptEDriver
• output_writer() : protocols::match::output::MatchProcessor
• output_writer_name() : protocols::match::MatcherTask
• Outputter() : protocols::outputter::Outputter
• OutputWriter() : protocols::match::output::OutputWriter
• outq() : protocols::wum2::EndPoint
• overall_cstfilter_weight() : protocols::abinitio::IterativeBase
• overall_energy0() : protocols::branch_angle::BranchCoef1
• overall_Ktheta() : protocols::branch_angle::BranchCoef1
• overall_params() : protocols::branch_angle::BranchAngleOptimizer
• overall_theta0() : protocols::branch_angle::BranchCoef1
• overlap() : protocols::comparative_modeling::AlignmentCluster , core::scoring::packstat::Circle
• overlap_exposed() : core::pack::interaction_graph::InvRotamerDots
• overlaps() : core::pack::interaction_graph::RotamerDots , protocols::match::BumpGrid , core::pack::interaction_graph::HPatchNode< V, E, G >
• override_option_input() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• override_secstruct() : protocols::rna::RNA_StructureParameters
• owner() : protocols::topology_broker::DofClaim , core::scoring::Energies
• owner_nodes_and_locations() : protocols::toolbox::match_enzdes_util::InvrotCollector