Class Index

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A	DerivCheckDataPoint (core::optimization)	HeavyAtomWithPolarHydrogensFilter (core::chemical)	PattersonCorrEnergy (core::scoring::electron_density)	ScoreFileSilentStructCreator (core::io::silent)
	DerivedSequenceMapping (core::sequence)	Helices (core::scoring)	PattersonCorrEnergyCreator (core::scoring::electron_density)	ScoreFunction (core::scoring)
ABEGO (core::util)	DerivVectorPair (core::scoring)	HolesEnergy (core::scoring::packing)	PBLifetimeCache (core::scoring::methods)	ScoreFunctionFactory (core::scoring)
ABEGOEval (core::fragment::picking_old::vall::eval)	DescentDirectionAlgorithm (core::optimization)	HolesEnergyCreator (core::scoring::packing)	PDB_DReader (core::io::pdb)	ScoreFunctionInfo (core::scoring)
ABEGOManager (core::util)	DesignContrast (core::io::sequence_comparation)	HolesEnergyRes (core::scoring::packing)	PDB_DReaderOptions (core::io::pdb)	ScoreJumpFileSilentStruct (core::io::silent)
AbstractRotamerTrie (core::conformation)	DestructionEvent (core::pose::signals)	HolesParams (core::scoring::packing)	PDBInfo (core::pose)	ScoreJumpFileSilentStructCreator (core::io::silent)
AcceptorAtomFilter (core::chemical)	DFIRE_Energy (core::scoring::methods::dfire)	HolesParamsRes (core::scoring::packing)	PDBPoseInputStream (core::import_pose::pose_stream)	ScoreLessThanComparator (core::import_pose::atom_tree_diffs)
Accumulator (core::scoring::packstat)	DFIRE_EnergyCreator (core::scoring::methods::dfire)	HolesResult (core::scoring::packing)	PDBPoseMap (core::pose)	ScoreStruct (core::io::raw_data)
AddAtom (core::chemical)	DFIRE_Potential (core::scoring::methods::dfire)	HPatchBackgroundEdge (core::pack::interaction_graph)	PDBSilentStruct (core::import_pose)	ScoreTypeManager (core::scoring)
AddBehaviorRLT (core::pack::task::operation)	DFPMinConvergedAbsolute (core::optimization)	HPatchBackgroundNode (core::pack::interaction_graph)	PDBSilentStructCreator (core::import_pose)	ScoringManager (core::scoring)
AddBehaviorRLTCreator (core::pack::task::operation)	DFPMinConvergedFractional (core::optimization)	HPatchEdge (core::pack::interaction_graph)	PDEdge (core::pack::interaction_graph)	ScoringScheme (core::sequence)
AddBond (core::chemical)	DihedralConstraint (core::scoring::constraints)	HPatchEnergy (core::pack::interaction_graph)	PDInteractionGraph (core::pack::interaction_graph)	ScoringSchemeFactory (core::sequence)
AddChi (core::chemical)	DihedralConstraintCreator (core::scoring::constraints)	HPatchEnergyCreator (core::pack::interaction_graph)	PDNode (core::pack::interaction_graph)	SDFParser (core::chemical::sdf)
AddChiRotamer (core::chemical)	DihedralPairConstraint (core::scoring::constraints)	HPatchInteractionGraph (core::pack::interaction_graph)	PeptideBondedEnergyContainer (core::scoring)	SecondaryStructure (core::fragment)
AddConnect (core::chemical)	DihedralPairConstraintCreator (core::scoring::constraints)	HPatchNode (core::pack::interaction_graph)	PeptideBondedNeighborConstIterator (core::scoring)	SecondaryStructureEnergy (core::scoring::methods)
AddEdgeVisitor (core::conformation)	DimerPairing (core::scoring)	HTL_EventX (core::scoring::packstat)	PeptideBondedNeighborIterator (core::scoring)	SecondaryStructureEnergyCreator (core::scoring::methods)
AdditionalBackgroundNodesInteractionGraph (core::pack::interaction_graph)	DipolarCoupling (core::scoring)	HybridVDW_Energy (core::scoring::methods)	PeptideBondEnergy (core::scoring::methods)	SecondaryStructurePotential (core::scoring)
AddProperty (core::chemical)	DipolarCouplingEnergy (core::scoring::methods)	HybridVDW_EnergyCreator (core::scoring::methods)	PeptideBondEnergyCreator (core::scoring::methods)	SecondaryStructureWeights (core::scoring)
AddProtonChi (core::chemical)	DipolarCouplingEnergyCreator (core::scoring::methods)	HydrogenAtomFilter (core::chemical)	PeriodicBoundFunc (core::scoring::constraints)	SecStructGen (core::fragment::picking_old::vall::gen)
AddResiduesRotamerSetOperation (core::pack::rotamer_set)	DirectReadoutEnergy (core::scoring::methods)	I	PeriodicFunc (core::scoring::func)	SecstructSRFD (core::fragment)
Adduct (core::chemical)	DirectReadoutEnergyCreator (core::scoring::methods)		PerSphereAccumulator (core::scoring::packstat)	SelectedResPredicate (core::scoring)
Aligner (core::sequence)	DirectReadoutPotential (core::scoring::dna)	APBSConfig::I_PARAM (core::scoring)	PhenixInterface (core::scoring::cryst)	Selector_AA (core::chemical)
AlignerFactory (core::sequence)	DisallowIfNonnative (core::pack::task::operation)	ICoorAtomID (core::chemical)	PIKAA (core::pack::task)	Selector_CMDFLAG (core::chemical)
ALLAA (core::pack::task)	DisallowIfNonnativeCreator (core::pack::task::operation)	ICoorOrbitalData (core::chemical::orbitals)	PIKNA (core::pack::task)	Selector_MATCH_VARIANTS (core::chemical)
ALLAAwc (core::pack::task)	DisallowIfNonnativeRLT (core::pack::task::operation)	IdealBondLengthSet (core::chemical)	PIKRNA (core::pack::task)	Selector_NAME1 (core::chemical)
ALLAAxc (core::pack::task)	DisallowIfNonnativeRLTCreator (core::pack::task::operation)	IdealParametersDatabase (core::scoring::methods)	Point (core::scoring::packstat)	Selector_NAME3 (core::chemical)
AllResFilter (core::pack::task::operation)	DisjointSets (core::graph)	IdentityEval (core::fragment::picking_old::vall::eval)	PointGraphEdgeData (core::conformation)	Selector_NO_VARIANTS (core::chemical)
AllResFilterCreator (core::pack::task::operation)	DistanceChainbreakEnergy (core::scoring::methods)	IdentityEvent (core::conformation::signals)	PointGraphVertexData (core::conformation)	Selector_PROPERTY (core::chemical)
AmberPeriodicFunc (core::scoring::func)	DistanceChainbreakEnergyCreator (core::scoring::methods)	IdentityFunc (core::scoring::func)	PointPair (core::scoring::packstat)	Selector_UPPER_POSITION (core::chemical)
AmbiguousConstraint (core::scoring::constraints)	DistanceFunc (core::scoring::custom_pair_distance)	IGEdgeReweightContainer (core::pack::task)	PoissonBoltzmannEnergy (core::scoring::methods)	Selector_VARIANT_TYPE (core::chemical)
AmbiguousConstraintCreator (core::scoring::constraints)	DistanceHistogram (core::scoring::saxs)	IGEdgeReweighter (core::pack::task)	PoissonBoltzmannEnergyCreator (core::scoring::methods)	SemiRotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)
AmbiguousNMRConstraint (core::scoring::constraints)	DistancePairConstraint (core::scoring::constraints)	ImportPoseOptions (core::import_pose)	PoissonBoltzmannPotential (core::scoring)	Sequence (core::sequence)
AmbiguousNMRConstraintCreator (core::scoring::constraints)	DisulfideAtomIndices (core::scoring::disulfides)	ImportPoseOptionsCreator (core::import_pose)	POLAR (core::pack::task)	SequenceAlignment (core::sequence)
AmbiguousNMRDistanceConstraint (core::scoring::constraints)	DisulfideFile (core::io::raw_data)	IncludeCurrent (core::pack::task::operation)	PolarHydrogenFilter (core::chemical)	SequenceAlignmentHasher (core::sequence)
AmbiguousNMRDistanceConstraintCreator (core::scoring::constraints)	DisulfideMatchingDatabase (core::scoring::disulfides)	IncludeCurrentCreator (core::pack::task::operation)	Polynomial_1d (core::scoring::hbonds)	SequenceAnnotation (core::environment)
AminoAcidNeighborSparseMatrix (core::pack::interaction_graph)	DisulfideMatchingEnergy (core::scoring::disulfides)	IndependentBBTorsionSRFD (core::fragment)	Pose (core::pose)	SequenceCoupling (core::sequence)
AnalyticEtableEnergy (core::scoring::etable)	DisulfideMatchingEnergyComponents (core::scoring::disulfides)	InitializeExtraRotsFromCommandline (core::pack::task::operation)	PoseBalls (core::scoring::packing)	SequenceCouplingCreator (core::sequence)
AnalyticEtableEvaluator (core::scoring::etable)	DisulfideMatchingEnergyContainer (core::scoring::disulfides)	InitializeExtraRotsFromCommandlineCreator (core::pack::task::operation)	PoseBallsLite (core::scoring::packing)	SequenceCreator (core::sequence)
AndResidueSelector (core::pack::task::residue_selector)	DisulfideMatchingEnergyCreator (core::scoring::disulfides)	InitializeFromCommandline (core::pack::task::operation)	PoseFromPDBLoader (core::import_pose)	SequenceDependentRefEnergy (core::scoring::methods)
AndResidueSelectorCreator (core::pack::task::residue_selector)	DisulfideMatchingNeighborConstIterator (core::scoring::disulfides)	InitializeFromCommandlineCreator (core::pack::task::operation)	PoseFromPDBLoaderCreator (core::import_pose)	SequenceDependentRefEnergyCreator (core::scoring::methods)
AngleConstraint (core::scoring::constraints)	DisulfideMatchingNeighborIterator (core::scoring::disulfides)	InteractionGraphBase (core::pack::interaction_graph)	PoseInputStream (core::import_pose::pose_stream)	SequenceFactory (core::sequence)
AngleConstraintCreator (core::scoring::constraints)	DisulfideMatchingPotential (core::scoring::disulfides)	InteractionGraphFactory (core::pack::interaction_graph)	PoseMetricCalculator (core::pose::metrics)	SequenceMapping (core::id)
AnnealerFactory (core::pack::annealer)	DisulfMinData (core::scoring::disulfides)	InterfaceDefinitionCalculator (core::pose::metrics::simple_calculators)	PoseMetricContainer (core::pose::metrics)	SequenceProfile (core::sequence)
AnnotatedFragData (core::fragment)	DisulfResNeighbConstIterator (core::scoring::disulfides)	InterfaceDeltaEnergeticsCalculator (core::pose::metrics::simple_calculators)	PoseOutputStream (core::import_pose::pose_stream)	SequenceProfileConstraint (core::scoring::constraints)
AnnotatedSequence (core::sequence)	DisulfResNeighbIterator (core::scoring::disulfides)	InterfaceNeighborDefinitionCalculator (core::pose::metrics::simple_calculators)	PosePackData (core::scoring::packstat)	SequenceProfileConstraintCreator (core::scoring::constraints)
AnyResFilter (core::pack::task::operation)	DNA_BaseEnergy (core::scoring::methods)	InterfaceSasaDefinitionCalculator (core::pose::metrics::simple_calculators)	PositionConservedResiduesStore (core::pose::datacache)	SequenceProfileCreator (core::sequence)
AnyResFilterCreator (core::pack::task::operation)	DNA_BaseEnergyCreator (core::scoring::methods)	InterGroupInterfaceByVectorSelector (core::pack::task::residue_selector)	PositionDdGInfo (core::io::PositionDdGInfo)	SequenceRegistrator (core::sequence)
APBSConfig (core::scoring)	DNA_BasePotential (core::scoring::dna)	InterGroupInterfaceByVectorSelectorCreator (core::pack::task::residue_selector)	PossibleAtomTypesForAtom (core::chemical::gasteiger)	SetAtomicCharge (core::chemical)
APBSResult (core::scoring)	DNABFormPotential (core::scoring::dna)	IntermolEnergy (core::scoring::methods)	PQR (core::scoring)	SetAtomType (core::chemical)
APBSWrapper (core::scoring)	DNAChiEnergy (core::scoring::dna)	IntermolEnergyCreator (core::scoring::methods)	PrecomputedPairEnergiesEdge (core::pack::interaction_graph)	SetBackboneHeavyatom (core::chemical)
APOLA (core::pack::task)	DNAChiEnergyCreator (core::scoring::dna)	Invoker (core::scoring::etable::count_pair)	PrecomputedPairEnergiesInteractionGraph (core::pack::interaction_graph)	SetICoor (core::chemical)
APOLAR (core::pack::task)	DNATorsionEnergy (core::scoring::dna)	InvRotamerDots (core::pack::interaction_graph)	PrecomputedPairEnergiesNode (core::pack::interaction_graph)	SetInterchangeabilityGroup_String (core::chemical)
APolarHydrogenFilter (core::chemical)	DNATorsionEnergyCreator (core::scoring::dna)	IsProteinCAPredicate (core::scoring)	Predicate (core::scoring)	SetIO_String (core::chemical)
AppendInterchangeabilityGroup_String (core::chemical)	DNATorsionPotential (core::scoring::dna)	J	PrependMainchainAtom (core::chemical)	SetMMAtomType (core::chemical)
AppendMainchainAtom (core::chemical)	DockingNoRepack1 (core::pack::task::operation)		PreserveCBeta (core::pack::task::operation)	SetNbrAtom (core::chemical)
AppendResidueRotamerSet (core::pack::task::operation)	DockingNoRepack2 (core::pack::task::operation)	JJH_Minimizer (core::optimization)	PreserveCBetaCreator (core::pack::task::operation)	SetNbrRadius (core::chemical)
AppendResidueRotamerSetCreator (core::pack::task::operation)	DockingScoreFunction (core::scoring)	Jump (core::kinematics)	PreventRepacking (core::pack::task::operation)	SetOrientAtom (core::chemical)
AppendRotamer (core::pack::task::operation)	DOF_Constraint (core::scoring::constraints)	JumpAtom (core::kinematics::tree)	PreventRepackingCreator (core::pack::task::operation)	SetPolymerConnectAtom (core::chemical)
AppendRotamerCreator (core::pack::task::operation)	DOF_DataPoint (core::optimization)	JumpDownstreamSelector (core::pack::task::residue_selector)	PreventRepackingRLT (core::pack::task::operation)	SetRotamerCouplings (core::pack::task::operation)
AppendRotamerSet (core::pack::task::operation)	DOF_ID (core::id)	JumpDownstreamSelectorCreator (core::pack::task::residue_selector)	PreventRepackingRLTCreator (core::pack::task::operation)	SetRotamerCouplingsCreator (core::pack::task::operation)
AppendRotamerSetCreator (core::pack::task::operation)	DOF_ID_Map (core::id)	JumpID (core::id)	ProbSortClass (core::pack::dunbrack)	SetRotamerLinks (core::pack::task::operation)
AreaAccumulator (core::scoring::packstat)	DOF_ID_Range (core::id)	JumpingFrame (core::fragment)	ProClosureEnergy (core::scoring::methods)	SetRotamerLinksCreator (core::pack::task::operation)
ArmijoLineMinimization (core::optimization)	DOF_Node (core::optimization)	JumpUpstreamSelector (core::pack::task::residue_selector)	ProClosureEnergyCreator (core::scoring::methods)	SG_Dist_Func (core::scoring::disulfides)
AromaticAtomFilter (core::chemical)	DofPassport (core::environment)	JumpUpstreamSelectorCreator (core::pack::task::residue_selector)	ProfSimScoringScheme (core::sequence)	SGSG_Dihedral_Func (core::scoring::disulfides)
Array0 (core::graph)	DotSphere (core::pack::interaction_graph)	K	ProQ_Energy (core::scoring::methods)	ShapeComplementarityCalculator (core::scoring::sc)
Array2D (core::scoring::packstat)	DoubleDensePDEdge (core::pack::interaction_graph)		ProQ_EnergyCreator (core::scoring::methods)	ShapeComplementarityCalculatorException (core::scoring::sc)
ArrayPool (core::graph)	DoubleDensePDInteractionGraph (core::pack::interaction_graph)	KarplusFunc (core::scoring::func)	ProQPotential (core::scoring)	SharedSilentData (core::io::silent)
ArrayPoolElement (core::graph)	DoubleDensePDNode (core::pack::interaction_graph)	KofNConstraint (core::scoring::constraints)	ProteinSilentStruct_SinglePrecCreator (core::io::silent)	ShortestPathInFoldTree (core::kinematics)
AssignOrbitals (core::chemical::orbitals)	DoubleLazyEdge (core::pack::interaction_graph)	KofNConstraintCreator (core::scoring::constraints)	ProteinSilentStruct_Template (core::io::silent)	ShortRangeTwoBodyEnergy (core::scoring::methods)
Atom (core::scoring::sc)	DoubleLazyInteractionGraph (core::pack::interaction_graph)	KromerMann (core::scoring::electron_density)	ProteinSilentStructCreator (core::io::silent)	SidechainStateAssignment (core::pack::scmin)
Atom (core::chemical)	DoubleLazyNode (core::pack::interaction_graph)	L	PseudoBond (core::conformation)	SigmoidFunc (core::scoring::func)
Atom (core::conformation)	DownJumpSRFD (core::fragment)		PseudoBondCollection (core::conformation)	SigmoidWeightedCenList (core::scoring)
Atom (core::kinematics::tree)	DP_Matrix (core::sequence)	L1ScoringScheme (core::sequence)	PyContextIndependentOneBodyEnergy (core::scoring::methods)	SilentEnergy (core::io::silent)
Atom_ (core::kinematics::tree)	DPScoringScheme (core::sequence)	LazyEdge (core::pack::interaction_graph)	PyContextIndependentTwoBodyEnergy (core::scoring::methods)	SilentFileData (core::io::silent)
AtomGraphEdgeData (core::conformation)	DS_Node (core::graph)	LazyInteractionGraph (core::pack::interaction_graph)	PyEnergyMethodRegistrator (core::scoring::methods)	SilentFileLoader (core::io::silent)
AtomGraphVertexData (core::conformation)	Dssp (core::scoring::dssp)	LazyNode (core::pack::interaction_graph)	R	SilentFileLoaderCreator (core::io::silent)
AtomICoor (core::chemical)	DunbrackConstraint (core::pack::dunbrack)	LazySilentFilePoseInputStream (core::import_pose::pose_stream)		SilentFileOptions (core::io::silent)
AtomID (core::id)	DunbrackConstraintCreator (core::pack::dunbrack)	LeeRichards (core::scoring::packstat)	APBSConfig::R_PARAM (core::scoring)	SilentFileOptionsCreator (core::io::silent)
AtomID_Map (core::id)	DunbrackEnergy (core::pack::dunbrack)	LeGrandSasa (core::scoring::sasa)	Rama2BOffset (core::scoring)	SilentFilePoseInputStream (core::import_pose::pose_stream)
AtomID_Map_AtomID (core::id)	DunbrackEnergyCreator (core::pack::dunbrack)	LengthChecker (core::environment)	Rama2BOffsetEnergy (core::scoring::methods)	SilentStruct (core::io::silent)
AtomInformation (core::io::pdb)	DunbrackRotamer (core::pack::dunbrack)	LengthEvent (core::conformation::signals)	Rama2BOffsetEnergyCreator (core::scoring::methods)	SilentStructCreator (core::io::silent)
AtomNeighbor (core::scoring)	DunbrackRotamerMeanSD (core::pack::dunbrack)	LengthEventCollector (core::pose::datacache)	Ramachandran (core::scoring)	SilentStructFactory (core::io::silent)
AtomNode (core::optimization)	DunbrackRotamerSampleData (core::pack::dunbrack)	LengthGen (core::fragment::picking_old::vall::gen)	Ramachandran2B (core::scoring)	SilentStructRegistrator (core::io::silent)
AtomPairConstraint (core::scoring::constraints)	E	Librarian (core::fragment::picking_old::concepts)	RamachandranEnergy (core::scoring::methods)	SimAnnealerBase (core::pack::annealer)
AtomPairConstraintCreator (core::scoring::constraints)		Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary (core::fragment::picking_old::concepts)	RamachandranEnergy2B (core::scoring::methods)	SimpleDerivCheckResult (core::optimization)
AtomPairEnergy (core::scoring::etable)	Edge (core::graph)	Library (core::fragment::picking_old::concepts)	RamachandranEnergy2BCreator (core::scoring::methods)	SimpleEdge (core::pack::interaction_graph)
AtomPairFuncList (core::scoring::custom_pair_distance)	Edge (core::kinematics)	Library_VallSections (core::fragment::picking_old::concepts)	RamachandranEnergyCreator (core::scoring::methods)	SimpleInteractionGraph (core::pack::interaction_graph)
AtomRadiusMap (core::scoring::packstat)	EdgeBase (core::pack::interaction_graph)	Line (core::util)	RawFileData (core::io::raw_data)	SimpleNode (core::pack::interaction_graph)
PDBInfo::AtomRecord (core::pose)	EdgeList (core::graph)	LinearChainbreakEnergy (core::scoring::methods)	RawStruct (core::io::raw_data)	SimplePDB (core::scoring::packstat)
AtomTree (core::kinematics)	EdgeListConstIterator (core::graph)	LinearChainbreakEnergyCreator (core::scoring::methods)	RDC (core::scoring)	SimplePDB_Atom (core::scoring::packstat)
AtomTreeCollection (core::pack::scmin)	EdgeListElement (core::graph)	LinearMemEdge (core::pack::interaction_graph)	RDC_Rohl (core::scoring)	SimpleScoringScheme (core::sequence)
AtomTreeDiff (core::import_pose::atom_tree_diffs)	EdgeListIterator (core::graph)	LinearMemNode (core::pack::interaction_graph)	ReadResfile (core::pack::task::operation)	SimpleSequenceCreator (core::sequence)
AtomTreeMinimizer (core::optimization)	EItem (core::optimization)	LinearMemoryInteractionGraph (core::pack::interaction_graph)	ReadResfileAndObeyLengthEvents (core::pack::task::operation)	SimpleSequenceData (core::io::silent)
AtomTreeMultifunc (core::optimization)	ElecAtom (core::scoring::elec)	LinearPenaltyFunction (core::scoring::func)	ReadResfileAndObeyLengthEventsCreator (core::pack::task::operation)	SingleLigandRotamerLibrary (core::pack::dunbrack)
AtomTreeSCMinMinimizerMap (core::pack::scmin)	ElecDensAllAtomCenEnergy (core::scoring::electron_density)	LineMinimizationAlgorithm (core::optimization)	ReadResfileCreator (core::pack::task::operation)	SingleResidueCenrotLibrary (core::pack::dunbrack::cenrot)
AtomType (core::chemical)	ElecDensAllAtomCenEnergyCreator (core::scoring::electron_density)	LinkInformation (core::io::pdb)	RealFilter (core::chemical)	SingleResidueDunbrackLibrary (core::pack::dunbrack)
AtomTypeData	ElecDensAtomwiseEnergy (core::scoring::electron_density_atomwise)	LipidAccInfo (core::conformation::membrane)	RedefineChi (core::chemical)	SingleResidueDunbrackLibraryConcrete (core::pack::dunbrack)
AtomTypeDatabaseIO (core::chemical)	ElecDensAtomwiseEnergyCreator (core::scoring::electron_density_atomwise)	LipoFileFallbackConfiguration (core::membrane::io)	ReferenceCount	SingleResidueFragData (core::fragment)
AtomTypeSet (core::chemical)	ElecDensCenEnergy (core::scoring::electron_density)	LipoFileFallbackConfigurationCreator (core::membrane::io)	ReferenceEnergy (core::scoring::methods)	SingleResidueMultifunc (core::optimization)
AtomVDW (core::scoring)	ElecDensCenEnergyCreator (core::scoring::electron_density)	LipoFileIO (core::membrane::io)	ReferenceEnergyCreator (core::scoring::methods)	SingleResidueRotamerLibrary (core::pack::dunbrack)
AtomWithDOFChange (core::kinematics)	ElecDensEnergy (core::scoring::electron_density)	LipoFileLoader (core::membrane::io)	ReferenceEnergyNoncanonical (core::scoring::methods)	SinXOverX (core::scoring::saxs)
AUTO (core::pack::task)	ElecDensEnergyCreator (core::scoring::electron_density)	LipoFileLoaderCreator (core::membrane::io)	ReferenceEnergyNoncanonicalCreator (core::scoring::methods)	SiteConstraint (core::scoring::constraints)
AutomorphismIterator (core::chemical)	ElectronConfiguration (core::chemical)	LipoFileOptions (core::membrane::io)	RemarkInfo (core::pose)	SiteConstraintCreator (core::scoring::constraints)
B	ElectronDensity (core::scoring::electron_density)	LipoFileOptionsCreator (core::membrane::io)	Remarks (core::pose)	SiteConstraintResidues (core::scoring::constraints)
	ElectronDensityAtomwise (core::scoring::electron_density_atomwise)	LK_BallEnergy (core::scoring::methods)	ReplicateTask (core::pack::task::operation)	SiteConstraintResiduesCreator (core::scoring::constraints)
BackboneStubConstraint (core::scoring::constraints)	ElectronDensityLoader (core::scoring::electron_density)	LK_BallEnergyCreator (core::scoring::methods)	ReplicateTaskCreator (core::pack::task::operation)	SkipViolFunc (core::scoring::func)
BackboneStubLinearConstraint (core::scoring::constraints)	ElectronDensityLoaderCreator (core::scoring::electron_density)	LK_hack (core::scoring::methods)	ResConnID (core::chemical)	Slice (core::scoring::packstat)
BackgroundNode (core::pack::interaction_graph)	ElectronDensityOptions (core::scoring::electron_density)	LK_hackCreator (core::scoring::methods)	ResfileCommand (core::pack::task)	SmallAtNb (core::scoring)
BackgroundToFirstClassEdge (core::pack::interaction_graph)	ElectronDensityOptionsCreator (core::scoring::electron_density)	LK_PolarNonPolarEnergy (core::scoring::methods)	ResfileContents (core::pack::task)	SmoothCenPairEnergy (core::scoring::methods)
Ball (core::scoring::packing)	Element (core::chemical)	LK_PolarNonPolarEnergyCreator (core::scoring::methods)	ResfileReaderException (core::pack::task)	SmoothCenPairEnergyCreator (core::scoring::methods)
Base_pair (core::scoring::rna)	ElementSet (core::chemical)	LK_SigmoidalFunc (core::scoring::methods)	ResFilter (core::pack::task::operation)	SmoothEnvEnergy (core::scoring::methods)
Base_stack (core::scoring::rna)	EMapVector (core::scoring)	LKB_ResidueInfo (core::scoring::methods)	ResFilterComposition (core::pack::task::operation)	SmoothEnvEnergyCreator (core::scoring::methods)
BaseCacheUnit (core::fragment)	EmbedConfigInfo (core::conformation::membrane)	LKB_ResiduesInfo (core::scoring::methods)	ResFilterCreator (core::pack::task::operation)	SmoothEnvPairPotential (core::scoring)
BaseEtableEnergy (core::scoring::etable)	EmbedDefFallbackConfiguration (core::membrane::io)	LKB_ResPairMinData (core::scoring::methods)	ResFilterFactory (core::pack::task::operation)	SmoothScoreTermCoeffs (core::scoring)
BasePartner (core::scoring::dna)	EmbedDefFallbackConfigurationCreator (core::membrane::io)	LocalCoordinateConstraint (core::scoring::constraints)	ResFilterRegistrator (core::pack::task::operation)	SoedingFunc (core::scoring::func)
BB_BB_EnergyInvoker (core::scoring::etable)	EmbedDefIO (core::membrane::io)	LocalCoordinateConstraintCreator (core::scoring::constraints)	ResidualDipolarCoupling (core::scoring)	SOGFunc (core::scoring::func)
BB_Pos (core::scoring)	EmbedDefLoader (core::membrane::io)	LocalPosition (core::environment)	ResidualDipolarCoupling_Rohl (core::scoring)	SOGFunc_Impl (core::scoring::func)
BBDepCartBondedParameters (core::scoring::methods)	EmbedDefLoaderCreator (core::membrane::io)	LongRangeTwoBodyEnergy (core::scoring::methods)	ResidualDipolarCouplingEnergy (core::scoring::methods)	SpanFileFallbackConfiguration (core::membrane::io)
BBDepNRChiSample (core::pack::dunbrack)	EmbedDefOptions (core::membrane::io)	Loop (core::scoring::loop_graph)	ResidualDipolarCouplingEnergy_Rohl (core::scoring::methods)	SpanFileFallbackConfigurationCreator (core::membrane::io)
BBDepScoreInterpData (core::pack::dunbrack)	EmbedDefOptionsCreator (core::membrane::io)	LoopCloseEnergy (core::scoring::loop_graph)	ResidualDipolarCouplingEnergy_RohlCreator (core::scoring::methods)	SpanFileIO (core::membrane::io)
BBDepSemiRotamericData (core::pack::dunbrack)	EmbeddingFactory (core::membrane::geometry)	LoopCloseEnergyCreator (core::scoring::loop_graph)	ResidualDipolarCouplingEnergyCreator (core::scoring::methods)	SpanFileLoader (core::membrane::io)
BBIndepCartBondedParameters (core::scoring::methods)	EmbedSearchParams (core::conformation::membrane)	LoopCycle (core::scoring::loop_graph)	ResidualDipolarCouplingEnergyRigidSegments (core::scoring::methods)	SpanFileLoaderCreator (core::membrane::io)
BBIndNRChiSample (core::pack::dunbrack)	EmbedSearchParamsFallbackConfiguration (core::membrane::io)	LoopGraph (core::scoring::loop_graph)	Residue (core::conformation)	SpanFileOptions (core::membrane::io)
BBIndSemiRotamericData (core::pack::dunbrack)	EmbedSearchParamsFallbackConfigurationCreator (core::membrane::io)	LoopScoreInfo (core::scoring::loop_graph)	ResidueAtomTreeCollection (core::pack::scmin)	SpanFileOptionsCreator (core::membrane::io)
BBTorsionAndAnglesSRFD (core::fragment)	EmbedSearchParamsIO (core::membrane::io)	LR_AtomData (core::scoring::packstat)	ResidueAtomTreeCollectionMomento (core::pack::scmin)	SpanningTopology (core::conformation::membrane)
BBTorsionSRFD (core::fragment)	EmbedSearchParamsLoader (core::membrane::io)	LR_MP_AtomData (core::scoring::packstat)	ResidueCartBondedParameters (core::scoring::methods)	SparseMatrixIndex (core::pack::interaction_graph)
Rule::BeadAdder (core::coarse)	EmbedSearchParamsLoaderCreator (core::membrane::io)	LREnergyContainer (core::scoring)	ResidueConnection (core::chemical)	SpecialSegmentsObserver (core::pose::datacache)
Translator::BeadAtom (core::coarse)	EmbedSearchParamsOptions (core::membrane::io)	M	ResidueConstraints (core::scoring::constraints)	Sphere (core::scoring::packstat)
BigBinConstraint (core::scoring::constraints)	EmbedSearchParamsOptionsCreator (core::membrane::io)		ResidueCoordinateChangeList (core::kinematics)	SplineFunc (core::scoring::func)
BigBinConstraintCreator (core::scoring::constraints)	EMPTY (core::pack::task)	MapCacheUnit (core::fragment)	ResidueDatabaseIO (core::chemical)	SplineParameters (core::scoring::etable)
BinarySilentStruct (core::io::silent)	Energies (core::scoring)	MatrixScoringScheme (core::sequence)	ResidueFactory (core::conformation)	SquareWell2Func (core::scoring::func)
BinarySilentStructCreator (core::io::silent)	EnergyDependentCalculator (core::pose::metrics)	MCAligner (core::sequence)	ResidueHasProperty (core::pack::task::operation)	SquareWellFunc (core::scoring::func)
Bond (core::chemical)	EnergyEdge (core::scoring)	MembEtable (core::scoring::etable)	ResidueHasPropertyCreator (core::pack::task::operation)	SS_Info (core::scoring)
BondData (core::chemical::sdf)	EnergyEval (core::fragment::picking_old::vall::eval)	Membrane_FAEmbed (core::scoring)	ResidueIndexIs (core::pack::task::operation)	SS_Killhairpins_Info (core::scoring)
BondedAtom (core::kinematics::tree)	EnergyEvent (core::pose::signals)	Membrane_FAPotential (core::scoring)	ResidueIndexIsCreator (core::pack::task::operation)	SSWeightParameters (core::scoring::hbonds)
BondID (core::id)	EnergyGraph (core::scoring)	MembraneCbetaEnergy (core::scoring::methods)	ResidueIndexIsnt (core::pack::task::operation)	StackElecEnergy (core::scoring::rna)
Book (core::fragment::picking_old::concepts)	EnergyMethod (core::scoring::methods)	MembraneCbetaEnergyCreator (core::scoring::methods)	ResidueIndexIsntCreator (core::pack::task::operation)	StackElecEnergyCreator (core::scoring::rna)
Book_VallResidues (core::fragment::picking_old::concepts)	EnergyMethodCreator (core::scoring::methods)	MembraneCenPairEnergy (core::scoring::methods)	ResidueIndexSelector (core::pack::task::residue_selector)	StrandPairing (core::scoring::dssp)
Bookmark (core::fragment::picking_old::concepts)	EnergyMethodOptions (core::scoring::methods)	MembraneCenPairEnergyCreator (core::scoring::methods)	ResidueIndexSelectorCreator (core::pack::task::residue_selector)	StrandPairingSet (core::scoring::dssp)
BoundFunc (core::scoring::constraints)	EnergyMethodRegistrator (core::scoring::methods)	MembraneEmbed (core::scoring)	ResidueInformation (core::io::pdb)	Strands (core::scoring)
BrentLineMinimization (core::optimization)	EnergyNames (core::io::silent)	MembraneEnvEnergy (core::scoring::methods)	PDBPoseMap::ResidueKey (core::pose)	StrongWolfeLineMinimization (core::optimization)
BUFFER (core::io::serialization)	EnergyNode (core::scoring)	MembraneEnvEnergyCreator (core::scoring::methods)	ResidueKinWriter (core::conformation)	StructureDependentCalculator (core::pose::metrics)
BumpSelector (core::pack::rotamer_set)	Entry	MembraneEnvPenalties (core::scoring::methods)	ResidueLacksProperty (core::pack::task::operation)	Stub (core::kinematics)
BurialEnergy (core::scoring::methods)	EnvCore (core::environment)	MembraneEnvPenaltiesCreator (core::scoring::methods)	ResidueLacksPropertyCreator (core::pack::task::operation)	StubID (core::id)
BurialEnergyCreator (core::scoring::methods)	EnvEnergy (core::scoring::methods)	MembraneEnvSmoothEnergy (core::scoring::methods)	ResidueLevelTask (core::pack::task)	SuckerEnergy (core::scoring::methods)
C	EnvEnergyCreator (core::scoring::methods)	MembraneEnvSmoothEnergyCreator (core::scoring::methods)	ResidueLevelTask_ (core::pack::task)	SuckerEnergyCreator (core::scoring::methods)
	EnvPairPotential (core::scoring)	MembraneInfo (core::conformation::membrane)	ResidueLoader (core::chemical)	SumFunc (core::scoring::func)
CaCbCb_Angle_Func (core::scoring::disulfides)	EnvSmoothEnergy (core::scoring::methods)	MembraneLipo (core::scoring::methods)	ResidueLoaderCreator (core::chemical)	SurfaceBackgroundEdge (core::pack::interaction_graph)
CaCbCbCa_Dihedral_Func (core::scoring::disulfides)	EnvSmoothEnergyCreator (core::scoring::methods)	MembraneLipoCreator (core::scoring::methods)	ResidueLoaderOptions (core::chemical)	SurfaceBackgroundNode (core::pack::interaction_graph)
CacheableAtomID_MapVector (core::id)	Etable (core::scoring::etable)	MembranePotential (core::scoring)	ResidueLoaderOptionsCreator (core::chemical)	SurfaceEdge (core::pack::interaction_graph)
CacheableDataType (core::pose::datacache)	EtableAtom (core::scoring::etable::etrie)	MembraneProteinFactory (core::membrane)	ResidueMatcher (core::conformation)	SurfaceEnergies (core::scoring::solid_surface)
CacheableObserver (core::pose::datacache)	EtableEnergyCreator (core::scoring::etable)	MembraneProtocolConfigLib (core::membrane::config)	ResidueName3Is (core::pack::task::operation)	SurfaceEnergy (core::pack::interaction_graph)
CacheableObserverType (core::pose::datacache)	EtableEvaluator (core::scoring::etable)	MembraneResidueFactory (core::membrane::geometry)	ResidueName3IsCreator (core::pack::task::operation)	SurfaceEnergyCreator (core::pack::interaction_graph)
CacheablePoseRawPtr (core::pose::datacache)	EtableFunc (core::scoring::func)	MembraneTopology (core::scoring)	ResidueName3Isnt (core::pack::task::operation)	SurfaceInteractionGraph (core::pack::interaction_graph)
CacheableSequenceProfile (core::sequence)	EtableOptions (core::scoring::etable)	MetalloPlacementEnergy (core::scoring::methods)	ResidueName3IsntCreator (core::pack::task::operation)	SurfaceNode (core::pack::interaction_graph)
CacheWrapper (core::fragment)	EtableParamsOnePair (core::scoring::etable)	MetaPoseInputStream (core::import_pose::pose_stream)	ResidueNblistData (core::scoring)	SurfacePotential (core::pack::interaction_graph)
CalculatorFactory (core::pose::metrics)	Event (core::scoring::packstat)	MinDebug (core::optimization::symmetry)	ResidueNeighborConstIterator (core::scoring)	SurfEnergy (core::scoring::packing)
CarbohydrateInfo (core::chemical::carbohydrates)	EX (core::pack::task)	MinimizationEdge (core::scoring)	ResidueNeighborIterator (core::scoring)	SurfEnergyCreator (core::scoring::packing)
CarbonHBondEnergy (core::scoring::carbon_hbonds)	EX_CUTOFF (core::pack::task)	MinimizationGraph (core::scoring)	ResiduePairNeighborList (core::scoring)	SurfVol (core::scoring::packing)
CarbonHBondEnergyCreator (core::scoring::carbon_hbonds)	ExactOccludedHbondSolEnergy (core::scoring::geometric_solvation)	MinimizationNode (core::scoring)	ResiduePairXYZ (core::scoring::func)	SurfVolDeriv (core::scoring::packing)
CarbonHBondPotential (core::scoring::carbon_hbonds)	ExactOccludedHbondSolEnergyCreator (core::scoring::geometric_solvation)	Minimizer (core::optimization)	ResiduePDBIndexIs (core::pack::task::operation)	SurfVolEnergy (core::scoring::packing)
CartBondedParameters (core::scoring::methods)	ExactResidueMatcher (core::conformation)	MinimizerMap (core::optimization)	ResiduePDBIndexIsCreator (core::pack::task::operation)	SurfVolEnergyCreator (core::scoring::packing)
CartesianBondedEnergy (core::scoring::methods)	ExcludedResPredicate (core::scoring)	MinimizerMapBase (core::kinematics)	ResiduePDBIndexIsnt (core::pack::task::operation)	SVNVersion (core)
CartesianBondedEnergyCreator (core::scoring::methods)	EXCN_AtomNotFound (core::id)	MinimizerOptions (core::optimization)	ResiduePDBIndexIsntCreator (core::pack::task::operation)	SWAligner (core::sequence)
CartesianMinimizer (core::optimization)	EXCN_Env_Exception (core::environment)	MiniPose (core::pose)	ResiduePDBInfoHasLabel (core::pack::task::operation)	SymAtomTreeMinimizer (core::optimization::symmetry)
CartesianMinimizerMap (core::optimization)	EXCN_FTSketchGraph (core::environment)	MinMultiHarmonicFunc (core::scoring::func)	ResiduePDBInfoHasLabelCreator (core::pack::task::operation)	SymAtomTreeMultifunc (core::optimization::symmetry)
CartesianMultifunc (core::optimization)	EXCN_Illegal_Arguments (core::conformation::membrane)	MinScoreScoreFunction (core::scoring)	ResiduePDBInfoLacksLabel (core::pack::task::operation)	SymDof (core::conformation::symmetry)
CartGrid (core::grid)	EXCN_InvalidFoldTree (core::kinematics)	MissingEnergy (core::scoring::methods)	ResiduePDBInfoLacksLabelCreator (core::pack::task::operation)	SymmData (core::conformation::symmetry)
CartSCMinMinimizerMap (core::pack::scmin)	EXCN_Membrane (core::conformation::membrane)	MissingEnergyCreator (core::scoring::methods)	PDBInfo::ResidueRecord (core::pose)	SymmDataFactory (core::conformation::symmetry)
CartSCMinMultifunc (core::pack::scmin)	EXCN_Membrane_Bounds (core::conformation::membrane)	MixtureFunc (core::scoring::func)	ResidueSelector (core::pack::task::residue_selector)	SymmDataLoader (core::conformation::symmetry)
CavityBall (core::scoring::packstat)	EXCN_MembraneFoldTree (core::conformation::membrane)	MMAtomType (core::chemical)	ResidueSelector (core::chemical)	SymmDataLoaderCreator (core::conformation::symmetry)
CavityBallCluster (core::scoring::packstat)	EXCN_NonMembrane (core::conformation::membrane)	MMAtomTypeSet (core::chemical)	ResidueSelectorCreator (core::pack::task::residue_selector)	SymmDataOptions (core::conformation::symmetry)
CB_Angle_Func (core::scoring::disulfides)	EXCN_Resource_Definition (core::conformation::membrane)	MMBondAngleEnergy (core::scoring::methods)	ResidueSelectorFactory (core::pack::task::residue_selector)	SymmDataOptionsCreator (core::conformation::symmetry)
Cb_Distance_Func (core::scoring::disulfides)	EXCN_VirtualRsd (core::conformation::membrane)	MMBondAngleEnergyCreator (core::scoring::methods)	ResidueSelectorRegistrator (core::pack::task::residue_selector)	SymmetricConformation (core::conformation::symmetry)
CBSG_Dihedral_Func (core::scoring::disulfides)	ExtendAlignerSW (core::sequence)	MMBondAngleLibrary (core::scoring::mm)	ResidueSelectorSingle (core::chemical)	SymmetricEnergies (core::scoring::symmetry)
Cell (core::sequence)	ExtendedPoseInputStream (core::import_pose::pose_stream)	MMBondAngleResidueTypeParam (core::scoring::mm)	ResidueType (core::chemical)	SymmetricLigandEnergy (core::scoring::methods)
Cen_Distance_Func (core::scoring::disulfides)	Extent (core::fragment::picking_old::concepts)	MMBondAngleResidueTypeParamSet (core::scoring::mm)	ResidueTypeConstraint (core::scoring::constraints)	SymmetricLigandEnergyCreator (core::scoring::methods)
CenHBEnergy (core::scoring::methods)	ExtentEvaluator (core::fragment::picking_old::concepts)	MMBondAngleScore (core::scoring::mm)	ResidueTypeFilter (core::pack::task::operation)	SymmetricRotamerSet_ (core::pack::rotamer_set::symmetry)
CenHBEnergyCreator (core::scoring::methods)	ExtentGenerator (core::fragment::picking_old::concepts)	MMBondLengthEnergy (core::scoring::methods)	ResidueTypeFilterCreator (core::pack::task::operation)	SymmetricRotamerSetFactory (core::pack::rotamer_set::symmetry)
CenHBPotential (core::scoring)	ExtraChiCutoff (core::pack::task::operation)	MMBondLengthEnergyCreator (core::scoring::methods)	ResidueTypeKinWriter (core::chemical)	SymmetricRotamerSets (core::pack::rotamer_set::symmetry)
CenListInfo (core::scoring)	ExtraChiCutoffCreator (core::pack::task::operation)	MMBondLengthLibrary (core::scoring::mm)	ResidueTypeLinkingConstraint (core::scoring::constraints)	SymmetricScoreFunction (core::scoring::symmetry)
CenPairEnergy (core::scoring::methods)	ExtraQuadraticRepulsion (core::scoring::etable)	MMBondLengthScore (core::scoring::mm)	ResidueTypeSet (core::chemical)	SymmetryInfo (core::conformation::symmetry)
CenPairEnergyCreator (core::scoring::methods)	ExtraRotamers (core::pack::task::operation)	MMEnergyTableAtom (core::scoring::mm::mmtrie)	ResidueXYZ (core::scoring::func)	SymMinimizerMap (core::optimization::symmetry)
CenRotDunEnergy (core::pack::dunbrack::cenrot)	ExtraRotamersCreator (core::pack::task::operation)	MMLJEnergyInter (core::scoring::methods)	ResLvlTaskOperation (core::pack::task::operation)	SymmLinearMemEdge (core::pack::interaction_graph)
CenRotDunEnergyCreator (core::pack::dunbrack::cenrot)	ExtraRotamersGeneric (core::pack::task::operation)	MMLJEnergyInterCreator (core::scoring::methods)	ResLvlTaskOperationCreator (core::pack::task::operation)	SymmLinearMemNode (core::pack::interaction_graph)
CenRotEnvEnergy (core::scoring::methods)	ExtraRotamersGenericCreator (core::pack::task::operation)	MMLJEnergyIntra (core::scoring::methods)	ResLvlTaskOperationFactory (core::pack::task::operation)	SymmLinearMemoryInteractionGraph (core::pack::interaction_graph)
CenRotEnvEnergyCreator (core::scoring::methods)	F	MMLJEnergyIntraCreator (core::scoring::methods)	ResLvlTaskOperationRegistrator (core::pack::task::operation)	SymmMinimalistEdge (core::pack::interaction_graph)
CenRotEnvPairPotential (core::scoring)		MMLJEnergyTable (core::scoring::mm)	DisulfideFile::ResNum (core::io::raw_data)	SymmMinimalistInteractionGraph (core::pack::interaction_graph)
CenRotPairEnergy (core::scoring::methods)	FA_ElecEnergy (core::scoring::elec)	MMLJLibrary (core::scoring::mm)	RespairInteractions (core::scoring::custom_pair_distance)	SymmMinimalistNode (core::pack::interaction_graph)
CenRotPairEnergyCreator (core::scoring::methods)	FA_ElecEnergyAroAll (core::scoring::elec)	MMLJScore (core::scoring::mm)	ResPairMinimizationData (core::scoring)	SymmOnTheFlyEdge (core::pack::interaction_graph)
CentroidDisulfideEnergy (core::scoring::disulfides)	FA_ElecEnergyAroAllCreator (core::scoring::elec)	MMTorsionEnergy (core::scoring::methods)	ResRangePredicate (core::scoring)	SymmOnTheFlyInteractionGraph (core::pack::interaction_graph)
CentroidDisulfideEnergyComponents (core::scoring::disulfides)	FA_ElecEnergyAroAro (core::scoring::elec)	MMTorsionEnergyCreator (core::scoring::methods)	ResResEnergyInvoker (core::scoring::etable)	SymmOnTheFlyNode (core::pack::interaction_graph)
CentroidDisulfideEnergyContainer (core::scoring::disulfides)	FA_ElecEnergyAroAroCreator (core::scoring::elec)	MMTorsionLibrary (core::scoring::mm)	ResSingleMinimizationData (core::scoring)	SymSlideInfo (core::conformation::symmetry)
CentroidDisulfideEnergyCreator (core::scoring::disulfides)	FA_ElecEnergyCreator (core::scoring::elec)	MMTorsionScore (core::scoring::mm)	RestrictAbsentCanonicalAAS (core::pack::task::operation)	T
CentroidDisulfideNeighborConstIterator (core::scoring::disulfides)	Fa_MbenvEnergy (core::scoring::methods)	MolData (core::chemical::sdf)	RestrictAbsentCanonicalAASCreator (core::pack::task::operation)
CentroidDisulfideNeighborIterator (core::scoring::disulfides)	Fa_MbenvEnergyCreator (core::scoring::methods)	MolecularSurfaceCalculator (core::scoring::sc)	RestrictAbsentCanonicalAASRLT (core::pack::task::operation)	TableLookupEtableEnergy (core::scoring::etable)
CentroidDisulfidePotential (core::scoring::disulfides)	Fa_MbsolvEnergy (core::scoring::methods)	MolFileParser (core::chemical::sdf)	RestrictAbsentCanonicalAASRLTCreator (core::pack::task::operation)	TableLookupEvaluator (core::scoring::etable)
CentroidRotamerSampleData (core::pack::dunbrack::cenrot)	Fa_MbsolvEnergyCreator (core::scoring::methods)	MolWriter (core::chemical::sdf)	RestrictResidueToRepacking (core::pack::task::operation)	TARGET (core::pack::task)
ChainbreakEnergy (core::scoring::methods)	FabConstraint (core::scoring::constraints)	MoveMap (core::kinematics)	RestrictResidueToRepackingCreator (core::pack::task::operation)	TaskFactory (core::pack::task)
ChainbreakEnergyCreator (core::scoring::methods)	FabConstraintCreator (core::scoring::constraints)	MultiConstraint (core::scoring::constraints)	RestrictToInterface (core::pack::task::operation)	TaskOperation (core::pack::task::operation)
ChainbreakUtil (core::util)	FACTSEnergy (core::scoring::methods)	MultiConstraintCreator (core::scoring::constraints)	RestrictToRepacking (core::pack::task::operation)	TaskOperationCreator (core::pack::task::operation)
ChainIs (core::pack::task::operation)	FACTSEnergyCreator (core::scoring::methods)	MultiCoolAnnealer (core::pack::annealer)	RestrictToRepackingCreator (core::pack::task::operation)	TaskOperationFactory (core::pack::task::operation)
ChainIsCreator (core::pack::task::operation)	FACTSPoseInfo (core::scoring)	Multifunc (core::optimization)	RestrictToRepackingRLT (core::pack::task::operation)	TaskOperationRegistrator (core::pack::task::operation)
ChainIsnt (core::pack::task::operation)	FACTSPotential (core::scoring)	MultiProbePerSphereAccumulator (core::scoring::packstat)	RestrictToRepackingRLTCreator (core::pack::task::operation)	TenANeighborEdge (core::scoring)
ChainIsntCreator (core::pack::task::operation)	FACTSResidueInfo (core::scoring)	MultiProbePoseAccumulator (core::scoring::packstat)	RestrictYSDesign (core::pack::task::operation)	TenANeighborGraph (core::scoring)
ResiduePDBIndexIs::ChainPos (core::pack::task::operation)	FACTSRotamerSetInfo (core::scoring)	N	RestrictYSDesignCreator (core::pack::task::operation)	TenANeighborNode (core::scoring)
ChainSelector (core::pack::task::residue_selector)	FACTSRsdTypeInfo (core::scoring)		RG_Energy (core::scoring::methods)	TMscore (core::scoring)
ChainSelectorCreator (core::pack::task::residue_selector)	FadeFunc (core::scoring::func)	NamedAtomID (core::id)	RG_Energy_Fast (core::scoring::methods)	TMscoreStore (core::scoring)
CharmmPeriodicFunc (core::scoring::func)	FadeInterval (core::scoring::hbonds)	NamedAtomPairConstraint (core::scoring::constraints)	RG_Energy_FastCreator (core::scoring::methods)	TopOutFunc (core::scoring::func)
ChemicalManager (core::chemical)	FastDensEnergy (core::scoring::electron_density)	NamedStubID (core::id)	RG_Energy_RNA (core::scoring::rna)	TorsionFourierComponent (core::scoring::dna)
ChemicalShiftAnisotropy (core::scoring)	FastDensEnergyCreator (core::scoring::electron_density)	NATAA (core::pack::task)	RG_Energy_RNACreator (core::scoring::rna)	TorsionID (core::id)
ChemicalShiftAnisotropyEnergy (core::scoring::methods)	FASTERAnnealer (core::pack::annealer)	NATRO (core::pack::task)	RG_Local_MinData (core::scoring::methods)	TorsionID_Range (core::id)
ChemicalShiftAnisotropyEnergyCreator (core::scoring::methods)	FASTEREdge (core::pack::interaction_graph)	NBListCache (core::scoring::symmetry)	RG_LocalEnergy (core::scoring::methods)	TorsionInfoSet (core::fragment)
ChemicalShiftData (core::scoring::rna::chemical_shift)	FASTERInteractionGraph (core::pack::interaction_graph)	NC (core::pack::task)	RG_LocalEnergyCreator (core::scoring::methods)	Translator (core::coarse)
ChemicalShiftScoringScheme (core::sequence)	FASTERNode (core::pack::interaction_graph)	NCAARotLibPath (core::chemical)	RG_MinData (core::scoring::methods)	TranslatorSet (core::coarse)
ChemicalShiftSequence (core::sequence)	FastSAXSEnergy (core::scoring::saxs)	NCaCaC_Dihedral_Func (core::scoring::disulfides)	RingConformer (core::chemical)	TreeVizBuilder (core::kinematics)
ChemicalShiftSequenceCreator (core::sequence)	FastSAXSEnergyCreator (core::scoring::saxs)	NegSpaceElement (core::graph)	RingConformerSet (core::chemical)	TrieCollection (core::scoring::trie)
ChiSet (core::pack::dunbrack)	Field (core::io::pdb)	NeighborhoodResidueSelector (core::pack::task::residue_selector)	RMS_Energy (core::scoring::methods)	TrieCountPair1BC3 (core::scoring::etable::etrie)
Circle (core::scoring::packstat)	FileData (core::io::pdb)	NeighborhoodResidueSelectorCreator (core::pack::task::residue_selector)	RMS_EnergyCreator (core::scoring::methods)	TrieCountPair1BC4 (core::scoring::etable::etrie)
CircularGeneral1D_Func (core::scoring::func)	FileDataOptions (core::io::pdb)	NeighborList (core::scoring)	RNA_AtomVDW (core::scoring::rna)	TrieCountPairAll (core::scoring::etable::etrie)
CircularHarmonicFunc (core::scoring::func)	FirstClassEdge (core::pack::interaction_graph)	NelderMeadSimplex (core::optimization)	RNA_BaseBaseEnergy (core::scoring::rna)	TrieCountPairBase (core::scoring::trie)
CircularPowerFunc (core::scoring::func)	FirstClassNode (core::pack::interaction_graph)	NMerPSSMEnergy (core::scoring::methods)	RNA_BulgeEnergy (core::scoring::rna)	TrieCountPairGeneric (core::scoring::etable::etrie)
CircularSigmoidalFunc (core::scoring::func)	FIX_HIS_TAUTOMER (core::pack::task)	NMerPSSMEnergyCreator (core::scoring::methods)	RNA_BulgeEnergyCreator (core::scoring::rna)	TrieCountPairNone (core::scoring::etable::etrie)
CoarseEtable (core::coarse)	FixbbCoupledRotamerSimAnnealer (core::pack::annealer)	NMerRefEnergy (core::scoring::methods)	RNA_CentroidInfo (core::scoring::rna)	TrieNode (core::scoring::trie)
CoarseEtableEnergy (core::scoring::etable)	FixbbLinkingRotamerSimAnnealer (core::pack::annealer)	NMerRefEnergyCreator (core::scoring::methods)	RNA_ChemicalShiftEnergy (core::scoring::rna::chemical_shift)	TwelveANeighborEdge (core::scoring)
CoarseEtableEnergyCreator (core::scoring::etable)	FixbbRotamerSets (core::pack::rotamer_set)	NMerSVMEnergy (core::scoring::methods)	RNA_ChemicalShiftEnergyCreator (core::scoring::rna::chemical_shift)	TwelveANeighborGraph (core::scoring)
CoarseRotamer (core::pack::dunbrack)	FixbbSimAnnealer (core::pack::annealer)	NMerSVMEnergyCreator (core::scoring::methods)	RNA_ChemicalShiftPotential (core::scoring::rna::chemical_shift)	TwelveANeighborNode (core::scoring)
CoarseRotamerSet (core::pack::dunbrack)	FixedBBEdge (core::pack::interaction_graph)	NO_ADDUCTS (core::pack::task)	RNA_CS_parameters (core::scoring::rna::chemical_shift)	TwoBodyEnergy (core::scoring::methods)
CoarseSingleResidueLibrary (core::pack::dunbrack)	FixedBBInteractionGraph (core::pack::interaction_graph)	Node (core::kinematics)	RNA_CS_residue_parameters (core::scoring::rna::chemical_shift)	U
CompassScoringScheme (core::sequence)	FixedBBNode (core::pack::interaction_graph)	FoldTreeSketch::Node (core::environment)	RNA_DataBackboneEnergy (core::scoring::rna)
CompositeScoringScheme (core::sequence)	FlatHarmonicFunc (core::scoring::func)	Node (core::graph)	RNA_DataBackboneEnergyCreator (core::scoring::rna)	UEEdge (core::graph)
CompositeSequence (core::sequence)	FoldTree (core::kinematics)	NodeBase (core::pack::interaction_graph)	RNA_DataInfo (core::scoring::rna)	UEVertex (core::graph)
CompositeSequenceCreator (core::sequence)	FoldTreeSketch (core::environment)	NonContinuousFrame (core::fragment)	RNA_Datum (core::scoring::rna)	UltraLightResidue (core::conformation)
Computes	FormFactor (core::scoring::saxs)	NonResidueTypeConstraint (core::scoring::constraints)	RNA_FA_ElecEnergy (core::scoring::elec)	UnboundRotamersOperation (core::pack::rotamer_set)
Conformation (core::conformation)	FormFactorManager (core::scoring::saxs)	NoRepackDisulfides (core::pack::task::operation)	RNA_FA_ElecEnergyCreator (core::scoring::elec)	UnfoldedStateEnergy (core::scoring::methods)
ConformationEvent (core::pose::signals)	FourPointsFunc (core::scoring::func)	NoRepackDisulfidesCreator (core::pack::task::operation)	RNA_FilteredBaseBaseInfo (core::scoring::rna)	UnfoldedStateEnergyCreator (core::scoring::methods)
ConformationKinWriter (core::conformation)	FragCache (core::fragment)	NoResFilter (core::pack::task::operation)	RNA_FittedTorsionInfo (core::chemical::rna)	UnfoldedStatePotential (core::scoring)
ConformationXYZ (core::scoring::func)	FragData (core::fragment)	NoResFilterCreator (core::pack::task::operation)	RNA_FullAtomStackingEnergy (core::scoring::rna)	UnrecognizedAtomRecord (core::pose)
ConnectionEvent (core::conformation::signals)	FragFactory (core::fragment)	NOTAA (core::pack::task)	RNA_FullAtomStackingEnergyCreator (core::scoring::rna)	UpJumpSRFD (core::fragment)
ConstantConstraint (core::scoring::constraints)	FragID (core::fragment)	NotResidueSelector (core::pack::task::residue_selector)	RNA_FullAtomVDW_BasePhosphate (core::scoring::rna)	UpperEdgeGraph (core::graph)
ConstantFunc (core::scoring::func)	FragID_Iterator (core::fragment)	NotResidueSelectorCreator (core::pack::task::residue_selector)	RNA_FullAtomVDW_BasePhosphateCreator (core::scoring::rna)	USE_INPUT_SC (core::pack::task)
ConstantLengthFragSet (core::fragment)	FragmentIO (core::fragment)	NumDerivCheckData (core::optimization)	RNA_IdealCoord (core::pose::rna)	USOGFunc (core::scoring::func)
ConstantLengthFragSetIterator_ (core::fragment)	FragmentLibraryManager (core::fragment::picking_old)	NumericalDerivCheckResult (core::optimization)	RNA_LJ_BaseEnergy (core::scoring::rna)	V
ConstFrameIterator (core::fragment)	FragmentRmsd (core::fragment)	NumNeighborsSelector (core::pack::task::residue_selector)	RNA_LJ_BaseEnergyCreator (core::scoring::rna)
Constraint (core::scoring::constraints)	FragSet (core::fragment)	NumNeighborsSelectorCreator (core::pack::task::residue_selector)	RNA_LowResolutionPotential (core::scoring::rna)	V2Parser (core::chemical::sdf)
ConstraintCreator (core::scoring::constraints)	FragSetCollection (core::fragment)	NVlookup (core::scoring::nv)	RNA_Mg_Energy (core::scoring::rna)	V3Parser (core::chemical::sdf)
ConstraintEdge (core::scoring::constraints)	FragStore (core::fragment)	NVscore (core::scoring::nv)	RNA_Mg_EnergyCreator (core::scoring::rna)	VallFragmentEval (core::fragment::picking_old::vall::eval)
ConstraintFactory (core::scoring::constraints)	Frame (core::fragment)	NVscoreCreator (core::scoring::nv)	RNA_Mg_KnowledgeBasedPotential (core::scoring::rna)	VallFragmentGen (core::fragment::picking_old::vall::gen)
ConstraintGraph (core::scoring::constraints)	FrameIterator (core::fragment)	NWAligner (core::sequence)	RNA_PairwiseLowResolutionEnergy (core::scoring::rna)	VallFragmentScore (core::fragment::picking_old::vall::scores)
ConstraintIO (core::scoring::constraints)	FrameIteratorWorker_ (core::fragment)	O	RNA_PairwiseLowResolutionEnergyCreator (core::scoring::rna)	VallLibrarian (core::fragment::picking_old::vall)
ConstraintNode (core::scoring::constraints)	FrameList (core::fragment)		RNA_RawBaseBaseInfo (core::scoring::rna)	VallLibrary (core::fragment::picking_old::vall)
ConstraintRegistrator (core::scoring::constraints)	FrameListIterator_ (core::fragment)	ObserverCache (core::pose::datacache)	RNA_ResidueLevelTask (core::pack::task::rna)	VallResidue (core::fragment::picking_old::vall)
Constraints (core::scoring::constraints)	FreeMoietyEnergy (core::scoring::methods)	Obsolet_NamedAtomPairConstraint (core::scoring::constraints)	RNA_ResidueType (core::chemical::rna)	VallResidues (core::fragment::picking_old::vall)
ConstraintsEnergy (core::scoring::constraints)	FreeMoietyEnergyCreator (core::scoring::methods)	OccludedHbondSolEnergy (core::scoring::geometric_solvation)	RNA_ScoringInfo (core::scoring::rna)	VallSection (core::fragment::picking_old::vall)
ConstraintsEnergyCreator (core::scoring::constraints)	FreeResidueBonusEnergy (core::scoring::methods)	OccludedHbondSolEnergy_onebody (core::scoring::geometric_solvation)	RNA_SilentStruct (core::io::silent)	VallSections (core::fragment::picking_old::vall)
ConstraintSet (core::scoring::constraints)	FreeResidueBonusEnergyCreator (core::scoring::methods)	OccludedHbondSolEnergy_onebodyCreator (core::scoring::geometric_solvation)	RNA_SilentStructCreator (core::io::silent)	VDW_Energy (core::scoring::vdwaals)
ContactOrderEnergy (core::scoring::methods)	FullatomCustomPairDistanceEnergy (core::scoring::custom_pair_distance)	OccludedHbondSolEnergyCreator (core::scoring::geometric_solvation)	RNA_SugarCloseEnergy (core::scoring::rna)	VDW_EnergyCreator (core::scoring::vdwaals)
ContactOrderEnergyCreator (core::scoring::methods)	FullatomCustomPairDistanceEnergyCreator (core::scoring::custom_pair_distance)	Octree2D (core::scoring::packstat)	RNA_SugarCloseEnergyCreator (core::scoring::rna)	VDWAtom (core::scoring::vdwaals)
ContextDependentLRTwoBodyEnergy (core::scoring::methods)	FullatomDisulfideEnergy (core::scoring::disulfides)	OffsetPeriodicBoundFunc (core::scoring::constraints)	RNA_SuiteAssignment (core::pose::rna)	VDWTrieCountPair1B (core::scoring::vdwaals)
ContextDependentOneBodyEnergy (core::scoring::methods)	FullatomDisulfideEnergyComponents (core::scoring::disulfides)	OmegaTether (core::scoring)	RNA_SuiteInfo (core::pose::rna)	VDWTrieEvaluator (core::scoring::vdwaals)
ContextDependentTwoBodyEnergy (core::scoring::methods)	FullatomDisulfideEnergyContainer (core::scoring::disulfides)	OmegaTetherEnergy (core::scoring::methods)	RNA_SuiteName (core::pose::rna)	VectorCacheUnit (core::fragment)
ContextGraph (core::scoring)	FullatomDisulfideEnergyCreator (core::scoring::disulfides)	OmegaTetherEnergyCreator (core::scoring::methods)	RNA_TorsionEnergy (core::scoring::rna)	VirtualCoordinate (core::conformation::symmetry)
ContextGraphFactory (core::scoring)	FullatomDisulfideParams13 (core::scoring::disulfides)	OneBodyEnergy (core::scoring::methods)	RNA_TorsionEnergyCreator (core::scoring::rna)	VirtualCoordinates (core::conformation::symmetry)
ContextIndependentGeometricSolEnergy (core::scoring::geometric_solvation)	FullatomDisulfidePotential (core::scoring::disulfides)	OneGaussianScattering (core::scoring::electron_density)	RNA_TorsionPotential (core::scoring::rna)	W
ContextIndependentGeometricSolEnergyCreator (core::scoring::geometric_solvation)	FullModelInfo (core::pose::full_model_info)	OneToAllEnergyContainer (core::scoring)	RNA_VDW_Energy (core::scoring::rna)
ContextIndependentLRTwoBodyEnergy (core::scoring::methods)	FullModelParameters (core::pose::full_model_info)	OneToAllNeighborConstIterator (core::scoring)	RNA_VDW_EnergyCreator (core::scoring::rna)	WaterAdductHBondEnergy (core::scoring::methods)
ContextIndependentOneBodyEnergy (core::scoring::methods)	Func (core::scoring::func)	OneToAllNeighborIterator (core::scoring)	RotamerAssigningAnnealer (core::pack::annealer)	WaterAdductHBondEnergyCreator (core::scoring::methods)
ContextIndependentTwoBodyEnergy (core::scoring::methods)	FuncFactory (core::scoring::func)	OnTheFlyEdge (core::pack::interaction_graph)	RotamerBuildingData (core::pack::dunbrack)	WaterAdductHBondPotential (core::scoring)
ContinuousRotamerSet (core::pack::rotamer_set)	G	OnTheFlyInteractionGraph (core::pack::interaction_graph)	RotamerConstraint (core::pack::dunbrack)	WaterAdductIntraEnergy (core::scoring::methods)
ContinuousRotamerSets (core::pack::rotamer_set)		OnTheFlyNode (core::pack::interaction_graph)	RotamerCouplings (core::pack::rotamer_set)	WaterAdductIntraEnergyCreator (core::scoring::methods)
ConvergenceTest (core::optimization)	G	OperateOnCertainResidues (core::pack::task::operation)	RotamerDescriptor (core::scoring::trie)	WaterAnchorInfo (core::pack::rotamer_set)
CoordinateConstraint (core::scoring::constraints)	GA_Minimizer (core::optimization)	OperateOnCertainResiduesCreator (core::pack::task::operation)	RotamerDescriptorAtom (core::scoring::trie)	WaterBuilder (core::scoring::methods)
CoordinateConstraintCreator (core::scoring::constraints)	GasteigerAtomTypeData (core::chemical::gasteiger)	OperateOnResidueSubset (core::pack::task::operation)	RotamerDots (core::pack::interaction_graph)	WaterPackingInfo (core::pack::rotamer_set)
CopyDofs (core::pose::copydofs)	GasteigerAtomTypeSet (core::chemical::gasteiger)	OperateOnResidueSubsetCreator (core::pack::task::operation)	RotamerDotsCache (core::pack::interaction_graph)	WaterWeightGridSet (core::scoring::geometric_solvation)
Coulomb (core::scoring::etable::coulomb)	GaussianChainDoubleFunc (core::scoring::func)	OptCysHG (core::pack::task::operation)	RotamerDotsRadiusData (core::pack::interaction_graph)	WatsonCrickResidueMatcher (core::conformation)
CountPair1B (core::scoring::etable::count_pair)	GaussianChainFunc (core::scoring::func)	OptCysHGCreator (core::pack::task::operation)	RotamerExplosion (core::pack::task::operation)	WholeStructureEnergy (core::scoring::methods)
CountPairAll (core::scoring::etable::count_pair)	GaussianChainQuadrupleFunc (core::scoring::func)	OptH (core::pack::task::operation)	RotamerExplosionCreator (core::pack::task::operation)	WholeWholeEnergyInvoker (core::scoring::etable)
CountPairCrossover3 (core::scoring::etable::count_pair)	GaussianChainSingleFunc (core::scoring::func)	OptHCreator (core::pack::task::operation)	RotamericData (core::pack::dunbrack)	X
CountPairCrossover4 (core::scoring::etable::count_pair)	GaussianChainTripleFunc (core::scoring::func)	Orbital (core::chemical)	RotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)
CountPairData_1_1 (core::scoring::etable::etrie)	GaussianFunc (core::scoring::func)	OrbitalsAssigned (core::scoring::orbitals)	RotamerLibrary (core::pack::dunbrack)	XtalMLEnergy (core::scoring::cryst)
CountPairData_1_2 (core::scoring::etable::etrie)	GaussianOverlapEnergy (core::scoring::methods)	OrbitalsLookup (core::scoring::orbitals)	RotamerLibraryScratchSpace (core::pack::dunbrack)	XtalMLEnergyCreator (core::scoring::cryst)
CountPairData_1_3 (core::scoring::etable::etrie)	GaussianOverlapEnergyCreator (core::scoring::methods)	OrbitalsScore (core::scoring::orbitals)	RotamerLinks (core::pack::rotamer_set)	XYZ_Func (core::scoring::func)
CountPairDataGeneric (core::scoring::etable::etrie)	GaussianParameter (core::chemical::rna)	OrbitalsScoreCreator (core::scoring::orbitals)	RotamerOperation (core::pack::rotamer_set)	XYZEvent (core::conformation::signals)
CountPairFactory (core::scoring::etable::count_pair)	GenBornEnergy (core::scoring::methods)	OrbitalsStatistics (core::scoring::orbitals)	RotamerSet (core::pack::rotamer_set)	Y
CountPairFunction (core::scoring::etable::count_pair)	GenBornEnergyCreator (core::scoring::methods)	OrbitalType (core::chemical::orbitals)	RotamerSet_ (core::pack::rotamer_set)
CountPairGeneric (core::scoring::etable::count_pair)	GenBornPoseInfo (core::scoring)	OrbitalTypeMapper (core::chemical::orbitals)	RotamerSetBase (core::conformation)	YHHPlanarityEnergy (core::scoring::methods)
CountPairIntraRes (core::scoring::etable::count_pair)	GenBornPotential (core::scoring)	OrbitalTypeSet (core::chemical::orbitals)	RotamerSetFactory (core::pack::rotamer_set)	YHHPlanarityEnergyCreator (core::scoring::methods)
CountPairIntraResC3 (core::scoring::etable::count_pair)	GenBornResidueInfo (core::scoring)	OrbitalXYZCoords (core::conformation::orbitals)	RotamerSetOperation (core::pack::rotamer_set)	_
CountPairIntraResC4 (core::scoring::etable::count_pair)	GenBornRotamerSetInfo (core::scoring)	OrderCavBallOnR (core::scoring::packstat)	RotamerSets (core::pack::rotamer_set)
CountPairNone (core::scoring::etable::count_pair)	GeneralEvent (core::pose::signals)	OrderCavBallOnRmAnb (core::scoring::packstat)	RotamerSetsBase (core::pack::rotamer_set)	_ATOM_RADIUS (core::scoring::sc)
CountViolFunc (core::scoring::func)	GeneralEvent (core::conformation::signals)	OrderCavBallOnRmE (core::scoring::packstat)	RotamerSubset (core::pack::rotamer_set)	_DOT (core::scoring::sc)
CPDataCorrespondence (core::scoring::trie)	GenericResidueConnectionData (core::scoring::etable::etrie)	OrderCavBallOnX (core::scoring::packstat)	RotamerSubsets (core::pack::rotamer_set)	_PROBE (core::scoring::sc)
CrossoverBehavior	GenericRule (core::coarse)	OrderCBC (core::scoring::packstat)	RotamerTrie (core::scoring::trie)	_RESULTS (core::scoring::sc)
CrystInfo (core::pose)	GeometricSolEnergy (core::scoring::geometric_solvation)	OrderedFragSet (core::fragment)	RotamerTrieBase (core::scoring::trie)	a
CSA (core::scoring)	GeometricSolEnergyCreator (core::scoring::geometric_solvation)	OrderedFragSetIterator_ (core::fragment)	RotSub (core::pack::annealer)
CSD_TorsionEnergy (core::scoring::methods)	GeometricSolEnergyEvaluator (core::scoring::geometric_solvation)	OrderSphereOnID (core::scoring::packstat)	RT (core::kinematics)	addedH (core::chemical::sdf)
CstEnergyContainer (core::scoring::constraints)	GoapEnergy (core::scoring::methods)	OrderSphereOnX (core::scoring::packstat)	RT_helper (core::scoring::disulfides)	atoms_and_func_struct (core::scoring::custom_pair_distance)
CstMinimizationData (core::scoring::constraints)	GoapEnergyCreator (core::scoring::methods)	OrResidueSelector (core::pack::task::residue_selector)	RTMin (core::pack)	atomTyper (core::chemical::sdf)
CstResNeighbConstIterator (core::scoring::constraints)	GoapRsdType (core::scoring::methods)	OrResidueSelectorCreator (core::pack::task::residue_selector)	Rule (core::coarse)	c
CstResNeighbIterator (core::scoring::constraints)	Graph (core::graph)	OtherPoseEnergy (core::scoring::methods)	RuleSet (core::coarse)
CtabBase (core::chemical::sdf)	GridInfo (core::scoring::geometric_solvation)	OtherPoseEnergyCreator (core::scoring::methods)	S	RawFileData::const_iterator (core::io::raw_data)
CubicPolynomial (core::scoring::etable)	H	P		SilentFileData::const_iterator (core::io::silent)
CustomAtomPairEnergy (core::scoring::methods)			SA_Energy (core::scoring::methods)	ctabV2000Parser (core::chemical::sdf)
CustomAtomPairEnergyCreator (core::scoring::methods)	HackAroEnergy (core::scoring::hackaro)	P_AA (core::scoring)	SA_EnergyCreator (core::scoring::methods)	ctabV3000Parser (core::chemical::sdf)
D	HackAroEnergyCreator (core::scoring::hackaro)	P_AA_Energy (core::scoring::methods)	SasaCalc (core::scoring::sasa)	d
	Hairpin (core::scoring)	P_AA_EnergyCreator (core::scoring::methods)	SasaCalculator2 (core::pose::metrics::simple_calculators)
D2H_SA_Energy (core::scoring::methods)	Hairpins (core::scoring)	P_AA_pp_Energy (core::scoring::methods)	SasaCalculatorLegacy (core::pose::metrics::simple_calculators)	data_struct (core::scoring)
D2H_SA_EnergyCreator (core::scoring::methods)	HarmonicFunc (core::scoring::func)	P_AA_pp_EnergyCreator (core::scoring::methods)	SasaMethod (core::scoring::sasa)	data_structDa (core::scoring)
DatabaseOccSolEne (core::scoring::geometric_solvation)	HBAtom (core::scoring::hbonds::hbtrie)	PackedDunbrackRotamer (core::pack::dunbrack)	SasaOptions (core::scoring::packstat)	data_structDaR (core::scoring)
DC (core::scoring)	HBCountPairFunction (core::scoring::hbonds::hbtrie)	PackerTask (core::pack::task)	SasaResult (core::scoring::packstat)	data_structR (core::scoring)
DDPlookup (core::scoring::interface_)	HBCPData (core::scoring::hbonds::hbtrie)	PackerTask_ (core::pack::task)	SAXSEnergy (core::scoring::saxs)	e
DDPscore (core::scoring::interface_)	HBEvalTuple (core::scoring::hbonds)	PackingScore (core::scoring::packstat)	SAXSEnergyCEN (core::scoring::saxs)
DDPscoreCreator (core::scoring::interface_)	HBond (core::scoring::hbonds)	PackingScoreResData (core::scoring::packstat)	SAXSEnergyCreator (core::scoring::saxs)	elementToType (core::chemical::sdf)
DebuggingAnnealer (core::pack::annealer)	HBondDatabase (core::scoring::hbonds)	PackStatEnergy (core::scoring::methods)	SAXSEnergyCreatorCEN (core::scoring::saxs)	exposed_hydrophobic_data (core::pack::interaction_graph)
DecoyFileData (core::io::raw_data)	HBondDerivs (core::scoring::hbonds)	PackStatEnergyCreator (core::scoring::methods)	SAXSEnergyCreatorFA (core::scoring::saxs)	f
DecoyStruct (core::io::raw_data)	HBondEnergy (core::scoring::hbonds)	PairEnergy (core::scoring::methods)	SAXSEnergyFA (core::scoring::saxs)
DefaultCubeHash (core::conformation)	HBondEnergyCreator (core::scoring::hbonds)	PairEnergyCreator (core::scoring::methods)	SC_BB_EnergyInvoker (core::scoring::etable)	func_1d (core::optimization)
DeleteAtom (core::chemical)	HBondOptions (core::scoring::hbonds)	PairEPotential (core::scoring)	SC_SC_EnergyInvoker (core::scoring::etable)	h
DeleteProperty (core::chemical)	HBondResidueMinData (core::scoring::hbonds)	Pairing (core::scoring::dssp)	SC_Whole_EnergyInvoker (core::scoring::etable)
DenseEnergyContainer (core::scoring)	HBondResPairMinData (core::scoring::hbonds)	PairScoringScheme (core::sequence)	ScalarWeightedFunc (core::scoring::func)	history_queue_struct (core::pack::interaction_graph)
DenseNeighborConstIterator (core::scoring)	HBondSet (core::scoring::hbonds)	Particle (core::optimization)	SCAN (core::pack::task)	i
DenseNeighborIterator (core::scoring)	HBondTypeManager (core::scoring::hbonds)	ParticleSwarmMinimizer (core::optimization)	SCMinMinimizerMap (core::pack::scmin)
DensePDEdge (core::pack::interaction_graph)	HeaderInformation (core::io::pdb)	Patch (core::chemical)	SCMinMultifunc (core::pack::scmin)	RawFileData::iterator (core::io::raw_data)
DensePDInteractionGraph (core::pack::interaction_graph)	HeavyAtomFilter (core::chemical)	PatchCase (core::chemical)	ScoreFileData (core::io::raw_data)	SilentFileData::iterator (core::io::silent)
DensePDNode (core::pack::interaction_graph)	HeavyAtomWithHydrogensFilter (core::chemical)	PatchOperation (core::chemical)	ScoreFileSilentStruct (core::io::silent)	l
				lbfgs_iteration_data (core::optimization)

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