Classes
class	APBSConfig

class	APBSResult

class	APBSWrapper

class	AtomNeighbor
	an atom-atom neighborlist object More...

class	AtomVDW

class	BB_Pos

class	BondOrderParser

class	CenHBPotential

class	CenListInfo
	Keep track of the cenlist information. More...

class	CenRotEnvPairPotential

class	ChemicalShiftAnisotropy
	ChemicalShiftAnisotropys are mainly handled by this class related classed: CSA — a single line in an CSA file - representing a single csa coupling ChemicalShiftAnisotropyEnergy – an energy method which triggers computations handled by this class. More...

class	ContextGraph

class	ContextGraphFactory

class	CSA

class	data_struct

class	DC

class	DenseEnergyContainer

class	DenseNeighborConstIterator

class	DenseNeighborIterator

class	DerivVectorPair
	A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms. More...

class	DimerPairing

class	DipolarCoupling
	DipolarCouplings are mainly handled by this class related classed: DC — a single line in an DC file - representing a single dc coupling DipolarCouplingEnergy – an energy method which triggers computations handled by this class. More...

class	DockingScoreFunction

class	EMapVector
	A vector for storing energy data, initially all values are 0. More...

class	Energies
	A cached energies object. More...

class	EnergyEdge

class	EnergyGraph
	Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method. More...

class	EnergyNode

class	EnvPairPotential

class	ExcludedResPredicate

class	FACTSPoseInfo

class	FACTSPotential

class	FACTSResidueInfo

class	FACTSRotamerSetInfo

class	FACTSRsdTypeInfo

class	FACTSRsdTypeMap
	The FACTSRsdTypeMap is a collection of FACTSRsdTypeInfo for a number of residue types (This is a separate class to shield the raw pointer usage here. More...

class	GenBondedExclInfo

class	GenBornPoseInfo

class	GenBornPotential

class	GenBornResidueInfo

class	GenBornRotamerSetInfo

class	GenericBondedPotential
	Potential for core/scoring/methods/GenericBondedEnergy method. More...

class	GenTorsionParams
	Parameter set for one torsion angle. More...

struct	Hairpin

struct	Hairpins

struct	Helices

class	HydroxylTorsionPotential

class	IsMainAtomPredicate

class	IsProteinCAPredicate

class	LREnergyContainer

class	Membrane_FAEmbed
	Membrane Fullatom embedding info. More...

class	Membrane_FAPotential
	Mmebrane Fullatom Potential - Scoring Class. More...

class	MembraneEmbed
	Whole Pose Membrane Embedding. More...

class	MembranePotential
	Rosetta Membrane Low Resolution Scoring Methods. More...

class	MembraneTopology

class	MinimizationEdge

class	MinimizationGraph
	Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity. More...

class	MinimizationNode

class	MinScoreScoreFunction

class	MultipoleElecPoseInfo

class	MultipoleElecPotential

class	MultipoleElecResidueInfo

class	MultipoleElecRotamerSetInfo

class	MultipoleParameter

class	NeighborList

class	OmegaTether

class	OneToAllEnergyContainer

class	OneToAllNeighborConstIterator

class	OneToAllNeighborIterator

class	P_AA

class	P_AA_ABEGO3

class	P_AA_ss

class	PairEPotential

class	PDatom

class	PDinter

class	PDvertex

class	PointWaterPotential

class	PoissonBoltzmannPotential

class	PolymerBondedEnergyContainer

class	PolymerBondedNeighborConstIterator

class	PolymerBondedNeighborIterator

class	PQR

class	Predicate

class	ProQPotential

class	Ramachandran

class	Ramachandran2B

class	RamaPrePro

class	RDC

class	RDC_Rohl

class	ResidualDipolarCoupling
	ResidualDipolarCouplings are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy – an energy method which triggers computations handled by this class. More...

class	ResidualDipolarCoupling_Rohl

class	ResidueExclParams

class	ResidueNblistData

class	ResidueNeighborConstIterator

class	ResidueNeighborIterator

class	ResiduePairNeighborList

class	ResPairMinimizationData

class	ResRangePredicate

class	ResSingleMinimizationData

class	SAnode

class	SASAPotential

class	ScoreFunction
	This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated. More...

class	ScoreFunctionFactory
	A collection of functions for making a single score_function. More...

class	ScoreFunctionInfo
	Info on the scorefunction settings. More...

class	ScoreTypeManager

class	ScoringManager

class	SecondaryStructurePotential
	secondary structure scoring cut from classic rosetta structure.h/structure.cc More...

class	SecondaryStructureWeights
	Holds weights and flags for configuring a SecondaryStructureEnergy evaluation. More...

class	SelectedResPredicate

class	SigmoidWeightedCenList
	Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) More...

class	SmallAtNb

class	SmoothEnvPairPotential

class	SmoothScoreTermCoeffs

class	SplitUnfoldedTwoBodyPotential

class	SpringParams
	Parameter set for one torsion angle. More...

class	SS_Info

class	SS_Killhairpins_Info

struct	Strands

struct	tableID

class	TenANeighborEdge

class	TenANeighborGraph

class	TenANeighborNode

class	TMscore

class	TMscoreStore

struct	TorsionParams

class	TwelveANeighborEdge

class	TwelveANeighborGraph

class	TwelveANeighborNode

class	UnfoldedStatePotential

class	VdWTinkerPoseInfo

class	VdWTinkerPotential

class	VdWTinkerResidueInfo

class	VdWTinkerRotamerSetInfo

class	WaterAdductHBondPotential

Typedefs
typedef utility::pointer::shared_ptr < APBSWrapper >	APBSWrapperOP

typedef utility::pointer::shared_ptr < APBSWrapper const >	APBSWrapperCOP

typedef utility::pointer::weak_ptr < APBSWrapper >	APBSWrapperAP

typedef utility::pointer::weak_ptr < APBSWrapper const >	APBSWrapperCAP

typedef utility::pointer::shared_ptr < APBSConfig >	APBSConfigOP

typedef utility::pointer::shared_ptr < APBSConfig const >	APBSConfigCOP

typedef utility::pointer::weak_ptr < APBSConfig >	APBSConfigAP

typedef utility::pointer::weak_ptr < APBSConfig const >	APBSConfigCAP

typedef utility::pointer::shared_ptr < APBSResult >	APBSResultOP

typedef utility::pointer::shared_ptr < APBSResult const >	APBSResultCOP

typedef utility::pointer::weak_ptr < APBSResult >	APBSResultAP

typedef utility::pointer::weak_ptr < APBSResult const >	APBSResultCAP

typedef utility::pointer::shared_ptr < PQR >	PQROP

typedef utility::pointer::shared_ptr < PQR const >	PQRCOP

typedef utility::pointer::weak_ptr < PQR >	PQRAP

typedef utility::pointer::weak_ptr < PQR const >	PQRCAP

typedef utility::pointer::shared_ptr < AtomVDW >	AtomVDWOP

typedef utility::pointer::shared_ptr < AtomVDW const >	AtomVDWCOP

typedef utility::pointer::shared_ptr < CenHBPotential >	CenHBPotentialOP

typedef utility::pointer::shared_ptr < CenHBPotential const >	CenHBPotentialCOP

typedef utility::pointer::shared_ptr < CenRotEnvPairPotential >	CenRotEnvPairPotentialOP

typedef utility::pointer::shared_ptr < CenRotEnvPairPotential const >	CenRotEnvPairPotentialCOP

typedef utility::pointer::shared_ptr < ChemicalShiftAnisotropy >	ChemicalShiftAnisotropyOP

typedef utility::pointer::shared_ptr < ChemicalShiftAnisotropy const >	ChemicalShiftAnisotropyCOP

typedef utility::pointer::shared_ptr < ContextGraph >	ContextGraphOP

typedef utility::pointer::shared_ptr < ContextGraph const >	ContextGraphCOP

typedef utility::pointer::shared_ptr < DenseNeighborIterator >	DenseNeighborIteratorOP

typedef utility::pointer::shared_ptr < DenseEnergyContainer >	DenseEnergyContainerOP

typedef utility::pointer::shared_ptr < DipolarCoupling >	DipolarCouplingOP

typedef utility::pointer::shared_ptr < DipolarCoupling const >	DipolarCouplingCOP

typedef utility::pointer::shared_ptr < DockingScoreFunction >	DockingScoreFunctionOP

typedef utility::pointer::shared_ptr < DockingScoreFunction const >	DockingScoreFunctionCOP

typedef utility::pointer::shared_ptr < Energies >	EnergiesOP

typedef utility::pointer::shared_ptr < Energies const >	EnergiesCOP

typedef utility::pointer::shared_ptr < EnergyGraph >	EnergyGraphOP

typedef EMapVector	EnergyMap

typedef utility::pointer::shared_ptr < CenListInfo >	CenListInfoOP

typedef utility::pointer::shared_ptr < EnvPairPotential >	EnvPairPotentialOP

typedef utility::pointer::shared_ptr < EnvPairPotential const >	EnvPairPotentialCOP

typedef utility::pointer::shared_ptr < FACTSRsdTypeInfo >	FACTSRsdTypeInfoOP

typedef utility::pointer::shared_ptr < FACTSRsdTypeInfo const >	FACTSRsdTypeInfoCOP

typedef utility::pointer::shared_ptr < FACTSResidueInfo >	FACTSResidueInfoOP

typedef utility::pointer::shared_ptr < FACTSPoseInfo >	FACTSPoseInfoOP

typedef utility::pointer::shared_ptr < FACTSRotamerSetInfo >	FACTSRotamerSetInfoOP

typedef utility::pointer::shared_ptr < FACTSPotential >	FACTSPotentialOP

typedef utility::pointer::shared_ptr < GenBornResidueInfo >	GenBornResidueInfoOP

typedef utility::pointer::shared_ptr < GenBornPoseInfo >	GenBornPoseInfoOP

typedef utility::pointer::shared_ptr < GenBornRotamerSetInfo >	GenBornRotamerSetInfoOP

typedef utility::pointer::shared_ptr < GenBornPotential >	GenBornPotentialOP

typedef utility::pointer::shared_ptr < GenBornPotential const >	GenBornPotentialCOP

typedef utility::pointer::shared_ptr < GenericBondedPotential >	GenericBondedPotentialOP

typedef utility::pointer::shared_ptr < ResidueExclParams >	ResidueExclParamsOP

typedef utility::pointer::shared_ptr < ResidueExclParams const >	ResidueExclParamsCOP

typedef utility::pointer::shared_ptr < GenBondedExclInfo >	GenBondedExclInfoOP

typedef utility::pointer::shared_ptr < GenBondedExclInfo const >	GenBondedExclInfoCOP

typedef utility::pointer::shared_ptr < HydroxylTorsionPotential >	HydroxylTorsionPotentialOP

typedef utility::pointer::shared_ptr < HydroxylTorsionPotential const >	HydroxylTorsionPotentialCOP

typedef utility::pointer::shared_ptr < ResidueNeighborIterator >	ResidueNeighborIteratorOP

typedef utility::pointer::shared_ptr < ResidueNeighborIterator const >	ResidueNeighborIteratorCOP

typedef utility::pointer::shared_ptr < ResidueNeighborConstIterator >	ResidueNeighborConstIteratorOP

typedef utility::pointer::shared_ptr < ResidueNeighborConstIterator const >	ResidueNeighborConstIteratorCOP

typedef utility::pointer::shared_ptr < LREnergyContainer >	LREnergyContainerOP

typedef utility::pointer::shared_ptr < LREnergyContainer const >	LREnergyContainerCOP

typedef utility::pointer::shared_ptr < Membrane_FAEmbed >	Membrane_FAEmbedOP

typedef utility::pointer::shared_ptr < Membrane_FAEmbed const >	Membrane_FAEmbedCOP

typedef utility::pointer::shared_ptr < Membrane_FAPotential >	Membrane_FAPotentialOP

typedef utility::pointer::shared_ptr < Membrane_FAPotential const >	Membrane_FAPotentialCOP

typedef utility::pointer::shared_ptr < MembraneEmbed >	MembraneEmbedOP

typedef utility::pointer::shared_ptr < MembraneEmbed const >	MembraneEmbedCOP

typedef utility::pointer::shared_ptr < MembranePotential >	MembranePotentialOP

typedef utility::pointer::shared_ptr < MembranePotential const >	MembranePotentialCOP

typedef utility::pointer::shared_ptr < MembraneTopology >	MembraneTopologyOP

typedef utility::pointer::shared_ptr < MembraneTopology const >	MembraneTopologyCOP

typedef utility::pointer::shared_ptr < PoissonBoltzmannPotential >	PoissonBoltzmannPotentialOP

typedef utility::pointer::shared_ptr < PoissonBoltzmannPotential const >	PoissonBoltzmannPotentialCOP

typedef utility::pointer::shared_ptr < ResSingleMinimizationData >	ResSingleMinimizationDataOP

typedef utility::pointer::shared_ptr < ResSingleMinimizationData const >	ResSingleMinimizationDataCOP

typedef utility::pointer::shared_ptr < ResPairMinimizationData >	ResPairMinimizationDataOP

typedef utility::pointer::shared_ptr < ResPairMinimizationData const >	ResPairMinimizationDataCOP

typedef utility::pointer::shared_ptr < MinimizationGraph >	MinimizationGraphOP

typedef utility::pointer::shared_ptr < MinimizationGraph const >	MinimizationGraphCOP

typedef utility::pointer::shared_ptr < MinScoreScoreFunction >	MinScoreScoreFunctionOP

typedef utility::pointer::shared_ptr < MinScoreScoreFunction const >	MinScoreScoreFunctionCOP

typedef utility::pointer::shared_ptr < MultipoleElecResidueInfo >	MultipoleElecResidueInfoOP

typedef utility::pointer::shared_ptr < MultipoleElecResidueInfo const >	MultipoleElecResidueInfoCOP

typedef utility::pointer::shared_ptr < MultipoleElecPoseInfo >	MultipoleElecPoseInfoOP

typedef utility::pointer::shared_ptr < MultipoleElecPoseInfo const >	MultipoleElecPoseInfoCOP

typedef utility::pointer::shared_ptr < MultipoleElecRotamerSetInfo >	MultipoleElecRotamerSetInfoOP

typedef utility::pointer::shared_ptr < MultipoleParameter >	MultipoleParameterOP

typedef utility::pointer::shared_ptr < MultipoleElecPotential >	MultipoleElecPotentialOP

typedef utility::pointer::shared_ptr < MultipoleElecPotential const >	MultipoleElecPotentialCOP

typedef utility::pointer::shared_ptr < NeighborList >	NeighborListOP

typedef utility::pointer::shared_ptr < NeighborList const >	NeighborListCOP

typedef utility::vector1 < AtomNeighbor >	AtomNeighbors

typedef utility::pointer::shared_ptr < OmegaTether >	OmegaTetherOP

typedef utility::pointer::shared_ptr < OmegaTether const >	OmegaTetherCOP

typedef utility::pointer::shared_ptr < OneToAllNeighborIterator >	OneToAllNeighborIteratorOP

typedef utility::pointer::shared_ptr < OneToAllEnergyContainer >	OneToAllEnergyContainerOP

typedef utility::pointer::shared_ptr < P_AA >	P_AAOP

typedef utility::pointer::shared_ptr < P_AA const >	P_AACOP

typedef utility::pointer::shared_ptr < P_AA_ABEGO3 >	P_AA_ABEGO3_OP

typedef utility::pointer::shared_ptr < P_AA_ABEGO3 const >	P_AA_ABEGO3_COP

typedef utility::pointer::shared_ptr < P_AA_ss >	P_AA_ssOP

typedef utility::pointer::shared_ptr < P_AA_ss const >	P_AA_ssCOP

typedef utility::pointer::shared_ptr < PairEPotential >	PairEPotentialOP

typedef utility::pointer::shared_ptr < PairEPotential const >	PairEPotentialCOP

typedef utility::pointer::shared_ptr < PointWaterPotential >	PointWaterPotentialOP

typedef utility::pointer::shared_ptr < PointWaterPotential const >	PointWaterPotentialCOP

using	PB = PoissonBoltzmannPotential

typedef utility::pointer::weak_ptr < PoissonBoltzmannPotential >	PoissonBoltzmannPotentialAP

typedef utility::pointer::weak_ptr < PoissonBoltzmannPotential const >	PoissonBoltzmannPotentialCAP

typedef utility::pointer::shared_ptr < PolymerBondedNeighborIterator >	PolymerBondedNeighborIteratorOP

typedef utility::pointer::shared_ptr < const PolymerBondedNeighborIterator >	PolymerBondedNeighborIteratorCOP

typedef utility::pointer::shared_ptr < PolymerBondedEnergyContainer >	PolymerBondedEnergyContainerOP

typedef utility::pointer::shared_ptr < const PolymerBondedEnergyContainer >	PolymerBondedEnergyContainerCOP

typedef utility::pointer::shared_ptr < ProQPotential >	ProQPotentialOP

using	R = Ramachandran

typedef utility::pointer::shared_ptr < Ramachandran >	RamachandranOP

typedef utility::pointer::shared_ptr < Ramachandran const >	RamachandranCOP

typedef utility::pointer::shared_ptr < Ramachandran2B >	Ramachandran2BOP

typedef utility::pointer::shared_ptr < Ramachandran2B const >	Ramachandran2BCOP

typedef utility::pointer::shared_ptr < RamaPrePro >	RamaPreProOP

typedef utility::pointer::shared_ptr < RamaPrePro const >	RamaPreProCOP

typedef core::Real	matrix [3][3]

typedef core::Real	rvec [3]

typedef core::Real	rvec5 [5]

typedef utility::pointer::shared_ptr < ResidualDipolarCoupling >	ResidualDipolarCouplingOP

typedef utility::pointer::shared_ptr < ResidualDipolarCoupling const >	ResidualDipolarCouplingCOP

typedef utility::pointer::shared_ptr < ResidualDipolarCoupling_Rohl >	ResidualDipolarCoupling_RohlOP

typedef utility::pointer::shared_ptr < ResidualDipolarCoupling_Rohl const >	ResidualDipolarCoupling_RohlCOP

typedef utility::pointer::shared_ptr < ResidueNblistData >	ResidueNblistDataOP

typedef utility::pointer::shared_ptr < ResidueNblistData const >	ResidueNblistDataCOP

typedef utility::pointer::shared_ptr < ResiduePairNeighborList >	ResiduePairNeighborListOP

typedef utility::pointer::shared_ptr < ResiduePairNeighborList const >	ResiduePairNeighborListCOP

typedef std::list< core::Size >	ResidueSelection

typedef utility::vector1 < core::Size >	ResidueSelectionVector

typedef utility::pointer::shared_ptr < Predicate >	PredicateOP

typedef utility::pointer::shared_ptr < Predicate const >	PredicateCOP

typedef utility::pointer::shared_ptr < PDatom >	PDatomOP

typedef utility::pointer::shared_ptr < PDatom const >	PDatomCOP

typedef utility::pointer::shared_ptr < PDvertex >	PDvertexOP

typedef utility::pointer::shared_ptr < PDvertex const >	PDvertexCOP

typedef utility::pointer::shared_ptr < PDinter >	PDinterOP

typedef utility::pointer::shared_ptr < PDinter const >	PDinterCOP

typedef utility::pointer::shared_ptr < SASAPotential >	SASAPotentialOP

typedef utility::pointer::shared_ptr < SASAPotential const >	SASAPotentialCOP

typedef numeric::xyzVector < core::Real >	Vector

typedef numeric::xyzMatrix < core::Real >	Matrix

typedef utility::pointer::shared_ptr < ScoreFunction >	ScoreFunctionOP

typedef utility::pointer::shared_ptr < ScoreFunction const >	ScoreFunctionCOP

typedef utility::pointer::shared_ptr < ScoreFunctionInfo >	ScoreFunctionInfoOP

typedef utility::pointer::shared_ptr < ScoreFunctionInfo const >	ScoreFunctionInfoCOP

typedef utility::vector1 < ScoreType >	ScoreTypes

using	DimerPairingOP = utility::pointer::shared_ptr< DimerPairing >

typedef utility::pointer::shared_ptr < SecondaryStructurePotential >	SecondaryStructurePotentialOP

typedef utility::pointer::shared_ptr < SecondaryStructurePotential const >	SecondaryStructurePotentialCOP

typedef utility::pointer::shared_ptr < SigmoidWeightedCenList< Real > >	SigmoidWeightedCenListRealOP

typedef utility::pointer::shared_ptr < SigmoidWeightedCenList < numeric::xyzVector< Real > > >	SigmoidWeightedCenListVectorOP

typedef utility::pointer::shared_ptr < SmoothEnvPairPotential >	SmoothEnvPairPotentialOP

typedef utility::pointer::shared_ptr < SmoothEnvPairPotential const >	SmoothEnvPairPotentialCOP

typedef utility::pointer::shared_ptr < SplitUnfoldedTwoBodyPotential >	SplitUnfoldedTwoBodyPotentialOP

typedef utility::pointer::shared_ptr < SS_Info >	SS_InfoOP

typedef utility::pointer::shared_ptr < SS_Info const >	SS_InfoCOP

typedef utility::pointer::shared_ptr < SS_Killhairpins_Info >	SS_Killhairpins_InfoOP

typedef utility::pointer::shared_ptr < SS_Killhairpins_Info const >	SS_Killhairpins_InfoCOP

typedef utility::pointer::shared_ptr < TenANeighborGraph >	TenANeighborGraphOP

typedef utility::pointer::shared_ptr < TenANeighborGraph const >	TenANeighborGraphCOP

typedef utility::pointer::shared_ptr < TwelveANeighborGraph >	TwelveANeighborGraphOP

typedef utility::pointer::shared_ptr < TwelveANeighborGraph const >	TwelveANeighborGraphCOP

typedef core::Real	Probability

typedef Real	Weight

typedef Real	Score

typedef float	TableEnergy

typedef float	TableProbability

typedef ObjexxFCL::CArray< Energy >	CArray_Energy

typedef ObjexxFCL::CArrayP < Energy >	CArrayP_Energy

typedef ObjexxFCL::CArray < TableEnergy >	CArray_TableEnergy

typedef ObjexxFCL::CArrayP < TableEnergy >	CArrayP_TableEnergy

typedef ObjexxFCL::FArray1D < Length >	FArray1D_Length

typedef ObjexxFCL::FArray2D < Length >	FArray2D_Length

typedef ObjexxFCL::FArray3D < Length >	FArray3D_Length

typedef ObjexxFCL::FArray4D < Length >	FArray4D_Length

typedef ObjexxFCL::FArray5D < Length >	FArray5D_Length

typedef ObjexxFCL::FArray1D < Weight >	FArray1D_Weight

typedef ObjexxFCL::FArray2D < Weight >	FArray2D_Weight

typedef ObjexxFCL::FArray3D < Weight >	FArray3D_Weight

typedef ObjexxFCL::FArray4D < Weight >	FArray4D_Weight

typedef ObjexxFCL::FArray5D < Weight >	FArray5D_Weight

typedef ObjexxFCL::FArray1D < Energy >	FArray1D_Energy

typedef ObjexxFCL::FArray2D < Energy >	FArray2D_Energy

typedef ObjexxFCL::FArray3D < Energy >	FArray3D_Energy

typedef ObjexxFCL::FArray4D < Energy >	FArray4D_Energy

typedef ObjexxFCL::FArray5D < Energy >	FArray5D_Energy

typedef ObjexxFCL::FArray1D < TableEnergy >	FArray1D_TableEnergy

typedef ObjexxFCL::FArray2D < TableEnergy >	FArray2D_TableEnergy

typedef ObjexxFCL::FArray3D < TableEnergy >	FArray3D_TableEnergy

typedef ObjexxFCL::FArray4D < TableEnergy >	FArray4D_TableEnergy

typedef ObjexxFCL::FArray5D < TableEnergy >	FArray5D_TableEnergy

typedef ObjexxFCL::FArray2D < CArrayP_TableEnergy >	AtomPairEnergyTable

typedef ObjexxFCL::FArray1D < Probability >	FArray1D_Probability

typedef ObjexxFCL::FArray2D < Probability >	FArray2D_Probability

typedef ObjexxFCL::FArray3D < Probability >	FArray3D_Probability

typedef ObjexxFCL::FArray4D < Probability >	FArray4D_Probability

typedef ObjexxFCL::FArray5D < Probability >	FArray5D_Probability

typedef ObjexxFCL::FArray1D < TableProbability >	FArray1D_TableProbability

typedef ObjexxFCL::FArray2D < TableProbability >	FArray2D_TableProbability

typedef ObjexxFCL::FArray3D < TableProbability >	FArray3D_TableProbability

typedef ObjexxFCL::FArray4D < TableProbability >	FArray4D_TableProbability

typedef ObjexxFCL::FArray5D < TableProbability >	FArray5D_TableProbability

typedef ObjexxFCL::KeyFArray1D < Real >	KeyFArray1D_Real

typedef ObjexxFCL::KeyFArray2D < Real >	KeyFArray2D_Real

typedef ObjexxFCL::KeyFArray3D < Real >	KeyFArray3D_Real

typedef ObjexxFCL::KeyFArray1D < Weight >	KeyFArray1D_Weight

typedef ObjexxFCL::KeyFArray2D < Weight >	KeyFArray2D_Weight

typedef ObjexxFCL::KeyFArray3D < Weight >	KeyFArray3D_Weight

typedef ObjexxFCL::KeyFArray1D < Energy >	KeyFArray1D_Energy

typedef ObjexxFCL::KeyFArray2D < Energy >	KeyFArray2D_Energy

typedef ObjexxFCL::KeyFArray3D < Energy >	KeyFArray3D_Energy

typedef ObjexxFCL::KeyFArray1D < Probability >	KeyFArray1D_Probability

typedef ObjexxFCL::KeyFArray2D < Probability >	KeyFArray2D_Probability

typedef ObjexxFCL::KeyFArray3D < Probability >	KeyFArray3D_Probability

typedef utility::pointer::shared_ptr < UnfoldedStatePotential >	UnfoldedStatePotentialOP

typedef utility::pointer::shared_ptr < VdWTinkerResidueInfo >	VdWTinkerResidueInfoOP

typedef utility::pointer::shared_ptr < VdWTinkerResidueInfo const >	VdWTinkerResidueInfoCOP

typedef utility::pointer::shared_ptr < VdWTinkerPoseInfo >	VdWTinkerPoseInfoOP

typedef utility::pointer::shared_ptr < VdWTinkerPoseInfo const >	VdWTinkerPoseInfoCOP

typedef utility::pointer::shared_ptr < VdWTinkerRotamerSetInfo >	VdWTinkerRotamerSetInfoOP

typedef utility::pointer::shared_ptr < VdWTinkerPotential >	VdWTinkerPotentialOP

typedef utility::pointer::shared_ptr < VdWTinkerPotential const >	VdWTinkerPotentialCOP

typedef utility::pointer::shared_ptr < WaterAdductHBondPotential >	WaterAdductHBondPotentialOP

typedef utility::pointer::shared_ptr < WaterAdductHBondPotential const >	WaterAdductHBondPotentialCOP

typedef utility::pointer::shared_ptr < SetupPoissonBoltzmannPotential >	SetupPoissonBoltzmannPotentialOP

typedef utility::pointer::shared_ptr < SetupPoissonBoltzmannPotential const >	SetupPoissonBoltzmannPotentialCOP

typedef utility::pointer::weak_ptr < SetupPoissonBoltzmannPotential >	SetupPoissonBoltzmannPotentialAP

typedef utility::pointer::weak_ptr < SetupPoissonBoltzmannPotential const >	SetupPoissonBoltzmannPotentialCAP

Enumerations
enum	ContextGraphType { ten_A_neighbor_graph = 1, twelve_A_neighbor_graph, centroid_neighbor_graph, num_context_graph_types = centroid_neighbor_graph }

enum	ReadMode { rmNONE, rmATOM, rmBOND, rmANGLE, rmTORSION, rmIMPROPER }

enum	min_single_data { etab_single_nblist = 1, etab_classic_intrares_single_nblist, mm_lj_intra_nblist, cst_res_data, lkb_res_data, vdw_res_data, mp_res_data, hbond_res_data, n_min_single_data = hbond_res_data }

enum	min_pair_data { etab_pair_nblist = 1, etab_classic_intrares_pair_nblist, lkball_nblist, cst_respair_data, elec_pair_nblist, rna_elec_pair_nblist, geom_solv_pair_nblist, fa_stack_pair_nblist, lk_PolarNonPolar_pair_nblist, fa_dslf_respair_data, fa_custom_pair_dist_data, lkb_respair_data, vdw_respair_data, mp_respair_data, mg_pair_nblist, hbond_respair_data, n_min_pair_data = hbond_respair_data }

enum	MultipoleAxisType { none =1, z_axis_only, three_fold, bisector, z_then_bisector, z_then_x }

enum	ABEGO_index { ABEGO_index_INVALID =0, ABEGO_index_A, ABEGO_index_START = ABEGO_index_A, ABEGO_index_B, ABEGO_index_E, ABEGO_index_G, ABEGO_index_O, ABEGO_index_COUNT = ABEGO_index_O }

enum	ProteinTorsion { PHI = 1, PSI, OMEGA, CHI1, CHI2, CHI3, CHI4, protein_torsion_end }

enum	Rama_Table_Type { flat_l_aa_ramatable =1, flat_d_aa_ramatable, flat_symm_dl_aa_ramatable, flat_symm_gly_ramatable, flat_symm_pro_ramatable, flat_l_aa_ramatable_stringent, flat_d_aa_ramatable_stringent, flat_symm_dl_aa_ramatable_stringent, flat_symm_gly_ramatable_stringent, flat_symm_pro_ramatable_stringent, unknown_ramatable_type, end_of_ramatable_type_list =unknown_ramatable_type }

enum	rmsd_atoms { rmsd_protein_bb_heavy = 1, rmsd_protein_bb_heavy_including_O, rmsd_protein_bb_ca, rmsd_sc_heavy, rmsd_sc, rmsd_all_heavy, rmsd_all, rmsd_atom_total = rmsd_all }

enum	ScoreType { fa_atr = 1, fa_rep, fa_sol, fa_intra_atr, fa_intra_rep, fa_intra_sol, fa_intra_atr_xover4, fa_intra_rep_xover4, fa_intra_sol_xover4, fa_intra_atr_nonprotein, fa_intra_rep_nonprotein, fa_intra_sol_nonprotein, fa_intra_RNA_base_phos_atr, fa_intra_RNA_base_phos_rep, fa_intra_RNA_base_phos_sol, fa_atr_dummy, fa_rep_dummy, fa_sol_dummy, fa_vdw_tinker, lk_hack, lk_ball, lk_ball_wtd, lk_ball_iso, lk_ball_bridge, lk_ball_bridge_uncpl, coarse_fa_atr, coarse_fa_rep, coarse_fa_sol, coarse_beadlj, mm_lj_intra_rep, mm_lj_intra_atr, mm_lj_inter_rep, mm_lj_inter_atr, mm_twist, mm_bend, mm_stretch, lk_costheta, lk_polar, lk_nonpolar, lk_polar_intra_RNA, lk_nonpolar_intra_RNA, fa_elec, fa_elec_bb_bb, fa_elec_bb_sc, fa_elec_sc_sc, fa_intra_elec, h2o_hbond, dna_dr, dna_bp, dna_bs, dna_ref, peptide_bond, pcs, pcsTs1, pcsTs2, pcsTs3, pcsTs4, pcs2, fastsaxs, saxs_score, saxs_cen_score, saxs_fa_score, pddf_score, fiberdiffraction, fiberdiffractiondens, fa_mbenv, fa_mbsolv, fa_elec_rna_phos_phos, fa_elec_rna_phos_sugr, fa_elec_rna_phos_base, fa_elec_rna_sugr_sugr, fa_elec_rna_sugr_base, fa_elec_rna_base_base, fa_elec_rna_phos_phos_fast, fa_elec_rna_phos_sugr_fast, fa_elec_rna_phos_base_fast, fa_elec_rna_sugr_sugr_fast, fa_elec_rna_sugr_base_fast, fa_elec_rna_base_base_fast, fa_elec_aro_aro, fa_elec_aro_all, hack_aro, rna_fa_atr_base, rna_fa_rep_base, rna_data_backbone, ch_bond, ch_bond_bb_bb, ch_bond_sc_sc, ch_bond_bb_sc, pro_close, rama2b, vdw, cenpack, cenpack_smooth, cen_hb, hybrid_vdw, gauss, rna_vdw, rnp_vdw, rna_base_backbone, rna_backbone_backbone, rna_repulsive, rna_base_pair_pairwise, rna_base_axis_pairwise, rna_base_stagger_pairwise, rna_base_stack_pairwise, rna_base_stack_axis_pairwise, rna_data_base, rna_base_pair, rna_base_axis, rna_base_stagger, rna_base_stack, rna_base_stack_axis, rnp_base_pair, rnp_stack, rnp_stack_xy, rnp_pair, rnp_pair_dist, rnp_aa_to_rna_backbone, rna_mg_point, rna_mg_point_indirect, mg, mg_lig, mg_sol, mg_ref, hoh_ref, rna_torsion, rna_torsion_sc, rna_suite, rna_jr_suite, suiteness_bonus, tna_suite, rna_sugar_close, fa_stack, fa_stack_lower, fa_stack_upper, fa_stack_aro, fa_stack_ext, fa_stack_sol, fa_stack_lr, fa_stack_rna_protein, fa_stack_rna_protein_aro, ss_contact_worst, stack_elec, stack_elec_base_base, stack_elec_base_bb, alignment, dna_bb_torsion, dna_sugar_close, dna_base_distance, geom_sol_fast, geom_sol_fast_intra_RNA, fa_cust_pair_dist, custom_atom_pair, orbitals_hpol_bb, pci_cation_pi, pci_pi_pi, pci_salt_bridge, pci_hbond, arg_cation_pi, python, n_ci_2b_score_types = python, fa_pair, fa_pair_aro_aro, fa_pair_aro_pol, fa_pair_pol_pol, hbond_sr_bb, hbond_lr_bb, hbond_bb_sc, hbond_sr_bb_sc, hbond_lr_bb_sc, hbond_sc, hbond_intra, hbond_wat, wat_entropy, hbond, npd_hbond_sr_bb, npd_hbond_lr_bb, npd_hbond_bb_sc, npd_hbond_sr_bb_sc, npd_hbond_lr_bb_sc, npd_hbond_sc, npd_hbond_intra, npd_hbond, fa_grpelec, interface_dd_pair, geom_sol, geom_sol_intra_RNA, occ_sol_fitted, occ_sol_fitted_onebody, occ_sol_exact, cen_rot_pair, cen_rot_pair_ang, cen_rot_pair_dih, pair, cen_pair_smooth, Mpair, MPPair, FaMPSolv, suck, rna_rg, rna_motif, facts_elec, facts_solv, facts_sasa, motif_dock, pointwater, goap, goap_dist, goap_angle, approximate_buried_unsat_penalty, interchain_pair, interchain_vdw, n_shortranged_2b_score_types = interchain_vdw, gb_elec, multipole_elec, fa_sasa, dslf_ss_dst, dslf_cs_ang, dslf_ss_dih, dslf_ca_dih, dslf_cbs_ds, dslf_fa13, dslfc_cen_dst, dslfc_cb_dst, dslfc_ang, dslfc_cb_dih, dslfc_bb_dih, dslfc_rot, dslfc_trans, dslfc_RT, atom_pair_constraint, base_pair_constraint, coarse_chainbreak_constraint, constant_constraint, coordinate_constraint, angle_constraint, dihedral_constraint, big_bin_constraint, dunbrack_constraint, site_constraint, metalhash_constraint, metalbinding_constraint, rna_stub_coord_hack, bond_geometry, rna_bond_geometry, Hpol_bond_geometry, rama, omega, fa_dun, fa_dun_dev, fa_dun_rot, fa_dun_semi, cen_rot_dun, dna_chi, p_aa_pp, p_aa_ss, yhh_planarity, hxl_tors, h2o_intra, ref, ref_nc, seqdep_ref, nmer_ref, nmer_pssm, nmer_svm, envsmooth, e_pH, rna_bulge, dna_dihedral_bb, dna_dihedral_chi, dna_dihedral_sugar, sugar_bb, free_suite, free_2HOprime, free_side_chain, free_base, free_res, free_dof, intermol, other_pose, special_rot, PB_elec, cen_env_smooth, cbeta_smooth, cen_rot_env, cen_rot_cbeta, env, cbeta, DFIRE, Menv, Mcbeta, Menv_non_helix, Menv_termini, Menv_tm_proj, Mlipo, rg, rg_local, co, hs_pair, ss_pair, rsigma, sheet, burial_v2, burial, abego, covalent_labeling, covalent_labeling_fa, hrf_ms_labeling, rnp_env, loop_close, missing_res, MPEnv, MPCbeta, MPLipo, MPTermini, MPNonHelix, MPTMProj, FaMPEnv, FaMPEnvSmooth, fa_water_to_bilayer, MPResidueLipophilicity, span_ins, mp_span_ang, MPHelicality, natbias_ss, natbias_hs, natbias_hh, natbias_stwist, aa_cmp, dock_ens_conf, csa, dc, rdc, rdc_segments, rdc_rohl, nmr_pcs, nmr_rdc, nmr_pre, cen_pair_motifs, cen_pair_motif_degree, holes, holes_decoy, holes_resl, holes_min, holes_min_mean, rna_chem_shift, rna_chem_map, rna_chem_map_lores, rna_partition, dab_sasa, dab_sev, sa, d2h_sa, ProQM, ProQ, interchain_env, interchain_contact, chainbreak, linear_chainbreak, overlap_chainbreak, distance_chainbreak, dof_constraint, branch_conn, linear_branch_conn, rama_prepro, paa_abego3, cart_bonded, cart_bonded_angle, cart_bonded_length, cart_bonded_ring, cart_bonded_torsion, cart_bonded_proper, cart_bonded_improper, gen_bonded, gen_bonded_bond, gen_bonded_angle, gen_bonded_torsion, gen_bonded_improper, neigh_vect, neigh_count, neigh_vect_raw, symE_bonus, sym_lig, mhc_epitope, pack_stat, rms, res_type_constraint, res_type_linking_constraint, pocket_constraint, backbone_stub_constraint, backbone_stub_linear_constraint, surface, p_aa, unfolded, split_unfolded_two_body, fa_atr_ref, fa_rep_ref, fa_sol_ref, fa_elec_ref, hbond_ref, dslf_fa13_ref, fa_intra_atr_ref, fa_intra_rep_ref, fa_intra_sol_ref, pro_close_ref, fa_dun_ref, fa_dun_dev_ref, fa_dun_rot_ref, fa_dun_semi_ref, rama_ref, p_aa_pp_ref, omega_ref, mm_lj_intra_rep_ref, mm_lj_intra_atr_ref, mm_twist_ref, elec_dens_fast, elec_dens_window, elec_dens_whole_structure_ca, elec_dens_whole_structure_allatom, elec_dens_atomwise, grid_vdw, xtal_ml, xtal_rwork, xtal_rfree, hpatch, Menv_smooth, wat_desolv, ring_close, aa_repeat, aa_composition, aspartimide_penalty, hbnet, buried_unsatisfied_penalty, netcharge, voids_penalty, dna_env, dna_pair, dump_trajectory, sidechain_neighbors, membrane_span_constraint, membrane_span_term_z_constraint, aromatic_restraint, total_score, dummy_score_type, n_score_types = dummy_score_type, end_of_score_type_enumeration = dummy_score_type }
	Type for looking up cached energies. More...

Functions
static basic::Tracer	TR ("core.scoring.AtomVDW")

void	store_CSA_in_pose (ChemicalShiftAnisotropyOP csa_info, core::pose::Pose &pose)

ChemicalShiftAnisotropyCOP	retrieve_CSA_from_pose (core::pose::Pose const &pose)

ChemicalShiftAnisotropyOP	retrieve_CSA_from_pose (core::pose::Pose &pose)

std::ostream &	operator<< (std::ostream &out, CSA const &csa)

std::ostream &	operator<< (std::ostream &out, ChemicalShiftAnisotropy const &csa)

static Real const	BOGUS_ENERGY (99999.99)

DerivVectorPair	operator* (Real scale, DerivVectorPair const &dvp)

DerivVectorPair	operator* (DerivVectorPair const &dvp, Real scale)

void	store_DC_in_pose (DipolarCouplingOP dc_info, core::pose::Pose &pose)

DipolarCouplingCOP	retrieve_DC_from_pose (core::pose::Pose const &pose)

DipolarCouplingOP	retrieve_DC_from_pose (core::pose::Pose &pose)

std::ostream &	operator<< (std::ostream &out, DC const &dc)

std::ostream &	operator<< (std::ostream &out, DipolarCoupling const &dc)

std::string	element_string_dc (std::string const &atom)

std::ostream &	operator<< (std::ostream &out, const Energies &e)

std::ostream &	operator<< (std::ostream &ost, EMapVector const &emap)
	output operator (index;value) More...

template<class T , class T_Etable >
void	residue_fast_pair_energy_attached_H (conformation::Residue const &res1, int const atomno1, conformation::Residue const &res2, Size const atomno2, Size const at1hbegin, Size const at1hend, Size const at2hbegin, Size const at2hend, T const &count_pair, T_Etable const &etable_energy, EnergyMap &emap)
	class T must define More...

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap, int res1_start, int res1_end, int res2_start, int res2_end)
	templated atom pair energy calculations More...

template<class T , class T_Etable >
void	inline_intraresidue_atom_pair_energy (conformation::Residue const &res, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
	intraresidue atom pair energy evaluations More...

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_whole (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_backbone_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)

template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)

float	fastpow2 (float p)

float	fastlog2 (float x)

float	fastexp (float p)

float	fastpow (float x, float p)

static basic::Tracer	TR ("core.scoring.GenericBondedPotential")

uint64_t	get_parameter_hash (Size bondtypr, Size type1, Size type2, Size type3=0, Size type4=0)
	compress 5 values into one unsigned int; use 12 bits for each More...

core::Size	bin_from_bond (core::chemical::BondName bn, core::chemical::BondRingness br)
	convert a bond type to a bin index More...

utility::vector1< core::Size >	bondorders_map (std::string bt)
	helper function to convert string specification of bondorders to indices More...

static basic::Tracer	TR ("core.scoring.HydroxylTorsionPotential")

void	interpolate_value_and_deriv (ObjexxFCL::FArray1D< Real > const &potential, Real const &bin_width, Real const &r, Real &value, Real &deriv)

Membrane_FAEmbed const &	Membrane_FAEmbed_from_pose (pose::Pose const &pose)
	Return a Const Reference to the Embedding Object from the Pose Cache. More...

Membrane_FAEmbed &	nonconst_Membrane_FAEmbed_from_pose (pose::Pose &pose)
	Return a Non Const Reference to the Embedding Object from the Pose Cache. More...

MembraneEmbed const &	MembraneEmbed_from_pose (pose::Pose const &pose)
	Add Const Membrane Embedding to the pose cache. More...

MembraneEmbed &	nonconst_MembraneEmbed_from_pose (pose::Pose &pose)
	Add a non const membrane embedding object to the pose cache. More...

static basic::Tracer	TR ("core.scoring.MembraneTopology")

MembraneTopology const &	MembraneTopology_from_pose (pose::Pose const &pose)

MembraneTopology &	nonconst_MembraneTopology_from_pose (pose::Pose &pose)

void	eval_atom_derivatives_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &res_weights, utility::vector1< DerivVectorPair > &atom_derivs)
	Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node). More...

void	eval_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	Deprecated. More...

void	eval_atom_derivatives_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, ResSingleMinimizationData const &res1_min_data, ResSingleMinimizationData const &res2_min_data, pose::Pose const &pose, EnergyMap const &respair_weights, utility::vector1< DerivVectorPair > &r1atom_derivs, utility::vector1< DerivVectorPair > &r2atom_derivs)

void	eval_weighted_atom_derivatives_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, ResSingleMinimizationData const &res1_min_data, ResSingleMinimizationData const &res2_min_data, pose::Pose const &pose, EnergyMap const &respair_weights, utility::vector1< DerivVectorPair > &r1atom_derivs, utility::vector1< DerivVectorPair > &r2atom_derivs)

void	eval_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	Deprecated. More...

Real	eval_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights)

void	eval_weighted_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap)

void	eval_weighted_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap)

Real	eval_weighted_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights)

bool	ShouldItCount (conformation::Residue const &rsd, Size const &atm)

void	get_damped_scale_factors (MultipoleParameter::MultipoleParameterOP const &mp_param1, MultipoleParameter::MultipoleParameterOP const &mp_param2, core::Real dist, core::Real &scale3, core::Real &scale5, core::Real &scale7)

void	get_damped_scale_factors_with_derivs (MultipoleParameter::MultipoleParameterOP const &mp_param1, MultipoleParameter::MultipoleParameterOP const &mp_param2, core::Real dist, core::Real &scale3, core::Real &scale5, core::Real &scale7, core::Real &dscale3_dr, core::Real &dscale5_dr, core::Real &dscale7_dr)

bool	same_polarization_group (core::conformation::Residue const &rsd1, MultipoleElecResidueInfo const &mp1, core::Size atm1, core::conformation::Residue const &rsd2, core::Size atm2)

static basic::Tracer	tr ("core.scoring.NeighborList")

ABEGO_index	abego_to_index (char abego)

int	abego3aa_to_index (const char abego1, const char abego2, const char abego3, const core::chemical::AA aa_index)

int	abego3aa_to_index (const char abego1, const char abego2, const char abego3, const char aa)

static basic::Tracer	TR ("core.scoring.PolymerBondedEnergyContainer")

static basic::Tracer	TR_it ("core.scoring.PolymerBondedNeighborIterator")

std::ostream &	operator<< (std::ostream &os, PolymerBondedEnergyContainer const &t)
	Operator to allow object to be summarized. More...

static basic::Tracer	TR ("core.scoring.ProQPotential")

bool	polymeric_termini_incomplete (conformation::Residue res)

static basic::Tracer	T ("core.scoring.Ramachandran2B")

static basic::Tracer	TR ("core.scoring.RamaPrePro")

Real	sqr (Real x)

void	store_RDC_in_pose (ResidualDipolarCouplingOP rdc_info, core::pose::Pose &pose)

ResidualDipolarCouplingCOP	retrieve_RDC_from_pose (core::pose::Pose const &pose)

ResidualDipolarCouplingOP	retrieve_RDC_from_pose (core::pose::Pose &pose)

std::ostream &	operator<< (std::ostream &out, RDC const &rdc)

std::ostream &	operator<< (std::ostream &out, ResidualDipolarCoupling const &rdc)

std::string	element_string (std::string const &atom)

int	m_inv_gen (ResidualDipolarCoupling::Tensor5 const &m, int n, ResidualDipolarCoupling::Tensor5 &minv)

void	jacobi (ResidualDipolarCoupling::Tensor5 &a, ResidualDipolarCoupling::rvec5 &d, ResidualDipolarCoupling::Tensor5 &v, int &nrot)

void	jacobi3 (ResidualDipolarCoupling::Tensor &a, ResidualDipolarCoupling::rvec &d, ResidualDipolarCoupling::Tensor &v, int &nrot)

Real	iprod (const rvec a, const rvec b)

void	mvmul (matrix a, const rvec src, rvec dest)

int	compare_by_abs (const void a, const void b)

core::Real	frdc (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, const core::Real *par)

core::Real	frdcDa (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorDa, const core::Real *par)

core::Real	frdcR (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorR, const core::Real *par)

core::Real	frdcDaR (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorDa, core::Real const tensorR, const core::Real *par)

void	evaluaterdc (const core::Real par, int m_dat, const void data, core::Real fvec, int )

template<class T >
void	ROTATE (T &a, int i, int j, int k, int l, Real s, Real tau)

void	store_RDC_ROHL_in_pose (ResidualDipolarCoupling_RohlOP rdc_info, core::pose::Pose &pose)

ResidualDipolarCoupling_RohlCOP	retrieve_RDC_ROHL_from_pose (core::pose::Pose const &pose)

ResidualDipolarCoupling_RohlOP	retrieve_RDC_ROHL_from_pose (core::pose::Pose &pose)

static basic::Tracer	tr ("core.scoring.rms_util")

core::Real	gdtsc (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues)
	Returns a single, Global Distance Test-like value that measures the extent to which the functional ends of a model's sidechains agree with their counterparts in a given reference structure. More...

core::Real	gdtha (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues)
	Returns the average fraction of residues superimposable under a series of distance thresholds– 0.5, 1.0, 2.0, and 4.0 Angstroms. More...

void	invert_exclude_residues (Size nres, utility::vector1< int > const &exclude_list, ResidueSelection &residue_selection)

ResidueSelection	invert_exclude_residues (core::Size nres, utility::vector1< int > const &exclude_list)

Real	native_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose)

Real	native_CA_gdtmm (const core::pose::Pose &native_pose, const core::pose::Pose &pose)

core::Real	automorphic_rmsd (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, bool superimpose)
	RMSD between residues, accounting for automorphisms (symmetries). For example if you have something like a tyrosine, you won't get a higher rmsd just because you flipped the ring 180 degrees (Rocco). Does NOT include H atoms – they add lots of extra symmetries. More...

core::Real	residue_rmsd_super (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atom_map, bool skip_hydro)
	Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Superimposes the residues (remove rigid-body rotational/translational component of the rmsd.) More...

core::Real	residue_rmsd_nosuper (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atom_map, bool skip_hydro)
	Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Does not superimpose the residues. More...

bool	is_protein_CA (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_protein_CA_or_equiv (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_protein_CA_or_CB (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_protein_backbone (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_protein_backbone_including_O (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_protein_sidechain_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_ligand_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_ligand_heavyatom_residues (core::conformation::Residue const &residue1, core::conformation::Residue const &, core::Size atomno)

bool	is_polymer_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_non_peptide_heavy_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::uint const resno, core::uint const atomno)
	Return true if the pose residues and atoms specified are non-peptide heavy atoms. More...

bool	is_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_scatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

bool	is_nbr_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)

core::DistanceSquared	non_peptide_heavy_atom_RMSD (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Return the RMSD of the non-peptide heavy atoms of two poses. More...

core::Real	CA_or_equiv_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start=1, Size end=0)
	Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose. More...

core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start=1, Size end=0)
	Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose. More...

void	retrieve_coordinates (const core::pose::Pose &pose, const utility::vector1< core::Size > &residues, FArray2D< core::Real > *coords)

core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues)
	Compute the CA RMSD between two poses. More...

core::Real	CA_gdtmm (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues)
	Compute the CA RMSD between two poses. More...

core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end, utility::vector1< Size > const &exclude)

core::Real	bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
	Compute rmsd for only backbone residues (excluding carboxyl oxygen) More...

core::Real	bb_rmsd_including_O (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
	Compute rmsd for only backbone residues (including carboxyl oxygen) More...

core::Real	CA_or_equiv_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > const &residue_selection)

core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection)

core::Real	all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)

core::Real	all_scatom_rmsd_nosuper (const core::pose::Pose &pose1, const core::pose::Pose &pose2)

core::Real	all_atom_rmsd_nosuper (const core::pose::Pose &pose1, const core::pose::Pose &pose2)

core::Real	all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection)

core::Real	nbr_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)

int	CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Real rms=4.0)
	Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information. More...

int	CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection, Real rms)

int	xyz_maxsub (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, int natoms)

int	CA_maxsub_by_subset (const core::pose::Pose &pose1, const core::pose::Pose &pose2, utility::vector1< bool >)

core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > const &residue_selection, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)

core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score. More...

core::Real	xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a)

core::Real	xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)

core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. More...

core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > const &residue_selection)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. More...

void	CA_gdttm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &gdttm_score, core::Real &gdtha_score, std::list< Size > const &residue_selection)
	Calculate gdttm score based on the C-alpha positions in pose1 and pose2. More...

void	CA_gdttm (const core::pose::Pose &pose1, const core::pose::Pose &pose2, core::Real &gdttm_score, core::Real &gdtha_score, const std::map< core::Size, core::Size > &residues)

void	CA_gdttm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &gdttm_score, core::Real &gdtha_score)

void	xyz_gdttm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, core::Real &gdttm_score, core::Real &gdtha_score)

Real	superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map,core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false)
	Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map. More...

Real	superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< id::AtomID, id::AtomID > const &atom_map,core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false)
	Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by map< AtomID, AtomID > More...

Real	superimpose_pose (pose::Pose &mod_pose, pose::MiniPose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map,core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false)
	Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map. More...

Real	calpha_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose)
	Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.". More...

core::Real	CA_rmsd_symmetric (const core::pose::Pose &native_pose, const core::pose::Pose &pose)

void	create_shuffle_map_recursive_rms (std::vector< int > sequence, int const N, std::vector< std::vector< int > > &map)

Real	rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map)

Real	rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< Size > const &calc_rms_res)

Real	rms_at_all_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map)

Real	rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map)

Real	rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< Size > const &calc_rms_res)

std::map< core::Size, core::Real >	per_res_rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< bool > const &mask)
	Calculate RMSD for each residue in mask, return a map of res to value. More...

Real	rms_at_corresponding_heavy_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose)

void	setup_matching_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)

core::Real	residue_sc_rmsd_no_super (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2, bool const fxnal_group_only=false)
	utility function to calculate per-residue sidechain rmsd without superposition More...

void	setup_matching_CA_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)

void	setup_matching_protein_backbone_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)

void	setup_matching_atoms_with_given_names (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< std::string > const &atom_names_to_find, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)

void	compute_jump_rmsd (const core::pose::Pose &reference, const core::pose::Pose &model, boost::unordered_map< core::Size, core::Real > &rmsds)
	Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id. More...

std::map< rmsd_atoms, utility::vector1< std::string > >	setup_rmsd_atom_names ()

std::map< std::string, rmsd_atoms >	get_rmsd_type_name_map ()
	Setup a name mapping for rmsd_atoms. More...

utility::vector1< std::string >	get_rmsd_type_names ()
	Setup a name mapping for rmsd_atoms. More...

int	xyz_maxsub (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, int natoms)

core::Real	xyz_gdtmm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)
	Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a. More...

core::Real	xyz_gdtmm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a)
	Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a. More...

void	xyz_gdttm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, core::Real &gdttm_score, core::Real &gdtha_score)

template<class T >
core::Real	rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< core::Size > const &pose1_residues, utility::vector1< core::Size > const &pose2_residues, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...

template<class T >
core::Real	rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > const &subset_residues, T *predicate)

template<class T >
core::Real	rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...

template<class T >
core::Real	rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for RMS via a predicate function/functor. More...

template<class T >
core::Real	rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, core::id::SequenceMapping const &seqmap, T *predicate)
	like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way... More...

template<class T >
core::Real	rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< core::Size > const &pose1_residues, utility::vector1< core::Size > const &pose2_residues, T *predicate)
	Select atoms for RMS via a predicate function/functor at given residues. More...

template<class T >
core::Real	rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...

template<class T >
core::Real	rmsd_no_super (core::conformation::ResidueCOPs const &residues1, core::conformation::ResidueCOPs const &residues2, T *predicate)

template<class T >
core::Real	rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...

template<class T >
core::Real	rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, core::id::SequenceMapping const &seqmap, T *predicate)
	like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way... More...

template<class T >
core::Real	biggest_residue_deviation_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses, More...

template<class T >
core::Real	biggest_residue_deviation_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses, More...

template<class T >
void	fill_rmsd_coordinates (int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)

template<class T >
core::Real	sym_rmsd_with_super_subset (core::pose::Pose const &native_pose, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);. More...

ObjexxFCL::FArray2D_int	angles (num_phi, num_theta)

ObjexxFCL::FArray2D_ubyte	masks (num_bytes, num_overlaps *num_orientations)

void	input_sasa_dats ()
	Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above. More...

void	get_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int &degree_of_overlap)

void	get_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_index, int &theta_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More...

Real	calc_total_sasa (pose::Pose const &pose, Real const probe_radius)
	returns total sasa More...

Real	calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H=false)
	Return total SASA. More...

Real	calc_per_atom_sasa_sc (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, bool normalize)

Real	normalizing_area (char const res)
	Get the area of the sidechain. More...

Real	normalizing_area_total (char const res)
	Given a one-letter code for a canonical amino acid, return its total surface area. More...

Real	normalizing_area_total_hydrophobic_atoms_only (char const res)
	Given a one-letter code for a canonical amino acid, return its total surface area, computed only using hydrophobic atoms. More...

Real	normalizing_area_total_polar_atoms_only (char const res)
	Given a one-letter code for a canonical amino acid, return its total surface area, computed only using polar atoms. More...

Real	calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H, id::AtomID_Map< bool > &atom_subset, bool const use_naccess_sasa_radii=false, bool const expand_polar_radii=false, Real const polar_expansion_radius=1.0, bool const include_probe_radius_in_atom_radii=true, bool const use_lj_radii=false)
	returns total sasa More...

void	calc_atom_masks (core::conformation::Residue const &irsd, core::conformation::Residue const &jrsd, Real const probe_radius, Real const cutoff_distance, utility::vector1< Real > const &radii, id::AtomID_Map< bool > const &atom_subset, core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &atom_masks)

int	get_num_bytes ()
	Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...

ObjexxFCL::FArray2D_int const &	get_angles ()
	Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...

ObjexxFCL::FArray2D_ubyte const &	get_masks ()
	Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...

Real	calc_per_res_hydrophobic_sasa (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, utility::vector1< Real > &rsd_hydrophobic_sasa, Real const probe_radius, bool use_naccess_sasa_radii)
	Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj) More...

bool	SASAShouldItCount (conformation::Residue const &rsd, Size const &atm)

void	show_detail (std::ostream &out, EnergyMap &energies, EnergyMap weights)

template<class T >
void	vector1_remove (utility::vector1< T > &v, T const &t)
	private – handles setting the derived data More...

std::string	find_weights_file (std::string const &name, std::string const &extension)
	Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passed either with or without the optional extension. More...

ScoreFunctionOP	deep_copy (ScoreFunction const &source)

std::ostream &	operator<< (std::ostream &out, ScoreFunction const &sf)

std::string const	REF_2015 ("ref2015")

std::string const	TALARIS_2014 ("talaris2014")

std::string const	TALARIS_2013 ("talaris2013")

std::string const	TALARIS_2013_CART ("talaris2013_cart")

std::string const	PRE_TALARIS_2013_STANDARD_WTS ("pre_talaris_2013_standard")

std::string const	CENTROID_WTS ("cen_std")

std::string const	SOFT_REP_WTS ("soft_rep")

std::string const	SOFT_REP_DESIGN_WTS ("soft_rep_design")

std::string const	DNA_INT_WTS ("dna_no_gb")

std::string const	DNA_INT_WTS_GB ("dna")

std::string const	MM_STD_WTS ("mm_std")

std::string const	RNA_LORES_WTS ("rna/denovo/rna_lores")

std::string const	RNA_HIRES_WTS ("rna/denovo/rna_hires")

std::string const	RNA_LORES_PLUS_HIRES_WTS ("rna/denovo/rna_lores_plus_hires")

std::string const	MEMB_HIGHRES_WTS ("membrane_highres")

std::string const	SCORE12_PATCH ("score12")

std::string const	SCORE13 ("score13")

std::string const	DOCK_PATCH ("docking")

std::string const	DOCK_LOW_PATCH ("docking_cen")

std::string const	SCORE4_SMOOTH_CART ("score4_smooth_cart")

std::string const	BETA_GENPOT ("beta_genpot")

std::string const	BETA_NOV16 ("beta_nov16")

std::string const	BETA_NOV15 ("beta_nov15")

std::string const	BETA_JULY15 ("beta_july15")

core::scoring::ScoreFunctionOP	get_score_function (bool const is_fullatom=true)
	A helper function which returns a scoring function held in an owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=talaris2013 for fullatom, and weights=cen_std and patch="" for centroid. More...

core::scoring::ScoreFunctionOP	get_score_function (core::pose::Pose const &pose, bool const is_fullatom=true)
	Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. More...

core::scoring::ScoreFunctionOP	get_score_function (core::pose::Pose const &pose, utility::options::OptionCollection const &options, bool const is_fullatom=true)
	Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. Local Options collection. More...

core::scoring::ScoreFunctionOP	get_score_function (utility::options::OptionCollection const &options, bool const is_fullatom=true)
	A helper function which creates a scoring function held in an owning pointer reading from the input OptionCollection. More...

void	list_read_options_in_get_score_function (utility::options::OptionKeyList &opts)
	A documentation function which reports the set of options read by get_score_function. More...

core::scoring::ScoreFunctionOP	get_score_function_legacy (std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file="")
	A helper function that either returns a ScoreFunctionOP created by get_score_function() or the one specified by the protocol which is activated by the -restore_pre_talaris_2013_behavior flag. The purpose of this function is to preserve legacy behavior for the sake of reproducibility and so that a record of the old behavior is still preserved in the code to ease the process of reverting the change to get_score_function if that were the wrong behavior. More...

core::scoring::ScoreFunctionOP	get_score_function_legacy (utility::options::OptionCollection const &options, std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file)

void	list_read_options_in_get_score_function_legacy (utility::options::OptionKeyList &opts)
	A documentation function which reports the set of options read by get_score_function_legacy. More...

std::string	get_score_functionName (bool const is_fullatom=true)
	use the logic of get_score_function to get the name. The name format is <weights_tag>[_<patch_tag> ... ] More...

std::string	basename_for_score_function (std::string const &sfxn_name)
	returns family name for a specific score function. For example, ref2015_cart returns ref2015 and beta_nov16_cst returns beta_nov16 Returns an empty string if no match is found More...

void	apply_set_weights (ScoreFunctionOP scorefxn, utility::vector1< std::string > const &settings)

std::string	get_current_default_score_function_name ()

bool	operator== (ScoreFunctionInfo const &a, ScoreFunctionInfo const &b)

ScoreType	score_type_from_name (std::string const &name)
	give a ScoreType string name and return its enum type More...

std::istream &	operator>> (std::istream &is, ScoreType &score_type)
	input operator for ScoreType enum type More...

std::ostream &	operator<< (std::ostream &os, ScoreType const &score_type)
	output operator for ScoreType enum type More...

std::ostream &	operator<< (std::ostream &os, ScoreTypes const &score_types)
	output operator for ScoreTypes list type More...

std::string	name_from_score_type (ScoreType score_type)
	Returns the name of the ScoreType <score_type> More...

void	fill_score_range (std::map< std::string, ScoreType > &M, std::string const &prefix, int first, int last)

std::string const	FA_STANDARD_DEFAULT ("FA_STANDARD_DEFAULT")
	global etable_id More...

std::string const	FA_STANDARD_SOFT ("FA_STANDARD_SOFT")

std::string const	FA_STANDARD_MULTIPOLE ("FA_STANDARD_MULTIPOLE")

std::string const	UNFOLDED_SCORE12 ("UNFOLDED_SCORE12")

std::string const	UNFOLDED_MM_STD ("UNFOLDED_MM_STD")

std::string const	UNFOLDED_RNA ("UNFOLDED_RNA")

std::string const	UNFOLDED_SPLIT_TALARIS2013 ("UNFOLDED_SPLIT_TALARIS2013")

std::string const	UNFOLDED_SPLIT_MM_STD ("UNFOLDED_SPLIT_MM_STD")

std::string const	UNFOLDED_SPLIT_USER_DEFINED ("UNFOLDED_SPLIT_USER_DEFINED")

std::string const	SPLIT_UNFOLDED_ELE ("SPLIT_UNFOLDED_ELE")

std::string const	SPLIT_UNFOLDED_PDB ("SPLIT_UNFOLDED_PDB")

std::string const	SPLIT_UNFOLDED_ROSETTA ("SPLIT_UNFOLDED_ROSETTA")

std::string const	SPLIT_UNFOLDED_MM ("SPLIT_UNFOLDED_MM")

std::string const	SPLIT_UNFOLDED_UNIQUE ("SPLIT_UNFOLDED_UNIQUE")

std::string const	SPLIT_UNFOLDED_MEAN ("SPLIT_UNFOLDED_MEAN")

std::string const	SPLIT_UNFOLDED_MEDIAN ("SPLIT_UNFOLDED_MEDIAN")

std::string const	SPLIT_UNFOLDED_MODE ("SPLIT_UNFOLDED_MODE")

std::string const	SPLIT_UNFOLDED_BOLTZ ("SPLIT_UNFOLDED_BOLTZ")

std::string const	SPLIT_UNFOLDED_USER_DEFINED ("SPLIT_UNFOLDED_USER_DEFINED")

SS_Info const &	retrieve_const_ss_info_from_pose (pose::Pose const &pose)
	helper function More...

SS_Info &	retrieve_nonconst_ss_info_from_pose (pose::Pose &pose)
	helper function More...

void	fill_bb_pos (pose::Pose const &pose, BB_Pos &bb_pos)
	helper function More...

bool	dimer_pairing_pointer_sorter (DimerPairingOP const &a, DimerPairingOP const &b)

std::ostream &	operator<< (std::ostream &out, Strands const &s)

std::ostream &	operator<< (std::ostream &out, Helices const &s)

static basic::Tracer	trKillHairpinsIO ("core.score.SS_Killhairpins_Info")

std::ostream &	operator<< (std::ostream &out, Hairpin const &s)

std::ostream &	operator<< (std::ostream &out, Hairpins const &s)

static basic::Tracer	TR ("core.scoring.TMscore")

void	eval_scsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1sc_centroid, Vector const &r2sc_centroid, Real const &r1sc_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...

void	eval_bbsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2sc_centroid, Real const &r1bb_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...

void	eval_bbbb_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2bb_centroid, Real const &r1bb_radius, Real const &r2bb_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...

Vector	compute_bb_centroid (conformation::Residue const &r1)
	Compute the average coordinate of the backbone heavy atoms (aka center of mass). More...

Real	compute_bb_radius (conformation::Residue const &r1, Vector const &r1bb_centroid)
	Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point. More...

Vector	compute_sc_centroid (conformation::Residue const &r1)
	Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone. More...

Real	compute_sc_radius (conformation::Residue const &r1, Vector const &r1sc_centroid)
	Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point. More...

bool	check_score_function_sanity (utility::options::OptionCollection const &options, std::string const &scorefxn_key, bool throw_exception=false)
	Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false. More...

bool	VdWShouldItCount (conformation::Residue const &rsd, Size const &atm)

core::scoring::ScoreFunctionOP	parse_score_function (utility::tag::TagCOP tag, std::string const &option_name, basic::datacache::DataMap const &data, std::string const &dflt_key="commandline")
	Look up the score function defined in the <SCOREFXNS> through the given option. Defaults to 'commandline'. More...

core::scoring::ScoreFunctionOP	parse_score_function (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &dflt_key="commandline")
	Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Defaults to 'commandline'. More...

std::string	get_score_function_name (utility::tag::TagCOP tag, std::string const &option_name)
	Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols. More...

std::string	get_score_function_name (utility::tag::TagCOP tag)
	Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols. More...

void	attributes_for_get_score_function_name (utility::tag::AttributeList &attributes)
	Get attributes ( i.e. options ) for movers to build xml schemas. More...

void	attributes_for_get_score_function_name (utility::tag::AttributeList &attributes, std::string const &option_name)
	Appends the attributes read by get_score_function_name w/ name argument. More...

void	attributes_for_get_score_function_name_w_description (utility::tag::AttributeList &attributes, std::string const &description)
	Appends the attributes read by get_score_function_name. More...

void	attributes_for_get_score_function_name_w_description (utility::tag::AttributeList &attributes, std::string const &option_name, std::string const &description)
	Appends the attributes read by get_score_function_name w/ name argument. More...

void	attributes_for_parse_score_function (utility::tag::AttributeList &attributes)
	Appends the attributes read by parse_score_function. More...

void	attributes_for_parse_score_function (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name)
	Appends the attributes read by parse_score_function w/ name argument. More...

void	attributes_for_parse_score_function_w_description (utility::tag::AttributeList &attributes, std::string const &description)
	Appends the attributes read by parse_score_function with description. More...

void	attributes_for_parse_score_function_w_description (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name, std::string const &description)
	Appends the attributes read by parse_score_function w/ name argument and description. More...

void	attributes_for_parse_score_function_w_description_when_required (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name, std::string const &description="")
	Appends the attributes read by parse_score_function w/ name argument and description. More...

Variables
short const	bit_count []

int const	num_bytes = 21

int const	num_phi = 64

int const	num_theta = 64

int const	num_overlaps = 100

int const	num_orientations = 162

int const	maskbits = 162

std::string const	REF_2015

std::string const	TALARIS_2014

std::string const	TALARIS_2013

std::string const	TALARIS_2013_CART

std::string const	PRE_TALARIS_2013_STANDARD_WTS

std::string const	SCORE13

std::string const	CENTROID_WTS

std::string const	SOFT_REP_WTS

std::string const	SOFT_REP_DESIGN_WTS

std::string const	DNA_INT_WTS

std::string const	DNA_INT_WTS_GB

std::string const	MM_STD_WTS

std::string const	RNA_LORES_WTS

std::string const	RNA_HIRES_WTS

std::string const	RNA_LORES_PLUS_HIRES_WTS

std::string const	MEMB_HIGHRES_WTS

std::string const	SCORE12_PATCH

std::string const	DOCK_PATCH

std::string const	DOCK_LOW_PATCH

std::string const	SCORE4_SMOOTH_CART

std::string const	BETA_GENPOT

std::string const	BETA_NOV16

std::string const	BETA_NOV15

std::string const	BETA_JULY15

std::string const	FA_STANDARD_DEFAULT

std::string const	FA_STANDARD_SOFT

std::string const	FA_STANDARD_MULTIPOLE

std::string const	UNFOLDED_SCORE12

std::string const	UNFOLDED_MM_STD

std::string const	UNFOLDED_RNA

std::string const	UNFOLDED_SPLIT_TALARIS2013

std::string const	UNFOLDED_SPLIT_MM_STD

std::string const	UNFOLDED_SPLIT_USER_DEFINED

std::string const	SPLIT_UNFOLDED_ELE

std::string const	SPLIT_UNFOLDED_PDB

std::string const	SPLIT_UNFOLDED_ROSETTA

std::string const	SPLIT_UNFOLDED_MM

std::string const	SPLIT_UNFOLDED_UNIQUE

std::string const	SPLIT_UNFOLDED_MEAN

std::string const	SPLIT_UNFOLDED_MEDIAN

std::string const	SPLIT_UNFOLDED_MODE

std::string const	SPLIT_UNFOLDED_BOLTZ

std::string const	SPLIT_UNFOLDED_USER_DEFINED

Typedef Documentation

typedef utility::pointer::weak_ptr< APBSConfig > core::scoring::APBSConfigAP

typedef utility::pointer::weak_ptr< APBSConfig const > core::scoring::APBSConfigCAP

typedef utility::pointer::shared_ptr< APBSConfig const > core::scoring::APBSConfigCOP

typedef utility::pointer::shared_ptr< APBSConfig > core::scoring::APBSConfigOP

typedef utility::pointer::weak_ptr< APBSResult > core::scoring::APBSResultAP

typedef utility::pointer::weak_ptr< APBSResult const > core::scoring::APBSResultCAP

typedef utility::pointer::shared_ptr< APBSResult const > core::scoring::APBSResultCOP

typedef utility::pointer::shared_ptr< APBSResult > core::scoring::APBSResultOP

typedef utility::pointer::weak_ptr< APBSWrapper > core::scoring::APBSWrapperAP

typedef utility::pointer::weak_ptr< APBSWrapper const > core::scoring::APBSWrapperCAP

typedef utility::pointer::shared_ptr< APBSWrapper const > core::scoring::APBSWrapperCOP

typedef utility::pointer::shared_ptr< APBSWrapper > core::scoring::APBSWrapperOP

typedef utility::vector1< AtomNeighbor > core::scoring::AtomNeighbors

typedef ObjexxFCL::FArray2D< CArrayP_TableEnergy > core::scoring::AtomPairEnergyTable

typedef utility::pointer::shared_ptr< AtomVDW const > core::scoring::AtomVDWCOP

typedef utility::pointer::shared_ptr< AtomVDW > core::scoring::AtomVDWOP

typedef ObjexxFCL::CArray< Energy > core::scoring::CArray_Energy

typedef ObjexxFCL::CArray< TableEnergy > core::scoring::CArray_TableEnergy

typedef ObjexxFCL::CArrayP< Energy > core::scoring::CArrayP_Energy

typedef ObjexxFCL::CArrayP< TableEnergy > core::scoring::CArrayP_TableEnergy

typedef utility::pointer::shared_ptr< CenHBPotential const > core::scoring::CenHBPotentialCOP

typedef utility::pointer::shared_ptr< CenHBPotential > core::scoring::CenHBPotentialOP

typedef utility::pointer::shared_ptr< CenListInfo > core::scoring::CenListInfoOP

typedef utility::pointer::shared_ptr< CenRotEnvPairPotential const > core::scoring::CenRotEnvPairPotentialCOP

typedef utility::pointer::shared_ptr< CenRotEnvPairPotential > core::scoring::CenRotEnvPairPotentialOP

typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy const > core::scoring::ChemicalShiftAnisotropyCOP

typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy > core::scoring::ChemicalShiftAnisotropyOP

typedef utility::pointer::shared_ptr< ContextGraph const > core::scoring::ContextGraphCOP

typedef utility::pointer::shared_ptr< ContextGraph > core::scoring::ContextGraphOP

typedef utility::pointer::shared_ptr< DenseEnergyContainer > core::scoring::DenseEnergyContainerOP

typedef utility::pointer::shared_ptr< DenseNeighborIterator > core::scoring::DenseNeighborIteratorOP

using core::scoring::DimerPairingOP = typedef utility::pointer::shared_ptr<DimerPairing>

typedef utility::pointer::shared_ptr< DipolarCoupling const > core::scoring::DipolarCouplingCOP

typedef utility::pointer::shared_ptr< DipolarCoupling > core::scoring::DipolarCouplingOP

typedef utility::pointer::shared_ptr< DockingScoreFunction const > core::scoring::DockingScoreFunctionCOP

typedef utility::pointer::shared_ptr< DockingScoreFunction > core::scoring::DockingScoreFunctionOP

typedef utility::pointer::shared_ptr< Energies const > core::scoring::EnergiesCOP

typedef utility::pointer::shared_ptr< Energies > core::scoring::EnergiesOP

typedef utility::pointer::shared_ptr< EnergyGraph > core::scoring::EnergyGraphOP

typedef EMapVector core::scoring::EnergyMap

typedef utility::pointer::shared_ptr< EnvPairPotential const > core::scoring::EnvPairPotentialCOP

typedef utility::pointer::shared_ptr< EnvPairPotential > core::scoring::EnvPairPotentialOP

typedef utility::pointer::shared_ptr< FACTSPoseInfo > core::scoring::FACTSPoseInfoOP

typedef utility::pointer::shared_ptr< FACTSPotential > core::scoring::FACTSPotentialOP

typedef utility::pointer::shared_ptr< FACTSResidueInfo > core::scoring::FACTSResidueInfoOP

typedef utility::pointer::shared_ptr< FACTSRotamerSetInfo > core::scoring::FACTSRotamerSetInfoOP

typedef utility::pointer::shared_ptr< FACTSRsdTypeInfo const > core::scoring::FACTSRsdTypeInfoCOP

typedef utility::pointer::shared_ptr< FACTSRsdTypeInfo > core::scoring::FACTSRsdTypeInfoOP

typedef ObjexxFCL::FArray1D< Energy > core::scoring::FArray1D_Energy

typedef ObjexxFCL::FArray1D< Length > core::scoring::FArray1D_Length

typedef ObjexxFCL::FArray1D< Probability > core::scoring::FArray1D_Probability

typedef ObjexxFCL::FArray1D< TableEnergy > core::scoring::FArray1D_TableEnergy

typedef ObjexxFCL::FArray1D< TableProbability > core::scoring::FArray1D_TableProbability

typedef ObjexxFCL::FArray1D< Weight > core::scoring::FArray1D_Weight

typedef ObjexxFCL::FArray2D< Energy > core::scoring::FArray2D_Energy

typedef ObjexxFCL::FArray2D< Length > core::scoring::FArray2D_Length

typedef ObjexxFCL::FArray2D< Probability > core::scoring::FArray2D_Probability

typedef ObjexxFCL::FArray2D< TableEnergy > core::scoring::FArray2D_TableEnergy

typedef ObjexxFCL::FArray2D< TableProbability > core::scoring::FArray2D_TableProbability

typedef ObjexxFCL::FArray2D< Weight > core::scoring::FArray2D_Weight

typedef ObjexxFCL::FArray3D< Energy > core::scoring::FArray3D_Energy

typedef ObjexxFCL::FArray3D< Length > core::scoring::FArray3D_Length

typedef ObjexxFCL::FArray3D< Probability > core::scoring::FArray3D_Probability

typedef ObjexxFCL::FArray3D< TableEnergy > core::scoring::FArray3D_TableEnergy

typedef ObjexxFCL::FArray3D< TableProbability > core::scoring::FArray3D_TableProbability

typedef ObjexxFCL::FArray3D< Weight > core::scoring::FArray3D_Weight

typedef ObjexxFCL::FArray4D< Energy > core::scoring::FArray4D_Energy

typedef ObjexxFCL::FArray4D< Length > core::scoring::FArray4D_Length

typedef ObjexxFCL::FArray4D< Probability > core::scoring::FArray4D_Probability

typedef ObjexxFCL::FArray4D< TableEnergy > core::scoring::FArray4D_TableEnergy

typedef ObjexxFCL::FArray4D< TableProbability > core::scoring::FArray4D_TableProbability

typedef ObjexxFCL::FArray4D< Weight > core::scoring::FArray4D_Weight

typedef ObjexxFCL::FArray5D< Energy > core::scoring::FArray5D_Energy

typedef ObjexxFCL::FArray5D< Length > core::scoring::FArray5D_Length

typedef ObjexxFCL::FArray5D< Probability > core::scoring::FArray5D_Probability

typedef ObjexxFCL::FArray5D< TableEnergy > core::scoring::FArray5D_TableEnergy

typedef ObjexxFCL::FArray5D< TableProbability > core::scoring::FArray5D_TableProbability

typedef ObjexxFCL::FArray5D< Weight > core::scoring::FArray5D_Weight

typedef utility::pointer::shared_ptr< GenBondedExclInfo const > core::scoring::GenBondedExclInfoCOP

typedef utility::pointer::shared_ptr< GenBondedExclInfo > core::scoring::GenBondedExclInfoOP

typedef utility::pointer::shared_ptr< GenBornPoseInfo > core::scoring::GenBornPoseInfoOP

typedef utility::pointer::shared_ptr< GenBornPotential const > core::scoring::GenBornPotentialCOP

typedef utility::pointer::shared_ptr< GenBornPotential > core::scoring::GenBornPotentialOP

typedef utility::pointer::shared_ptr< GenBornResidueInfo > core::scoring::GenBornResidueInfoOP

typedef utility::pointer::shared_ptr< GenBornRotamerSetInfo > core::scoring::GenBornRotamerSetInfoOP

typedef utility::pointer::shared_ptr< GenericBondedPotential > core::scoring::GenericBondedPotentialOP

typedef utility::pointer::shared_ptr< HydroxylTorsionPotential const > core::scoring::HydroxylTorsionPotentialCOP

typedef utility::pointer::shared_ptr< HydroxylTorsionPotential > core::scoring::HydroxylTorsionPotentialOP

typedef ObjexxFCL::KeyFArray1D< Energy > core::scoring::KeyFArray1D_Energy

typedef ObjexxFCL::KeyFArray1D< Probability > core::scoring::KeyFArray1D_Probability

typedef ObjexxFCL::KeyFArray1D< Real > core::scoring::KeyFArray1D_Real

typedef ObjexxFCL::KeyFArray1D< Weight > core::scoring::KeyFArray1D_Weight

typedef ObjexxFCL::KeyFArray2D< Energy > core::scoring::KeyFArray2D_Energy

typedef ObjexxFCL::KeyFArray2D< Probability > core::scoring::KeyFArray2D_Probability

typedef ObjexxFCL::KeyFArray2D< Real > core::scoring::KeyFArray2D_Real

typedef ObjexxFCL::KeyFArray2D< Weight > core::scoring::KeyFArray2D_Weight

typedef ObjexxFCL::KeyFArray3D< Energy > core::scoring::KeyFArray3D_Energy

typedef ObjexxFCL::KeyFArray3D< Probability > core::scoring::KeyFArray3D_Probability

typedef ObjexxFCL::KeyFArray3D< Real > core::scoring::KeyFArray3D_Real

typedef ObjexxFCL::KeyFArray3D< Weight > core::scoring::KeyFArray3D_Weight

typedef utility::pointer::shared_ptr< LREnergyContainer const > core::scoring::LREnergyContainerCOP

typedef utility::pointer::shared_ptr< LREnergyContainer > core::scoring::LREnergyContainerOP

typedef numeric::xyzMatrix< core::Real > core::scoring::Matrix

typedef core::Real core::scoring::matrix[3][3]

typedef utility::pointer::shared_ptr< Membrane_FAEmbed const > core::scoring::Membrane_FAEmbedCOP

typedef utility::pointer::shared_ptr< Membrane_FAEmbed > core::scoring::Membrane_FAEmbedOP

typedef utility::pointer::shared_ptr< Membrane_FAPotential const > core::scoring::Membrane_FAPotentialCOP

typedef utility::pointer::shared_ptr< Membrane_FAPotential > core::scoring::Membrane_FAPotentialOP

typedef utility::pointer::shared_ptr< MembraneEmbed const > core::scoring::MembraneEmbedCOP

typedef utility::pointer::shared_ptr< MembraneEmbed > core::scoring::MembraneEmbedOP

typedef utility::pointer::shared_ptr< MembranePotential const > core::scoring::MembranePotentialCOP

typedef utility::pointer::shared_ptr< MembranePotential > core::scoring::MembranePotentialOP

typedef utility::pointer::shared_ptr< MembraneTopology const > core::scoring::MembraneTopologyCOP

typedef utility::pointer::shared_ptr< MembraneTopology > core::scoring::MembraneTopologyOP

typedef utility::pointer::shared_ptr< MinimizationGraph const > core::scoring::MinimizationGraphCOP

typedef utility::pointer::shared_ptr< MinimizationGraph > core::scoring::MinimizationGraphOP

typedef utility::pointer::shared_ptr< MinScoreScoreFunction const > core::scoring::MinScoreScoreFunctionCOP

typedef utility::pointer::shared_ptr< MinScoreScoreFunction > core::scoring::MinScoreScoreFunctionOP

typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo const > core::scoring::MultipoleElecPoseInfoCOP

typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo > core::scoring::MultipoleElecPoseInfoOP

typedef utility::pointer::shared_ptr< MultipoleElecPotential const > core::scoring::MultipoleElecPotentialCOP

typedef utility::pointer::shared_ptr< MultipoleElecPotential > core::scoring::MultipoleElecPotentialOP

typedef utility::pointer::shared_ptr< const MultipoleElecResidueInfo > core::scoring::MultipoleElecResidueInfoCOP

typedef utility::pointer::shared_ptr< MultipoleElecResidueInfo > core::scoring::MultipoleElecResidueInfoOP

typedef utility::pointer::shared_ptr< MultipoleElecRotamerSetInfo > core::scoring::MultipoleElecRotamerSetInfoOP

typedef utility::pointer::shared_ptr< MultipoleParameter > core::scoring::MultipoleParameterOP

typedef utility::pointer::shared_ptr< NeighborList const > core::scoring::NeighborListCOP

typedef utility::pointer::shared_ptr< NeighborList > core::scoring::NeighborListOP

typedef utility::pointer::shared_ptr< OmegaTether const > core::scoring::OmegaTetherCOP

typedef utility::pointer::shared_ptr< OmegaTether > core::scoring::OmegaTetherOP

typedef utility::pointer::shared_ptr< OneToAllEnergyContainer > core::scoring::OneToAllEnergyContainerOP

typedef utility::pointer::shared_ptr< OneToAllNeighborIterator > core::scoring::OneToAllNeighborIteratorOP

typedef utility::pointer::shared_ptr< P_AA_ABEGO3 const > core::scoring::P_AA_ABEGO3_COP

typedef utility::pointer::shared_ptr< P_AA_ABEGO3 > core::scoring::P_AA_ABEGO3_OP

typedef utility::pointer::shared_ptr< P_AA_ss const > core::scoring::P_AA_ssCOP

typedef utility::pointer::shared_ptr< P_AA_ss > core::scoring::P_AA_ssOP

typedef utility::pointer::shared_ptr< P_AA const > core::scoring::P_AACOP

typedef utility::pointer::shared_ptr< P_AA > core::scoring::P_AAOP

typedef utility::pointer::shared_ptr< PairEPotential const > core::scoring::PairEPotentialCOP

typedef utility::pointer::shared_ptr< PairEPotential > core::scoring::PairEPotentialOP

using core::scoring::PB = typedef PoissonBoltzmannPotential

typedef utility::pointer::shared_ptr< PDatom const > core::scoring::PDatomCOP

typedef utility::pointer::shared_ptr< PDatom > core::scoring::PDatomOP

typedef utility::pointer::shared_ptr< PDinter const > core::scoring::PDinterCOP

typedef utility::pointer::shared_ptr< PDinter > core::scoring::PDinterOP

typedef utility::pointer::shared_ptr< PDvertex const > core::scoring::PDvertexCOP

typedef utility::pointer::shared_ptr< PDvertex > core::scoring::PDvertexOP

typedef utility::pointer::shared_ptr< PointWaterPotential const > core::scoring::PointWaterPotentialCOP

typedef utility::pointer::shared_ptr< PointWaterPotential > core::scoring::PointWaterPotentialOP

typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialAP

typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCAP

typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCOP

typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialOP

typedef utility::pointer::shared_ptr< const PolymerBondedEnergyContainer > core::scoring::PolymerBondedEnergyContainerCOP

typedef utility::pointer::shared_ptr< PolymerBondedEnergyContainer > core::scoring::PolymerBondedEnergyContainerOP

typedef utility::pointer::shared_ptr< const PolymerBondedNeighborIterator > core::scoring::PolymerBondedNeighborIteratorCOP

typedef utility::pointer::shared_ptr< PolymerBondedNeighborIterator > core::scoring::PolymerBondedNeighborIteratorOP

typedef utility::pointer::weak_ptr< PQR > core::scoring::PQRAP

typedef utility::pointer::weak_ptr< PQR const > core::scoring::PQRCAP

typedef utility::pointer::shared_ptr< PQR const > core::scoring::PQRCOP

typedef utility::pointer::shared_ptr< PQR > core::scoring::PQROP

typedef utility::pointer::shared_ptr< Predicate const > core::scoring::PredicateCOP

typedef utility::pointer::shared_ptr< Predicate > core::scoring::PredicateOP

typedef core::Real core::scoring::Probability

typedef utility::pointer::shared_ptr< ProQPotential > core::scoring::ProQPotentialOP

using core::scoring::R = typedef Ramachandran

typedef utility::pointer::shared_ptr< Ramachandran2B const > core::scoring::Ramachandran2BCOP

typedef utility::pointer::shared_ptr< Ramachandran2B > core::scoring::Ramachandran2BOP

typedef utility::pointer::shared_ptr<Ramachandran const > core::scoring::RamachandranCOP

typedef utility::pointer::shared_ptr<Ramachandran > core::scoring::RamachandranOP

typedef utility::pointer::shared_ptr< RamaPrePro const > core::scoring::RamaPreProCOP

typedef utility::pointer::shared_ptr< RamaPrePro > core::scoring::RamaPreProOP

typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl const > core::scoring::ResidualDipolarCoupling_RohlCOP

typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl > core::scoring::ResidualDipolarCoupling_RohlOP

typedef utility::pointer::shared_ptr< ResidualDipolarCoupling const > core::scoring::ResidualDipolarCouplingCOP

typedef utility::pointer::shared_ptr< ResidualDipolarCoupling > core::scoring::ResidualDipolarCouplingOP

typedef utility::pointer::shared_ptr< ResidueExclParams const > core::scoring::ResidueExclParamsCOP

typedef utility::pointer::shared_ptr< ResidueExclParams > core::scoring::ResidueExclParamsOP

typedef utility::pointer::shared_ptr< ResidueNblistData const > core::scoring::ResidueNblistDataCOP

typedef utility::pointer::shared_ptr< ResidueNblistData > core::scoring::ResidueNblistDataOP

typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator const > core::scoring::ResidueNeighborConstIteratorCOP

typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator > core::scoring::ResidueNeighborConstIteratorOP

typedef utility::pointer::shared_ptr< ResidueNeighborIterator const > core::scoring::ResidueNeighborIteratorCOP

typedef utility::pointer::shared_ptr< ResidueNeighborIterator > core::scoring::ResidueNeighborIteratorOP

typedef utility::pointer::shared_ptr< ResiduePairNeighborList const > core::scoring::ResiduePairNeighborListCOP

typedef utility::pointer::shared_ptr< ResiduePairNeighborList > core::scoring::ResiduePairNeighborListOP

typedef std::list< core::Size > core::scoring::ResidueSelection

typedef utility::vector1< core::Size > core::scoring::ResidueSelectionVector

typedef utility::pointer::shared_ptr< ResPairMinimizationData const > core::scoring::ResPairMinimizationDataCOP

typedef utility::pointer::shared_ptr< ResPairMinimizationData > core::scoring::ResPairMinimizationDataOP

typedef utility::pointer::shared_ptr< ResSingleMinimizationData const > core::scoring::ResSingleMinimizationDataCOP

typedef utility::pointer::shared_ptr< ResSingleMinimizationData > core::scoring::ResSingleMinimizationDataOP

typedef core::Real core::scoring::rvec[3]

typedef core::Real core::scoring::rvec5[5]

typedef utility::pointer::shared_ptr< SASAPotential const > core::scoring::SASAPotentialCOP

typedef utility::pointer::shared_ptr< SASAPotential > core::scoring::SASAPotentialOP

typedef Real core::scoring::Score

typedef utility::pointer::shared_ptr< ScoreFunction const > core::scoring::ScoreFunctionCOP

typedef utility::pointer::shared_ptr< ScoreFunctionInfo const > core::scoring::ScoreFunctionInfoCOP

typedef utility::pointer::shared_ptr< ScoreFunctionInfo > core::scoring::ScoreFunctionInfoOP

typedef utility::pointer::shared_ptr< ScoreFunction > core::scoring::ScoreFunctionOP

typedef utility::vector1< ScoreType > core::scoring::ScoreTypes

typedef utility::pointer::shared_ptr< SecondaryStructurePotential const > core::scoring::SecondaryStructurePotentialCOP

typedef utility::pointer::shared_ptr< SecondaryStructurePotential > core::scoring::SecondaryStructurePotentialOP

typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialAP

typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCAP

typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCOP

typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialOP

typedef utility::pointer::shared_ptr< SigmoidWeightedCenList<Real> > core::scoring::SigmoidWeightedCenListRealOP

typedef utility::pointer::shared_ptr< SigmoidWeightedCenList<numeric::xyzVector<Real> > > core::scoring::SigmoidWeightedCenListVectorOP

typedef utility::pointer::shared_ptr< SmoothEnvPairPotential const > core::scoring::SmoothEnvPairPotentialCOP

typedef utility::pointer::shared_ptr< SmoothEnvPairPotential > core::scoring::SmoothEnvPairPotentialOP

typedef utility::pointer::shared_ptr< SplitUnfoldedTwoBodyPotential > core::scoring::SplitUnfoldedTwoBodyPotentialOP

typedef utility::pointer::shared_ptr< SS_Info const > core::scoring::SS_InfoCOP

typedef utility::pointer::shared_ptr< SS_Info > core::scoring::SS_InfoOP

typedef utility::pointer::shared_ptr< SS_Killhairpins_Info const > core::scoring::SS_Killhairpins_InfoCOP

typedef utility::pointer::shared_ptr< SS_Killhairpins_Info > core::scoring::SS_Killhairpins_InfoOP

typedef float core::scoring::TableEnergy

typedef float core::scoring::TableProbability

typedef utility::pointer::shared_ptr< TenANeighborGraph const > core::scoring::TenANeighborGraphCOP

typedef utility::pointer::shared_ptr< TenANeighborGraph > core::scoring::TenANeighborGraphOP

typedef utility::pointer::shared_ptr< TwelveANeighborGraph const > core::scoring::TwelveANeighborGraphCOP

typedef utility::pointer::shared_ptr< TwelveANeighborGraph > core::scoring::TwelveANeighborGraphOP

typedef utility::pointer::shared_ptr< UnfoldedStatePotential > core::scoring::UnfoldedStatePotentialOP

typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo const > core::scoring::VdWTinkerPoseInfoCOP

typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo > core::scoring::VdWTinkerPoseInfoOP

typedef utility::pointer::shared_ptr< VdWTinkerPotential const > core::scoring::VdWTinkerPotentialCOP

typedef utility::pointer::shared_ptr< VdWTinkerPotential > core::scoring::VdWTinkerPotentialOP

typedef utility::pointer::shared_ptr< const VdWTinkerResidueInfo > core::scoring::VdWTinkerResidueInfoCOP

typedef utility::pointer::shared_ptr< VdWTinkerResidueInfo > core::scoring::VdWTinkerResidueInfoOP

typedef utility::pointer::shared_ptr< VdWTinkerRotamerSetInfo > core::scoring::VdWTinkerRotamerSetInfoOP

typedef numeric::xyzVector< core::Real > core::scoring::Vector

typedef utility::pointer::shared_ptr< WaterAdductHBondPotential const > core::scoring::WaterAdductHBondPotentialCOP

typedef utility::pointer::shared_ptr< WaterAdductHBondPotential > core::scoring::WaterAdductHBondPotentialOP

typedef Real core::scoring::Weight

Enumeration Type Documentation

enum core::scoring::ABEGO_index

Enumerator
ABEGO_index_INVALID
ABEGO_index_A
ABEGO_index_START
ABEGO_index_B
ABEGO_index_E
ABEGO_index_G
ABEGO_index_O
ABEGO_index_COUNT

enum core::scoring::ContextGraphType

Enumerator
ten_A_neighbor_graph
twelve_A_neighbor_graph
centroid_neighbor_graph
num_context_graph_types

enum core::scoring::min_pair_data

Enumerator
etab_pair_nblist
etab_classic_intrares_pair_nblist
lkball_nblist
cst_respair_data
elec_pair_nblist
rna_elec_pair_nblist
geom_solv_pair_nblist
fa_stack_pair_nblist
lk_PolarNonPolar_pair_nblist
fa_dslf_respair_data
fa_custom_pair_dist_data
lkb_respair_data
vdw_respair_data
mp_respair_data
mg_pair_nblist
hbond_respair_data
n_min_pair_data

enum core::scoring::min_single_data

Enumerator
etab_single_nblist
etab_classic_intrares_single_nblist
mm_lj_intra_nblist
cst_res_data
lkb_res_data
vdw_res_data
mp_res_data
hbond_res_data
n_min_single_data

enum core::scoring::MultipoleAxisType

Enumerator
none
z_axis_only
three_fold
bisector
z_then_bisector
z_then_x

enum core::scoring::ProteinTorsion

Enumerator
PHI
PSI
OMEGA
CHI1
CHI2
CHI3
CHI4
protein_torsion_end

enum core::scoring::Rama_Table_Type

Enumerator
flat_l_aa_ramatable
flat_d_aa_ramatable
flat_symm_dl_aa_ramatable
flat_symm_gly_ramatable
flat_symm_pro_ramatable
flat_l_aa_ramatable_stringent
flat_d_aa_ramatable_stringent
flat_symm_dl_aa_ramatable_stringent
flat_symm_gly_ramatable_stringent
flat_symm_pro_ramatable_stringent
unknown_ramatable_type
end_of_ramatable_type_list

enum core::scoring::ReadMode

Enumerator
rmNONE
rmATOM
rmBOND
rmANGLE
rmTORSION
rmIMPROPER

enum core::scoring::rmsd_atoms

Enumerator
rmsd_protein_bb_heavy
rmsd_protein_bb_heavy_including_O
rmsd_protein_bb_ca
rmsd_sc_heavy
rmsd_sc
rmsd_all_heavy
rmsd_all
rmsd_atom_total

enum core::scoring::ScoreType

Type for looking up cached energies.

Remarks: I guess we could get rid of the fa_ prefix, except maybe for fa_pair, to distinguish from std::pair and the centroid pair score...

Enumerator
fa_atr
fa_rep
fa_sol
fa_intra_atr
fa_intra_rep
fa_intra_sol
fa_intra_atr_xover4
fa_intra_rep_xover4
fa_intra_sol_xover4
fa_intra_atr_nonprotein
fa_intra_rep_nonprotein
fa_intra_sol_nonprotein
fa_intra_RNA_base_phos_atr
fa_intra_RNA_base_phos_rep
fa_intra_RNA_base_phos_sol
fa_atr_dummy
fa_rep_dummy
fa_sol_dummy
fa_vdw_tinker
lk_hack
lk_ball
lk_ball_wtd
lk_ball_iso
lk_ball_bridge
lk_ball_bridge_uncpl
coarse_fa_atr
coarse_fa_rep
coarse_fa_sol
coarse_beadlj
mm_lj_intra_rep
mm_lj_intra_atr
mm_lj_inter_rep
mm_lj_inter_atr
mm_twist
mm_bend
mm_stretch
lk_costheta
lk_polar
lk_nonpolar
lk_polar_intra_RNA
lk_nonpolar_intra_RNA
fa_elec
fa_elec_bb_bb
fa_elec_bb_sc
fa_elec_sc_sc
fa_intra_elec
h2o_hbond
dna_dr
dna_bp
dna_bs
dna_ref
peptide_bond
pcs
pcsTs1
pcsTs2
pcsTs3
pcsTs4
pcs2
fastsaxs
saxs_score
saxs_cen_score
saxs_fa_score
pddf_score
fiberdiffraction
fiberdiffractiondens
fa_mbenv
fa_mbsolv
fa_elec_rna_phos_phos
fa_elec_rna_phos_sugr
fa_elec_rna_phos_base
fa_elec_rna_sugr_sugr
fa_elec_rna_sugr_base
fa_elec_rna_base_base
fa_elec_rna_phos_phos_fast
fa_elec_rna_phos_sugr_fast
fa_elec_rna_phos_base_fast
fa_elec_rna_sugr_sugr_fast
fa_elec_rna_sugr_base_fast
fa_elec_rna_base_base_fast
fa_elec_aro_aro
fa_elec_aro_all
hack_aro
rna_fa_atr_base
rna_fa_rep_base
rna_data_backbone
ch_bond
ch_bond_bb_bb
ch_bond_sc_sc
ch_bond_bb_sc
pro_close
rama2b
vdw
cenpack
cenpack_smooth
cen_hb
hybrid_vdw
gauss
rna_vdw
rnp_vdw
rna_base_backbone
rna_backbone_backbone
rna_repulsive
rna_base_pair_pairwise
rna_base_axis_pairwise
rna_base_stagger_pairwise
rna_base_stack_pairwise
rna_base_stack_axis_pairwise
rna_data_base
rna_base_pair
rna_base_axis
rna_base_stagger
rna_base_stack
rna_base_stack_axis
rnp_base_pair
rnp_stack
rnp_stack_xy
rnp_pair
rnp_pair_dist
rnp_aa_to_rna_backbone
rna_mg_point
rna_mg_point_indirect
mg
mg_lig
mg_sol
mg_ref
hoh_ref
rna_torsion
rna_torsion_sc
rna_suite
rna_jr_suite
suiteness_bonus
tna_suite
rna_sugar_close
fa_stack
fa_stack_lower
fa_stack_upper
fa_stack_aro
fa_stack_ext
fa_stack_sol
fa_stack_lr
fa_stack_rna_protein
fa_stack_rna_protein_aro
ss_contact_worst
stack_elec
stack_elec_base_base
stack_elec_base_bb
alignment
dna_bb_torsion
dna_sugar_close
dna_base_distance
geom_sol_fast
geom_sol_fast_intra_RNA
fa_cust_pair_dist
custom_atom_pair
orbitals_hpol_bb
pci_cation_pi
pci_pi_pi
pci_salt_bridge
pci_hbond
arg_cation_pi
python
n_ci_2b_score_types
fa_pair
fa_pair_aro_aro
fa_pair_aro_pol
fa_pair_pol_pol
hbond_sr_bb
hbond_lr_bb
hbond_bb_sc
hbond_sr_bb_sc
hbond_lr_bb_sc
hbond_sc
hbond_intra
hbond_wat
wat_entropy
hbond
npd_hbond_sr_bb
npd_hbond_lr_bb
npd_hbond_bb_sc
npd_hbond_sr_bb_sc
npd_hbond_lr_bb_sc
npd_hbond_sc
npd_hbond_intra
npd_hbond
fa_grpelec
interface_dd_pair
geom_sol
geom_sol_intra_RNA
occ_sol_fitted
occ_sol_fitted_onebody
occ_sol_exact
cen_rot_pair
cen_rot_pair_ang
cen_rot_pair_dih
pair
cen_pair_smooth
Mpair
MPPair
FaMPSolv
suck
rna_rg
rna_motif
facts_elec
facts_solv
facts_sasa
motif_dock
pointwater
goap
goap_dist
goap_angle
approximate_buried_unsat_penalty
interchain_pair
interchain_vdw
n_shortranged_2b_score_types
gb_elec
multipole_elec
fa_sasa
dslf_ss_dst
dslf_cs_ang
dslf_ss_dih
dslf_ca_dih
dslf_cbs_ds
dslf_fa13
dslfc_cen_dst
dslfc_cb_dst
dslfc_ang
dslfc_cb_dih
dslfc_bb_dih
dslfc_rot
dslfc_trans
dslfc_RT
atom_pair_constraint
base_pair_constraint
coarse_chainbreak_constraint
constant_constraint
coordinate_constraint
angle_constraint
dihedral_constraint
big_bin_constraint
dunbrack_constraint
site_constraint
metalhash_constraint
metalbinding_constraint
rna_stub_coord_hack
bond_geometry
rna_bond_geometry
Hpol_bond_geometry
rama
omega
fa_dun
fa_dun_dev
fa_dun_rot
fa_dun_semi
cen_rot_dun
dna_chi
p_aa_pp
p_aa_ss
yhh_planarity
hxl_tors
h2o_intra
ref
ref_nc
seqdep_ref
nmer_ref
nmer_pssm
nmer_svm
envsmooth
e_pH
rna_bulge
dna_dihedral_bb
dna_dihedral_chi
dna_dihedral_sugar
sugar_bb
free_suite
free_2HOprime
free_side_chain
free_base
free_res
free_dof
intermol
other_pose
special_rot
PB_elec
cen_env_smooth
cbeta_smooth
cen_rot_env
cen_rot_cbeta
env
cbeta
DFIRE
Menv
Mcbeta
Menv_non_helix
Menv_termini
Menv_tm_proj
Mlipo
rg
rg_local
co
hs_pair
ss_pair
rsigma
sheet
burial_v2
burial
abego
covalent_labeling
covalent_labeling_fa
hrf_ms_labeling
rnp_env
loop_close
missing_res
MPEnv
MPCbeta
MPLipo
MPTermini
MPNonHelix
MPTMProj
FaMPEnv
FaMPEnvSmooth
fa_water_to_bilayer
MPResidueLipophilicity
span_ins
mp_span_ang
MPHelicality
natbias_ss
natbias_hs
natbias_hh
natbias_stwist
aa_cmp
dock_ens_conf
csa
dc
rdc
rdc_segments
rdc_rohl
nmr_pcs
nmr_rdc
nmr_pre
cen_pair_motifs
cen_pair_motif_degree
holes
holes_decoy
holes_resl
holes_min
holes_min_mean
rna_chem_shift
rna_chem_map
rna_chem_map_lores
rna_partition
dab_sasa
dab_sev
sa
d2h_sa
ProQM
ProQ
interchain_env
interchain_contact
chainbreak
linear_chainbreak
overlap_chainbreak
distance_chainbreak
dof_constraint
branch_conn
linear_branch_conn
rama_prepro
paa_abego3
cart_bonded
cart_bonded_angle
cart_bonded_length
cart_bonded_ring
cart_bonded_torsion
cart_bonded_proper
cart_bonded_improper
gen_bonded
gen_bonded_bond
gen_bonded_angle
gen_bonded_torsion
gen_bonded_improper
neigh_vect
neigh_count
neigh_vect_raw
symE_bonus
sym_lig
mhc_epitope
pack_stat
rms
res_type_constraint
res_type_linking_constraint
pocket_constraint
backbone_stub_constraint
backbone_stub_linear_constraint
surface
p_aa
unfolded
split_unfolded_two_body
fa_atr_ref
fa_rep_ref
fa_sol_ref
fa_elec_ref
hbond_ref
dslf_fa13_ref
fa_intra_atr_ref
fa_intra_rep_ref
fa_intra_sol_ref
pro_close_ref
fa_dun_ref
fa_dun_dev_ref
fa_dun_rot_ref
fa_dun_semi_ref
rama_ref
p_aa_pp_ref
omega_ref
mm_lj_intra_rep_ref
mm_lj_intra_atr_ref
mm_twist_ref
elec_dens_fast
elec_dens_window
elec_dens_whole_structure_ca
elec_dens_whole_structure_allatom
elec_dens_atomwise
grid_vdw
xtal_ml
xtal_rwork
xtal_rfree
hpatch
Menv_smooth
wat_desolv
ring_close
aa_repeat
aa_composition
aspartimide_penalty
hbnet
buried_unsatisfied_penalty
netcharge
voids_penalty
dna_env
dna_pair
dump_trajectory
sidechain_neighbors
membrane_span_constraint
membrane_span_term_z_constraint
aromatic_restraint
total_score
dummy_score_type
n_score_types	This element marks the end of the active score types. Elements in the enumeration up to this point will have space allocated for them in the EnergyMap object. Elements past this point are considered inactive and will not have space allocated for them. If you wish to use an inactive score type, you must move that score type into its appropriate position in the ScoreType enumeration (described above) and then recompile. Inactive score types must still have their names included in the ScoreTypeManager's string-to-score-type map.
end_of_score_type_enumeration	This element marks the very end of the score type enumeration. Elements between the n_score_types element and this element are considered inactive. They may not be used by any EnergyMethod or they will result in an out-of-bounds write and unexpected behavior. To use an inactive score type, the score type must be moved to an earlier position in this enumeration, and the program must be recompiled. Keep this guy last.

Function Documentation

int core::scoring::abego3aa_to_index	(	const char	abego1,
		const char	abego2,
		const char	abego3,
		const core::chemical::AA	aa_index
	)

inline

References ABEGO_index_INVALID, abego_to_index(), core::chemical::first_l_aa, core::chemical::num_canonical_aas, and TR().

Referenced by abego3aa_to_index(), core::scoring::P_AA_ABEGO3::P_AA_ABEGO3_energy(), and core::scoring::P_AA_ABEGO3::read_P_AA_ABEGO3().

int core::scoring::abego3aa_to_index	(	const char	abego1,
		const char	abego2,
		const char	abego3,
		const char	aa
	)

inline

References core::chemical::aa_from_oneletter_code(), abego3aa_to_index(), and TR().

ABEGO_index core::scoring::abego_to_index ( char abego )

inline

References ABEGO_index_A, ABEGO_index_B, ABEGO_index_E, ABEGO_index_G, ABEGO_index_INVALID, and ABEGO_index_O.

Referenced by abego3aa_to_index().

core::Real core::scoring::all_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_heavyatom(), rms, and rmsd_with_super().

Referenced by protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::idealize::IdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::idealize::basic_idealize(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::check_for_closeness_without_working_parameters(), protocols::rna::denovo::movers::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::pose_reporters::RMSDReporter::report_property().

core::Real core::scoring::all_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection
	)

References is_heavyatom(), rms, and rmsd_with_super().

core::Real core::scoring::all_atom_rmsd_nosuper	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_heavyatom(), rms, and rmsd_no_super().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply(), and protocols::cluster::GatherPosesMover::get_distance_measure().

core::Real core::scoring::all_scatom_rmsd_nosuper	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_scatom(), rms, and rmsd_no_super().

ObjexxFCL::FArray2D_int core::scoring::angles	(	num_phi	,
		num_theta
	)

Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::nmr::pcs::PCSTensor::diagonalize_tensor(), core::scoring::nmr::rdc::RDCTensor::diagonalize_tensor(), get_angles(), input_sasa_dats(), core::scoring::packstat::old::input_sasa_dats(), core::scoring::nmr::order_tensor_parameters(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

void core::scoring::apply_set_weights	(	ScoreFunctionOP	scorefxn,
		utility::vector1< std::string > const &	settings
	)

References score_type_from_name(), protocols::hybridization::t, and TR().

Referenced by core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), and protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn().

void core::scoring::attributes_for_get_score_function_name ( utility::tag::AttributeList & attributes )

Get attributes ( i.e. options ) for movers to build xml schemas.

Appends the attributes read by get_score_function_name.

References attributes_for_get_score_function_name_w_description().

void core::scoring::attributes_for_get_score_function_name	(	utility::tag::AttributeList &	attributes,
		std::string const &	option_name
	)

Appends the attributes read by get_score_function_name w/ name argument.

References attributes_for_get_score_function_name_w_description().

void core::scoring::attributes_for_get_score_function_name_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	description
	)

Appends the attributes read by get_score_function_name.

Referenced by attributes_for_get_score_function_name().

void core::scoring::attributes_for_get_score_function_name_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	option_name,
		std::string const &	description
	)

Appends the attributes read by get_score_function_name w/ name argument.

void core::scoring::attributes_for_parse_score_function ( utility::tag::AttributeList & attributes )

Appends the attributes read by parse_score_function.

References attributes_for_parse_score_function_w_description().

void core::scoring::attributes_for_parse_score_function	(	utility::tag::AttributeList &	attributes,
		std::string const &	sfxn_option_name
	)

Appends the attributes read by parse_score_function w/ name argument.

References attributes_for_parse_score_function_w_description().

void core::scoring::attributes_for_parse_score_function_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	description
	)

Appends the attributes read by parse_score_function with description.

Referenced by attributes_for_parse_score_function(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::provide_xml_schema(), protocols::simple_filters::InterfaceHbondsFilter::provide_xml_schema(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema(), protocols::minimization_packing::MinPackMover::provide_xml_schema(), and protocols::fold_from_loops::NubInitioMover::provide_xml_schema().

void core::scoring::attributes_for_parse_score_function_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	sfxn_option_name,
		std::string const &	description
	)

Appends the attributes read by parse_score_function w/ name argument and description.

void core::scoring::attributes_for_parse_score_function_w_description_when_required	(	utility::tag::AttributeList &	attributes,
		std::string const &	sfxn_option_name,
		std::string const &	description = `""`
	)

Appends the attributes read by parse_score_function w/ name argument and description.

This version appends the attributes as required attributes.

Author: Vikram K. Mulligan.

Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema(), and protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema().

core::Real core::scoring::automorphic_rmsd	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		bool	superimpose
	)

RMSD between residues, accounting for automorphisms (symmetries). For example if you have something like a tyrosine, you won't get a higher rmsd just because you flipped the ring 180 degrees (Rocco). Does NOT include H atoms – they add lots of extra symmetries.

Just iterates over all automorphisms for this residue type and chooses the minimum RMS.

References core::chemical::ResidueTypeBase::name(), core::conformation::Residue::nheavyatoms(), residue_rmsd_nosuper(), residue_rmsd_super(), core::conformation::Residue::seqpos(), tr(), and core::conformation::Residue::type().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_ddg::ddG::calculate(), protocols::ligand_docking::check_RMSD(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::ligand_docking::ga_ligand_dock::distance_slow(), protocols::ligand_docking::get_automorphic_RMSDs(), protocols::motifs::MotifSearch::incorporate_motifs(), core::scoring::nmr::NMRDummySpinlabelEnsemble::init_from_database_file(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

std::string core::scoring::basename_for_score_function ( std::string const & sfxn_name )

returns family name for a specific score function. For example, ref2015_cart returns ref2015 and beta_nov16_cst returns beta_nov16 Returns an empty string if no match is found

References BETA_GENPOT, BETA_JULY15, BETA_NOV15, BETA_NOV16, CENTROID_WTS, DNA_INT_WTS, DNA_INT_WTS_GB, DOCK_LOW_PATCH, DOCK_PATCH, MEMB_HIGHRES_WTS, MM_STD_WTS, PRE_TALARIS_2013_STANDARD_WTS, REF_2015, RNA_HIRES_WTS, RNA_LORES_PLUS_HIRES_WTS, RNA_LORES_WTS, SCORE12_PATCH, SCORE13, SCORE4_SMOOTH_CART, SOFT_REP_DESIGN_WTS, SOFT_REP_WTS, TALARIS_2013, TALARIS_2014, and TR().

Referenced by protocols::relax::FastRelax::get_possible_relax_script_names().

core::Real core::scoring::bb_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

Compute rmsd for only backbone residues (excluding carboxyl oxygen)

References is_protein_backbone(), rms, and rmsd_with_super().

Referenced by protocols::membrane::MPQuickRelaxMover::apply(), and protocols::relax::RangeRelaxMover::apply().

core::Real core::scoring::bb_rmsd_including_O	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

Compute rmsd for only backbone residues (including carboxyl oxygen)

References is_protein_backbone_including_O(), rms, and rmsd_with_super().

Referenced by protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), and protocols::grafting::perturb_backbone_for_test().

std::string const core::scoring::BETA_GENPOT ( "beta_genpot" )

std::string const core::scoring::BETA_JULY15 ( "beta_july15" )

std::string const core::scoring::BETA_NOV15 ( "beta_nov15" )

std::string const core::scoring::BETA_NOV16 ( "beta_nov16" )

template<class T >

core::Real core::scoring::biggest_residue_deviation_no_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

function to return the biggest deviation between an atom in a pair of poses,

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf().

template<class T >

core::Real core::scoring::biggest_residue_deviation_no_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

function to return the biggest deviation between an atom in a pair of poses,

as specified by the predicate and the subset

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

core::Size core::scoring::bin_from_bond	(	core::chemical::BondName	bn,
		core::chemical::BondRingness	br
	)

convert a bond type to a bin index

References core::chemical::BondNotInRing, and core::chemical::UnknownRingness.

Referenced by core::scoring::BondOrderParser::factor(), core::scoring::BondOrderParser::invfactor(), and core::scoring::GenericBondedPotential::lookup_tors_params().

static Real const core::scoring::BOGUS_ENERGY ( 99999. 99 )

static

utility::vector1< core::Size > core::scoring::bondorders_map ( std::string bt )

helper function to convert string specification of bondorders to indices

References core::scoring::BondOrderParser::parse().

Referenced by core::scoring::GenericBondedPotential::modify_tors_params(), and core::scoring::GenericBondedPotential::read_database().

core::Real core::scoring::CA_gdtmm	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		const std::map< core::Size, core::Size > &	residues
	)

Compute the CA RMSD between two poses.

Computes the gdtmm between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.

References retrieve_coordinates(), and xyz_gdtmm().

Referenced by protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::cluster::GatherPosesMover::get_distance_measure(), native_CA_gdtmm(), and protocols::jobdist::not_universal_main().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< Size > const &	residue_selection,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

References fill_rmsd_coordinates(), core::pose::Pose::size(), tr(), and xyz_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score.

References fill_rmsd_coordinates(), is_protein_CA(), core::pose::Pose::size(), and xyz_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.

References CA_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< Size > const &	residue_selection
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.

Referenced by CA_gdtmm().

void core::scoring::CA_gdttm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Real &	gdttm_score,
		core::Real &	gdtha_score,
		std::list< Size > const &	residue_selection
	)

Calculate gdttm score based on the C-alpha positions in pose1 and pose2.

References core::scoring::TMscore::apply(), fill_rmsd_coordinates(), core::scoring::TMscore::get_GDTHA(), core::scoring::TMscore::get_GDTTS(), core::pose::Pose::size(), and tr().

Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), and protocols::md::CartesianMD::report_MD().

void core::scoring::CA_gdttm	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		core::Real &	gdttm_score,
		core::Real &	gdtha_score,
		const std::map< core::Size, core::Size > &	residues
	)

References core::scoring::TMscore::apply(), core::scoring::TMscore::get_GDTHA(), core::scoring::TMscore::get_GDTTS(), and retrieve_coordinates().

void core::scoring::CA_gdttm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Real &	gdttm_score,
		core::Real &	gdtha_score
	)

References core::scoring::TMscore::apply(), fill_rmsd_coordinates(), core::scoring::TMscore::get_GDTHA(), core::scoring::TMscore::get_GDTTS(), is_protein_CA(), and core::pose::Pose::size().

int core::scoring::CA_maxsub	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Real	rms
	)

Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information.

References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::size().

Referenced by protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectMaxsubEvaluator::apply(), and protocols::jobdist::not_universal_main().

int core::scoring::CA_maxsub	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection,
		Real	rms
	)

References fill_rmsd_coordinates(), and tr().

int core::scoring::CA_maxsub_by_subset	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		utility::vector1< bool >
	)

References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::size().

core::Real core::scoring::CA_or_equiv_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end
	)

Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose.

References fill_rmsd_coordinates(), protocols::mean_field::min(), rms, core::pose::Pose::size(), and tr().

Referenced by CA_rmsd(), core::scoring::methods::RMS_Energy::finalize_total_energy(), and native_CA_rmsd().

core::Real core::scoring::CA_or_equiv_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size > const &	residue_selection
	)

References fill_rmsd_coordinates(), and tr().

Referenced by CA_rmsd().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end
	)

Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose.

References CA_or_equiv_rmsd(), fill_rmsd_coordinates(), protocols::mean_field::min(), rms, core::pose::Pose::size(), and tr().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		const std::map< core::Size, core::Size > &	residues
	)

Compute the CA RMSD between two poses.

Computes the root mean squared deviation between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.

References retrieve_coordinates().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end,
		utility::vector1< Size > const &	exclude
	)

References fill_rmsd_coordinates(), and rms.

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection
	)

References CA_or_equiv_rmsd(), fill_rmsd_coordinates(), and tr().

Referenced by compute_jump_rmsd().

core::Real core::scoring::CA_rmsd_symmetric	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), fill_rmsd_coordinates(), is_protein_CA(), core::pose::symmetry::is_symmetric(), core::chemical::element::N, rms, and tr().

Referenced by protocols::simple_filters::SymmetricRmsdEvaluator::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::cluster::GatherPosesMover::get_distance_measure(), and protocols::relax::FastRelax::inner_loop_accept_to_best_command().

void core::scoring::calc_atom_masks	(	core::conformation::Residue const &	irsd,
		core::conformation::Residue const &	jrsd,
		Real const	probe_radius,
		Real const	cutoff_distance,
		utility::vector1< Real > const &	radii,
		id::AtomID_Map< bool > const &	atom_subset,
		core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &	atom_masks
	)

References angles(), core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), get_orientation(), get_overlap(), core::chemical::AtomType::is_h2o(), masks(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), num_bytes, core::conformation::Residue::seqpos(), and protocols::kinmatch::xyz().

Referenced by calc_per_atom_sasa().

Real core::scoring::calc_per_atom_sasa	(	pose::Pose const &	pose,
		id::AtomID_Map< Real > &	atom_sasa,
		utility::vector1< Real > &	rsd_sasa,
		Real const	probe_radius,
		bool const	use_big_polar_H
	)

Return total SASA.

References calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), and core::pose::initialize_atomid_map().

Referenced by protocols::task_operations::SelectBySASAOperation::apply(), protocols::fldsgn::topology::calc_delta_sasa(), calc_per_res_hydrophobic_sasa(), core::select::util::SelectResiduesByLayer::calc_rsd_sasa(), protocols::forge::methods::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::motif::get_sasa(), protocols::constel::FilterBySASA::init(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pose::metrics::simple_calculators::SasaCalculatorLegacy::recompute(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), protocols::features::ResidueBurialFeatures::report_features(), and protocols::features::HBondFeatures::report_features().

Real core::scoring::calc_per_atom_sasa	(	pose::Pose const &	pose,
		id::AtomID_Map< Real > &	atom_sasa,
		utility::vector1< Real > &	rsd_sasa,
		Real const	probe_radius,
		bool const	use_big_polar_H,
		id::AtomID_Map< bool > &	atom_subset,
		bool const	use_naccess_sasa_radii,
		bool const	expand_polar_radii,
		Real const	polar_expansion_radius,
		bool const	include_probe_radius_in_atom_radii,
		bool const	use_lj_radii
	)

Real core::scoring::calc_per_atom_sasa_sc	(	pose::Pose const &	pose,
		utility::vector1< Real > &	rsd_sasa,
		bool	normalize
	)

References calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::n_atom(), normalizing_area(), core::pose::Pose::residue(), and core::id::AtomID_Map< T >::size().

Referenced by protocols::task_operations::CrystalContactsOperation::apply(), core::scoring::methods::ProQ_Energy::calculate_feature_vector(), and core::scoring::methods::ProQ_Energy::calculate_feature_vector_proq2().

Real core::scoring::calc_per_res_hydrophobic_sasa	(	pose::Pose const &	pose,
		utility::vector1< Real > &	rsd_sasa,
		utility::vector1< Real > &	rsd_hydrophobic_sasa,
		Real const	probe_radius,
		bool	use_naccess_sasa_radii
	)

Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)

References core::conformation::Residue::atom_type(), calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::name3(), core::chemical::ResidueType::natoms(), core::conformation::Residue::natoms(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::size(), and TR().

Real core::scoring::calc_total_sasa	(	pose::Pose const &	pose,
		Real const	probe_radius
	)

returns total sasa

References calc_per_atom_sasa().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), and core::scoring::methods::SA_Energy::finalize_total_energy().

Real core::scoring::calpha_superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.".

both poses must have the same length.

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID::set(), core::pose::Pose::size(), and superimpose_pose().

Referenced by protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::simple_moves::CombinePoseMover::apply(), protocols::mpi_refinement::CA_Sscore(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::star::Extender::extend_unaligned(), protocols::mpi_refinement::superimpose_all(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

std::string const core::scoring::CENTROID_WTS ( "cen_std" )

bool core::scoring::check_score_function_sanity	(	utility::options::OptionCollection const &	options,
		std::string const &	scorefxn_key,
		bool	throw_exception
	)

Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false.

References TR().

Referenced by protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), and parse_score_function().

int core::scoring::compare_by_abs	(	const void *	a,
		const void *	b
	)

inline

Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().

Vector core::scoring::compute_bb_centroid ( conformation::Residue const & res )

Compute the average coordinate of the backbone heavy atoms (aka center of mass).

returns the origin if there are no backbone atoms

References core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by compute_sc_centroid(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().

Real core::scoring::compute_bb_radius	(	conformation::Residue const &	res,
		Vector const &	bb_centroid
	)

Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point.

References core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().

void core::scoring::compute_jump_rmsd	(	const core::pose::Pose &	reference,
		const core::pose::Pose &	model,
		boost::unordered_map< core::Size, core::Real > &	rmsds
	)

Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id.

Computes the RMSD of the jump residues (jump point +/- 1 residue) of <model> and <reference>. Jump residues are identified by scanning <reference>'s FoldTree. Results are stored in the output parameter <rmsds>, keyed by the index of the jump point. For example,

Jump 100 => 10 rmsds[10] = rmsd(residues 9-11 in reference, residues 9-11 in model)

References CA_rmsd(), core::pose::Pose::fold_tree(), and core::pose::Pose::size().

Referenced by protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd().

Vector core::scoring::compute_sc_centroid ( conformation::Residue const & res )

Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone.

References compute_bb_centroid(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::NeighTeller::isneigh(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().

Real core::scoring::compute_sc_radius	(	conformation::Residue const &	res,
		Vector const &	centroid
	)

Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point.

References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::NeighTeller::isneigh(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().

void core::scoring::create_shuffle_map_recursive_rms	(	std::vector< int >	sequence,
		int const	N,
		std::vector< std::vector< int > > &	map
	)

This is a recursive algorithm to generate all combinations of n digits where a number can only occur once in the sequence. The size scales as N! so don't use this for large values of N!!!

References core::chemical::element::N.

Referenced by CA_rmsd_symmetric(), and sym_rmsd_with_super_subset().

ScoreFunctionOP core::scoring::deep_copy ( ScoreFunction const & source )

inline

References core::scoring::ScoreFunction::clone().

bool core::scoring::dimer_pairing_pointer_sorter	(	DimerPairingOP const &	a,
		DimerPairingOP const &	b
	)

Referenced by core::scoring::SecondaryStructurePotential::sspair().

std::string const core::scoring::DNA_INT_WTS ( "dna_no_gb" )

std::string const core::scoring::DNA_INT_WTS_GB ( "dna" )

std::string const core::scoring::DOCK_LOW_PATCH ( "docking_cen" )

std::string const core::scoring::DOCK_PATCH ( "docking" )

std::string core::scoring::element_string ( std::string const & atom )

Referenced by core::scoring::RDC::get_RDC_data_type().

std::string core::scoring::element_string_dc ( std::string const & atom )

Referenced by core::scoring::DC::get_DC_data_type().

void core::scoring::eval_atom_derivatives_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		ResSingleMinimizationData const &	res1_min_data,
		ResSingleMinimizationData const &	res2_min_data,
		pose::Pose const &	pose,
		EnergyMap const &	respair_weights,
		utility::vector1< DerivVectorPair > &	r1atom_derivs,
		utility::vector1< DerivVectorPair > &	r2atom_derivs
	)

References core::scoring::MinimizationEdge::active_2benmeths_begin(), core::scoring::MinimizationEdge::active_2benmeths_end(), and core::scoring::MinimizationEdge::res_pair_min_data().

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::pack::scmin::SCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::dfunc().

void core::scoring::eval_atom_derivatives_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap const &	res_weights,
		utility::vector1< DerivVectorPair > &	atom_derivs
	)

Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node).

References core::scoring::MinimizationNode::active_1benmeths_begin(), core::scoring::MinimizationNode::active_1benmeths_end(), core::scoring::MinimizationNode::active_intrares2benmeths_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative().

void core::scoring::eval_bbbb_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1bb_centroid,
		Vector const &	r2bb_centroid,
		Real const &	r1bb_radius,
		Real const &	r2bb_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

void core::scoring::eval_bbsc_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1bb_centroid,
		Vector const &	r2sc_centroid,
		Real const &	r1bb_radius,
		Real const &	r2sc_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::scoring::eval_dof_deriv_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		id::DOF_ID const &	dof_id,
		id::TorsionID const &	torsion_id,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights
	)

References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative(), and core::scoring::ScoreFunction::eval_dof_derivative().

void core::scoring::eval_res_onebody_energies_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

Deprecated.

References core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::scmin::SCMinMultifunc::operator()(), and core::pack::scmin::CartSCMinMultifunc::operator()().

void core::scoring::eval_res_pair_energy_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

Deprecated.

References core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), and core::scoring::MinimizationEdge::res_pair_min_data().

Referenced by core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::scmin::SCMinMultifunc::operator()(), and core::pack::scmin::CartSCMinMultifunc::operator()().

void core::scoring::eval_scsc_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1sc_centroid,
		Vector const &	r2sc_centroid,
		Real const &	r1sc_radius,
		Real const &	r2sc_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and protocols::constel::NeighTeller::isneigh().

void core::scoring::eval_weighted_atom_derivatives_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		ResSingleMinimizationData const &	res1_min_data,
		ResSingleMinimizationData const &	res2_min_data,
		pose::Pose const &	pose,
		EnergyMap const &	respair_weights,
		utility::vector1< DerivVectorPair > &	r1atom_derivs,
		utility::vector1< DerivVectorPair > &	r2atom_derivs
	)

References core::scoring::MinimizationEdge::active_2benmeths_begin(), core::scoring::MinimizationEdge::active_2benmeths_end(), core::scoring::MinimizationEdge::dweight(), and core::scoring::MinimizationEdge::res_pair_min_data().

Referenced by core::optimization::cartesian_collect_atompairE_deriv().

Real core::scoring::eval_weighted_dof_deriv_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		id::DOF_ID const &	dof_id,
		id::TorsionID const &	torsion_id,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights
	)

References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), core::scoring::MinimizationNode::res_min_data(), and core::scoring::MinimizationNode::weight().

void core::scoring::eval_weighted_res_onebody_energies_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap,
		EnergyMap &	scratch_emap
	)

Referenced by core::scoring::ScoreFunction::sym_eval_onebody_energies().

void core::scoring::eval_weighted_res_pair_energy_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap,
		EnergyMap &	scratch_emap
	)

References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), core::scoring::MinimizationEdge::res_pair_min_data(), core::scoring::MinimizationEdge::weight(), and core::scoring::EMapVector::zero().

Referenced by core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().

void core::scoring::evaluaterdc	(	const core::Real *	par,
		int	m_dat,
		const void *	data,
		core::Real *	fvec,
		int *
	)

References frdc(), frdcDa(), frdcDaR(), frdcR(), NLS, NLSDA, NLSDAR, NLSR, core::scoring::data_struct::r0, core::scoring::data_struct::r1, core::scoring::data_struct::r2, core::scoring::data_struct::rdc, core::scoring::data_struct::rdcconst, core::scoring::data_struct::rdcweight, core::scoring::data_struct::tensorDa, core::scoring::data_struct::tensorR, and core::scoring::data_struct::type_of_computation.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().

std::string const core::scoring::FA_STANDARD_DEFAULT ( "FA_STANDARD_DEFAULT" )

global etable_id

std::string const core::scoring::FA_STANDARD_MULTIPOLE ( "FA_STANDARD_MULTIPOLE" )

std::string const core::scoring::FA_STANDARD_SOFT ( "FA_STANDARD_SOFT" )

float core::scoring::fastexp ( float p )

inline

References fastpow2().

Referenced by core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), and core::scoring::FACTSPotential::evaluate_polar_otf_energy().

float core::scoring::fastlog2 ( float x )

inline

Referenced by fastpow().

float core::scoring::fastpow	(	float	x,
		float	p
	)

inline

References fastlog2(), and fastpow2().

float core::scoring::fastpow2 ( float p )

inline

Referenced by fastexp(), and fastpow().

void core::scoring::fill_bb_pos	(	pose::Pose const &	pose,
		BB_Pos &	bb_pos
	)

helper function

References core::scoring::BB_Pos::take_coordinates_from_pose().

Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().

template<class T >

void core::scoring::fill_rmsd_coordinates	(	int &	natoms,
		ObjexxFCL::FArray2D< core::Real > &	p1a,
		ObjexxFCL::FArray2D< core::Real > &	p2a,
		core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

References core::conformation::Residue::is_virtual_residue(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_maxsub_by_subset(), CA_or_equiv_rmsd(), CA_rmsd(), and CA_rmsd_symmetric().

void core::scoring::fill_score_range	(	std::map< std::string, ScoreType > &	M,
		std::string const &	prefix,
		int	first,
		int	last
	)

Referenced by core::scoring::ScoreTypeManager::setup_score_type_names().

std::string core::scoring::find_weights_file	(	std::string const &	name,
		std::string const &	extension
	)

Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passed either with or without the optional extension.

Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passes either with or without the optional extension.

References core::scoring::ScoreFunction::name().

Referenced by core::scoring::ScoreFunction::add_weights_from_file(), and core::scoring::ScoreFunction::apply_patch_from_file().

core::Real core::scoring::frdc	(	core::Real	r0,
		core::Real	r1,
		core::Real	r2,
		core::Real	rdcconst,
		const core::Real *	par
	)

References core::pose::motif::a(), protocols::match::upstream::b, core::pack::dunbrack::c, and protocols::hybridization::r2.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), and evaluaterdc().

core::Real core::scoring::frdcDa	(	core::Real	r0,
		core::Real	r1,
		core::Real	r2,
		core::Real	rdcconst,
		core::Real const	tensorDa,
		const core::Real *	par
	)

References core::pose::motif::a(), protocols::match::upstream::b, core::pack::dunbrack::c, and protocols::hybridization::r2.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), and evaluaterdc().

core::Real core::scoring::frdcDaR	(	core::Real	r0,
		core::Real	r1,
		core::Real	r2,
		core::Real	rdcconst,
		core::Real const	tensorDa,
		core::Real const	tensorR,
		const core::Real *	par
	)

References core::pose::motif::a(), protocols::match::upstream::b, core::pack::dunbrack::c, and protocols::hybridization::r2.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), and evaluaterdc().

core::Real core::scoring::frdcR	(	core::Real	r0,
		core::Real	r1,
		core::Real	r2,
		core::Real	rdcconst,
		core::Real const	tensorR,
		const core::Real *	par
	)

References core::pose::motif::a(), protocols::match::upstream::b, core::pack::dunbrack::c, and protocols::hybridization::r2.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), and evaluaterdc().

core::Real core::scoring::gdtha	(	const core::pose::Pose &	ref,
		const core::pose::Pose &	mod,
		const std::map< core::Size, core::Size > &	residues
	)

Returns the average fraction of residues superimposable under a series of distance thresholds– 0.5, 1.0, 2.0, and 4.0 Angstroms.

References core::conformation::Residue::name1(), core::pose::Pose::residue(), core::simple_metrics::metrics::sum, tr(), and core::pose::Pose::xyz().

Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), and protocols::comparative_modeling::Align_RmsdEvaluator::apply().

core::Real core::scoring::gdtsc	(	const core::pose::Pose &	ref,
		const core::pose::Pose &	model,
		const std::map< core::Size, core::Size > &	residues
	)

Returns a single, Global Distance Test-like value that measures the extent to which the functional ends of a model's sidechains agree with their counterparts in a given reference structure.

Instead of comparing residue positions on the basis of CAs, gdtsc uses a characteristic atom near the end of each sidechain type for the evaluation of residue-residue distance deviations.

The traditional GDT score is a weighted sum of the fraction of residues superimposed within limits of 1, 2, 4, and 8Å. For gdtsc, the backbone superposition is used to calculate fractions of corresponding model-ref sidechain atom pairs that fit under 10 distance-limit values from 0.5A to 5A. Ambiguity in Asp or Glu terminal oxygen naming is not currently considered.

Reference: Keedy, DA. The other 90% of the protein. Proteins. 2009; 77 Suppl 9:29-49.

References core::pose::Pose::is_fullatom(), core::conformation::Residue::name1(), core::pose::Pose::residue(), core::simple_metrics::metrics::sum, tr(), and core::pose::Pose::xyz().

Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().

ObjexxFCL::FArray2D_int const & core::scoring::get_angles ( )

Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

References angles(), and input_sasa_dats().

std::string core::scoring::get_current_default_score_function_name ( )

inline

References REF_2015.

void core::scoring::get_damped_scale_factors	(	MultipoleParameter::MultipoleParameterOP const &	mp_param1,
		MultipoleParameter::MultipoleParameterOP const &	mp_param2,
		core::Real	dist,
		core::Real &	scale3,
		core::Real &	scale5,
		core::Real &	scale7
	)

inline

References protocols::mean_field::min().

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

void core::scoring::get_damped_scale_factors_with_derivs	(	MultipoleParameter::MultipoleParameterOP const &	mp_param1,
		MultipoleParameter::MultipoleParameterOP const &	mp_param2,
		core::Real	dist,
		core::Real &	scale3,
		core::Real &	scale5,
		core::Real &	scale7,
		core::Real &	dscale3_dr,
		core::Real &	dscale5_dr,
		core::Real &	dscale7_dr
	)

inline

References protocols::mean_field::min().

Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs().

ObjexxFCL::FArray2D_ubyte const & core::scoring::get_masks ( )

Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

References input_sasa_dats(), and masks().

int core::scoring::get_num_bytes ( )

Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

References num_bytes.

void core::scoring::get_orientation	(	Vector const &	a_xyz,
		Vector const &	b_xyz,
		int &	phi_index,
		int &	theta_index,
		Real	distance_ijxyz
	)

Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)

ronj This function is used to get two indexes (phi and theta) which are used to get the index of a dot on the ronj surface of the 'a' sphere. When calculating how much surface area sphere b covers on a, we can get the degree ronj of overlap from the function above, but it's not necessarily the case that the vector that connects the center ronj of atom 'a' and atom 'b' goes through one of the predetermined dot locations on the surface of 'a'. In fact, ronj it's very unlikely that the vector goes through a predetermined dot. Instead, what is done is the actual point ronj of intersection (the outermost point of a on the line from the center of 'a' to center of 'b') is converted ronj to spherical polar coordinates. Then, the values are used to find the location of the closest predetermined ronj point on the surface of 'a' using a lookup table. So what this function needs to do is convert the ronj cartesian coordinate of the actual point of intersection into polar coordinates. ronj ronj To get the spherical, polar coordinates of a cartesian point x,y,z, use these equations: ronj r = sqrt( x^2 + y^2 + z^2 ) ronj theta = arccos( z / r ) ronj phi = arctan( y / x )

ronj Then, once we have the true phi and theta, we need to translate this into an index (or offset) for the correct ronj value in the database file. There are 64 phi angle bin and 64 theta bins in the database file sampling/SASA-angles.dat. ronj We need to convert the phi and theta into indexes for this file by multiplying them by num_phi / 2*pi. ronj Note: I think phi and theta have been reversed in the function below. The code below uses the following: ronj phi = arccos( z ) ronj theta = arctan( y / x )

ronj After a couple of weeks trying to write tests for this function, I have been unsuccessful in figuring out why ronj it's doing what it does. Despite using the wrong equations, it seems to work. Comparing the total residue ronj SASA values calculated by calc_per_atom_sasa() below results in a correlation of 0.98 against what the program ronj NACCESS finds for the same residues. This test was done on a small 110aa protein. I also looked at the per-atom ronj total SASA and the correlation for all atoms (mini v. NACCESS) was approximately 0.94. I'm using exactly the same ronj van der Waals radii for both programs so I feel like the correlations should be 1.0. Explanations for the ronj differences can be 1) this method is doing something wrong in calculating the closest surface point, 2) this ronj method is correct but the masks that are in the database are not aligned to the surface points correctly, 3) the ronj differences are solely due to the different way that the two program calculate surface area.

References num_phi, and num_theta.

Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

void core::scoring::get_overlap	(	Real const	radius_a,
		Real const	radius_b,
		Real const	distance_ijxyz,
		int &	degree_of_overlap
	)

getting overlap from a to b (or i to j, as the atoms are referred to in calc_per_atom_sasa below). this returns the degree of overlap between two atoms adapted from erics code in area.c GetD2 and returns value from 1 to 100. This calculation is based on the law of cosines. See LeGrand and Merz, Journal of Computational Chemistry 14(3):349-52 (1993). Note that equation (4) is wrong, the denominator should be 2*ri*riq instead of 2*ri*rq (j)

The function gets passed in the sasa radius of atom i (plus the probe radius), the sasa radius of atom j (plus the probe radius), the distance between the atom centers, and a reference to the degree of overlap (represented as an int). The degree of overlap that's returned can be thought of as how much of atom a is covered by atom b. A value of 100 means that atom a is completely covered up by atom b. A value of 1 means that not much of the surface of 'a' is covered up by 'b'. The law of cosines relates the cosine of one angle of a triangle to the lengths of its sides. More specifically, c^2 = a^2 + b^2 - 2*a*b*cos theta, where theta is the angle between sides a and b. For the function we want to compute the angle of the cone of intersection between spheres 'a' and 'b'. Let the radius of atom a be ri, and the radius of atom b be rq, and the distance between atom centers be riq. Let the angle between ri and riq be theta_iq. The cosine of theta_iq will be equivalent to ( ri^2 + riq^2 - rq^2 ) / 2 * ri * riq

Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

uint64_t core::scoring::get_parameter_hash	(	Size	bondtypr,
		Size	type1,
		Size	type2,
		Size	type3,
		Size	type4
	)

compress 5 values into one unsigned int; use 12 bits for each

Referenced by core::scoring::ResidueExclParams::find_by_atmpairno(), core::scoring::GenBondedExclInfo::get_residue_pair_data(), core::scoring::GenericBondedPotential::lookup_angle_params(), core::scoring::GenericBondedPotential::lookup_bond_params(), core::scoring::GenericBondedPotential::lookup_improper_params(), core::scoring::GenericBondedPotential::lookup_tors_params(), core::scoring::GenericBondedPotential::modify_tors_params(), core::scoring::GenericBondedPotential::read_database(), and core::scoring::ResidueExclParams::store_by_atmpairno().

std::map< std::string, rmsd_atoms > core::scoring::get_rmsd_type_name_map ( )

Setup a name mapping for rmsd_atoms.

References rmsd_all, rmsd_all_heavy, rmsd_protein_bb_ca, rmsd_protein_bb_heavy, rmsd_protein_bb_heavy_including_O, rmsd_sc, and rmsd_sc_heavy.

Referenced by get_rmsd_type_names(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::setup_name_mapping(), and core::simple_metrics::metrics::RMSDMetric::setup_name_mapping().

utility::vector1< std::string > core::scoring::get_rmsd_type_names ( )

Setup a name mapping for rmsd_atoms.

References get_rmsd_type_name_map().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), and core::simple_metrics::metrics::RMSDMetric::provide_xml_schema().

core::scoring::ScoreFunctionOP core::scoring::get_score_function ( bool const is_fullatom )

A helper function which returns a scoring function held in an owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=talaris2013 for fullatom, and weights=cen_std and patch="" for centroid.

core::scoring::ScoreFunctionOP core::scoring::get_score_function	(	pose::Pose const &	pose,
		bool const	is_fullatom
	)

Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose.

References get_score_function().

core::scoring::ScoreFunctionOP core::scoring::get_score_function	(	pose::Pose const &	pose,
		utility::options::OptionCollection const &	options,
		bool const	is_fullatom
	)

Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. Local Options collection.

References get_score_function(), and core::pose::symmetry::is_symmetric().

core::scoring::ScoreFunctionOP core::scoring::get_score_function	(	utility::options::OptionCollection const &	options,
		bool const	is_fullatom
	)

A helper function which creates a scoring function held in an owning pointer reading from the input OptionCollection.

References CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), metalbinding_constraint, sugar_bb, and TR().

core::scoring::ScoreFunctionOP core::scoring::get_score_function_legacy	(	std::string const &	pre_talaris_2013_weight_set,
		std::string const &	pre_talaris_2013_patch_file
	)

A helper function that either returns a ScoreFunctionOP created by get_score_function() or the one specified by the protocol which is activated by the -restore_pre_talaris_2013_behavior flag. The purpose of this function is to preserve legacy behavior for the sake of reproducibility and so that a record of the old behavior is still preserved in the code to ease the process of reverting the change to get_score_function if that were the wrong behavior.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::minimization_packing::MinPackMover::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::sasa_scores::compute_avge_scores(), protocols::antibody::get_Pack_ScoreFxn(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::antibody::RefineBetaBarrel::init(), protocols::docking::TemperedDocking::init_from_options(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::antibody::LHRepulsiveRampLegacy::set_default(), protocols::symmetric_docking::SymDockProtocol::set_default(), protocols::symmetric_docking::SymSidechainMinMover::set_default_options(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes(), and protocols::motifs::IRCollection::try_for_more().

core::scoring::ScoreFunctionOP core::scoring::get_score_function_legacy	(	utility::options::OptionCollection const &	options,
		std::string const &	pre_talaris_2013_weight_set,
		std::string const &	pre_talaris_2013_patch_file
	)

References core::scoring::ScoreFunctionFactory::create_score_function(), and get_score_function().

std::string core::scoring::get_score_function_name	(	utility::tag::TagCOP	tag,
		std::string const &	option_name
	)

Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols.

std::string core::scoring::get_score_function_name ( utility::tag::TagCOP tag )

Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols.

References get_score_function_name().

std::string core::scoring::get_score_functionName ( bool const is_fullatom )

use the logic of get_score_function to get the name. The name format is <weights_tag>[_<patch_tag> ... ]

References CENTROID_WTS, PRE_TALARIS_2013_STANDARD_WTS, and SCORE12_PATCH.

Referenced by protocols::relax::FastRelax::get_possible_relax_script_names().

template<class T , class T_Etable >

void core::scoring::inline_intraresidue_atom_pair_energy	(	conformation::Residue const &	res,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

intraresidue atom pair energy evaluations

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), fa_atr, fa_rep, fa_sol, core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), residue_fast_pair_energy_attached_H(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >::residue_atom_pair_energy().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap,
		int	res1_start,
		int	res1_end,
		int	res2_start,
		int	res2_end
	)

inline

templated atom pair energy calculations

loops over the heavy atoms of residue1 and the heavy atoms of residue2, evaluates their energies, and if a pair of heavy atoms is close enough, descendes into the attached hydrogen atoms for each.

Templates are for count_pair type resolution and etable type resolution: there are no polymorphic lookups within these functions

class T must define class T_Etable must define atom_pair_energy( Atom const &, Atom const &, Real, EnergyMap &, Distance ) and

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), fa_atr, fa_rep, fa_sol, core::scoring::EMapVector::get(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::name(), residue_fast_pair_energy_attached_H(), core::conformation::Residue::seqpos(), and core::scoring::EMapVector::set().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

References inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_backbone_backbone	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

References inline_residue_atom_pair_energy(), and core::conformation::Residue::last_backbone_atom().

Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_backbone	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), core::conformation::Residue::last_backbone_atom(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_whole	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)

inline

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole().

void core::scoring::input_sasa_dats ( )

Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.

References angles(), core::init::init(), masks(), num_bytes, num_orientations, num_overlaps, num_phi, and num_theta.

Referenced by calc_per_atom_sasa(), core::scoring::packstat::compute_sasa(), get_angles(), and get_masks().

void core::scoring::interpolate_value_and_deriv	(	ObjexxFCL::FArray1D< Real > const &	potential,
		Real const &	bin_width,
		Real const &	r,
		Real &	value,
		Real &	deriv
	)

inline

Referenced by core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_axis_score(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_score(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stagger_score().

void core::scoring::invert_exclude_residues	(	Size	nres,
		utility::vector1< int > const &	exclude_list,
		ResidueSelection &	residue_selection
	)

Referenced by protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), and protocols::cluster::GatherPosesMover::get_distance_measure().

ResidueSelection core::scoring::invert_exclude_residues	(	core::Size	nres,
		utility::vector1< int > const &	exclude_list
	)

Referenced by native_CA_gdtmm(), and native_CA_rmsd().

Real core::scoring::iprod	(	const rvec	a,
		const rvec	b
	)

inline

References XX, YY, and ZZ.

bool core::scoring::is_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), and core::pose::Pose::residue().

Referenced by all_atom_rmsd(), all_atom_rmsd_nosuper(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::docking::calc_Irmsd(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_with_super(), and sym_rmsd_with_super_subset().

bool core::scoring::is_ligand_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

Note: "Ligand" here means not "polymer" in the Rosetta sense.

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().

Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), rmsd_no_super(), rmsd_with_super(), and sym_rmsd_with_super_subset().

bool core::scoring::is_ligand_heavyatom_residues	(	core::conformation::Residue const &	residue1,
		core::conformation::Residue const &	,
		core::Size	atomno
	)

Note: "Ligand" here means not "polymer" in the Rosetta sense.

References core::conformation::Residue::atom_is_hydrogen(), and core::conformation::Residue::is_polymer().

Referenced by protocols::ligand_docking::check_RMSD(), and rmsd_no_super().

bool core::scoring::is_nbr_atom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::nbr_atom(), and core::pose::Pose::residue().

Referenced by nbr_atom_rmsd(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().

bool core::scoring::is_non_peptide_heavy_atom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::uint const	resno,
		core::uint const	atomno
	)

Return true if the pose residues and atoms specified are non-peptide heavy atoms.

This is a "predicate" function intended for use with RMSD-calculating functions.

Remarks: This is useful for oligosaccharide ligands, which are "polymers" in the Rosetta sense and do not have CAs.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by non_peptide_heavy_atom_RMSD().

bool core::scoring::is_polymer_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().

Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_with_super(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), and sym_rmsd_with_super_subset().

bool core::scoring::is_protein_backbone	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), bb_rmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_Lrmsd(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::loop_modeling::utilities::TrajectoryLogger::calc_rmsd_to_native(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

bool core::scoring::is_protein_backbone_including_O	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by bb_rmsd_including_O(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save(), protocols::rpc::JSON_RPC::get_irms(), protocols::antibody::global_loop_rmsd(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().

bool core::scoring::is_protein_CA	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::symmetry::SymmetricRMSMover::apply(), CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd_symmetric(), protocols::docking::calc_CA_Irmsd(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), core::scoring::IsProteinCAPredicate::operator()(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

bool core::scoring::is_protein_CA_or_CB	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().

bool core::scoring::is_protein_CA_or_equiv	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), and core::pose::Pose::residue().

Referenced by core::scoring::IsMainAtomPredicate::operator()().

bool core::scoring::is_protein_sidechain_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueTypeBase::is_protein(), and core::pose::Pose::residue_type().

Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

bool core::scoring::is_scatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_backbone(), and core::pose::Pose::residue().

Referenced by all_scatom_rmsd_nosuper(), and protocols::pose_metric_calculators::compute_rmsd().

void core::scoring::jacobi	(	ResidualDipolarCoupling::Tensor5 &	a,
		ResidualDipolarCoupling::rvec5 &	d,
		ResidualDipolarCoupling::Tensor5 &	v,
		int &	nrot
	)

References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE(), and protocols::hybridization::t.

Referenced by protocols::evaluation::PCA::calc_fit_R(), and m_inv_gen().

void core::scoring::jacobi3	(	ResidualDipolarCoupling::Tensor &	a,
		ResidualDipolarCoupling::rvec &	d,
		ResidualDipolarCoupling::Tensor &	v,
		int &	nrot
	)

References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE(), and protocols::hybridization::t.

Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().

void core::scoring::list_read_options_in_get_score_function ( utility::options::OptionKeyList & opts )

A documentation function which reports the set of options read by get_score_function.

References core::scoring::ScoreFunctionFactory::list_read_options().

Referenced by protocols::rosetta_scripts::RosettaScriptsParser::list_options_read().

void core::scoring::list_read_options_in_get_score_function_legacy ( utility::options::OptionKeyList & opts )

A documentation function which reports the set of options read by get_score_function_legacy.

References core::scoring::ScoreFunctionFactory::list_read_options().

int core::scoring::m_inv_gen	(	ResidualDipolarCoupling::Tensor5 const &	m,
		int	n,
		ResidualDipolarCoupling::Tensor5 &	minv
	)

References jacobi().

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore().

ObjexxFCL::FArray2D_ubyte core::scoring::masks	(	num_bytes	,
		num_overlaps *	num_orientations
	)

Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::aa_composition_energy::AACompositionEnergy::finalize_total_energy(), core::scoring::netcharge_energy::NetChargeEnergy::finalize_total_energy(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::finalize_total_energy(), get_masks(), input_sasa_dats(), core::scoring::packstat::old::input_sasa_dats(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::MEMB_HIGHRES_WTS ( "membrane_highres" )

Membrane_FAEmbed const & core::scoring::Membrane_FAEmbed_from_pose ( pose::Pose const & pose )

Return a Const Reference to the Embedding Object from the Pose Cache.

Grab Const MP Fa Embedding data from the pose cache.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

MembraneEmbed const & core::scoring::MembraneEmbed_from_pose ( pose::Pose const & pose )

Add Const Membrane Embedding to the pose cache.

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

Referenced by protocols::rigid::MovePoseToMembraneCenterMover::apply(), protocols::rigid::MembraneCenterPerturbationMover::apply(), protocols::rigid::MembraneNormalPerturbationMover::apply(), core::scoring::methods::MembraneEnvSmoothEnergy::calc_energy(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::evaluate_env(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().

MembraneTopology const & core::scoring::MembraneTopology_from_pose ( pose::Pose const & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::init_membrane_center_normal(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::MembranePotential::score_normal_center(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().

std::string const core::scoring::MM_STD_WTS ( "mm_std" )

void core::scoring::mvmul	(	matrix	a,
		const rvec	src,
		rvec	dest
	)

inline

References XX, YY, and ZZ.

std::string core::scoring::name_from_score_type ( ScoreType score_type )

Returns the name of the ScoreType <score_type>

example(s): name_from_score_type(fa_sol) See also: ScoreFunction ScoreType Energies Energies.residue_total_energies score_type_from_name

References core::scoring::ScoreTypeManager::name_from_score_type().

core::Real core::scoring::native_CA_gdtmm	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References CA_gdtmm(), invert_exclude_residues(), and core::pose::Pose::size().

Referenced by protocols::relax::FastRelax::batch_apply().

core::Real core::scoring::native_CA_rmsd	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References CA_or_equiv_rmsd(), CA_rmsd(), invert_exclude_residues(), and core::pose::Pose::size().

Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::relax::FastRelax::inner_loop_accept_to_best_command(), protocols::jobdist::main_plain_pdb_mover(), and protocols::jobdist::universal_main().

core::Real core::scoring::nbr_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_nbr_atom(), rms, and rmsd_with_super().

core::DistanceSquared core::scoring::non_peptide_heavy_atom_RMSD	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Return the RMSD of the non-peptide heavy atoms of two poses.

This does NOT perform a superimposition first.

Note: This is simply a wrapper for use in PyRosetta, since PyRosetta cannot use the templated function rmsd_no_super() directly.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References is_non_peptide_heavy_atom(), and rmsd_no_super().

Membrane_FAEmbed & core::scoring::nonconst_Membrane_FAEmbed_from_pose ( pose::Pose & pose )

Return a Non Const Reference to the Embedding Object from the Pose Cache.

Grab Const MP Fa embedding data from the pose cache.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::Membrane_FAPotential::fa_projection(), and core::scoring::Membrane_FAPotential::finalize().

MembraneEmbed & core::scoring::nonconst_MembraneEmbed_from_pose ( pose::Pose & pose )

Add a non const membrane embedding object to the pose cache.

Add Non Const Membrane Embedding to the pose cache.

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::Membrane_FAPotential::finalize(), core::scoring::MembranePotential::finalize(), and protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_embed().

MembraneTopology & core::scoring::nonconst_MembraneTopology_from_pose ( pose::Pose & pose )

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenlist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

Real core::scoring::normalizing_area ( char const res )

Get the area of the sidechain.

Threadsafe now, but these values are suspect.

Referenced by calc_per_atom_sasa_sc().

Real core::scoring::normalizing_area_total ( char const res )

Given a one-letter code for a canonical amino acid, return its total surface area.

Threadsafe now, but these values are suspect.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Real core::scoring::normalizing_area_total_hydrophobic_atoms_only ( char const res )

Given a one-letter code for a canonical amino acid, return its total surface area, computed only using hydrophobic atoms.

Threadsafe now. Based on Gabe Rocklin's values (grock.nosp@m.lin@.nosp@m.gmail.nosp@m..com).

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe now.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by protocols::simple_filters::BuriedSurfaceAreaFilter::compute().

Real core::scoring::normalizing_area_total_polar_atoms_only ( char const res )

Given a one-letter code for a canonical amino acid, return its total surface area, computed only using polar atoms.

Threadsafe. Based on Gabe Rocklin's values (grock.nosp@m.lin@.nosp@m.gmail.nosp@m..com).

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by protocols::simple_filters::BuriedSurfaceAreaFilter::compute().

DerivVectorPair core::scoring::operator*	(	Real	scale,
		DerivVectorPair const &	dvp
	)

inline

References core::scoring::DerivVectorPair::f1(), and core::scoring::DerivVectorPair::f2().

DerivVectorPair core::scoring::operator*	(	DerivVectorPair const &	dvp,
		Real	scale
	)

inline

References core::scoring::DerivVectorPair::f1(), and core::scoring::DerivVectorPair::f2().

std::ostream & core::scoring::operator<<	(	std::ostream &	os,
		ScoreType const &	score_type
	)

output operator for ScoreType enum type

example usage: std::cout << score_type_gly << std::endl;

References core::scoring::ScoreTypeManager::name_from_score_type().

std::ostream & core::scoring::operator<<	(	std::ostream &	os,
		ScoreTypes const &	score_types
	)

output operator for ScoreTypes list type

output operator for ScoreTypes list

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Hairpin const &	s
	)

References core::chemical::element::I, core::conformation::membrane::out, core::scoring::Hairpin::s1_end(), core::scoring::Hairpin::s1_start(), core::scoring::Hairpin::s2_end(), and core::scoring::Hairpin::s2_start().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		CSA const &	csa
	)

References core::conformation::membrane::out, and core::scoring::CSA::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		DC const &	dc
	)

References core::conformation::membrane::out, and core::scoring::DC::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		ChemicalShiftAnisotropy const &	csa
	)

References core::conformation::membrane::out, and core::scoring::ChemicalShiftAnisotropy::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		DipolarCoupling const &	dc
	)

References core::conformation::membrane::out, and core::scoring::DipolarCoupling::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		RDC const &	rdc
	)

References core::conformation::membrane::out, and core::scoring::RDC::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		ResidualDipolarCoupling const &	rdc
	)

References core::conformation::membrane::out, and core::scoring::ResidualDipolarCoupling::show().

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Hairpins const &	s
	)

References core::chemical::element::I, core::scoring::Hairpins::list(), and core::conformation::membrane::out.

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Strands const &	s
	)

References core::chemical::element::I, core::conformation::membrane::out, core::scoring::Strands::SS_dimer, core::scoring::Strands::SS_resnum, core::scoring::Strands::SS_strand, core::scoring::Strands::SS_strand_end, core::scoring::Strands::total_SS_dimer, and core::scoring::Strands::total_strands.

std::ostream& core::scoring::operator<<	(	std::ostream &	os,
		PolymerBondedEnergyContainer const &	t
	)

Operator to allow object to be summarized.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::scoring::PolymerBondedEnergyContainer::chemical_edges_, and core::scoring::PolymerBondedEnergyContainer::size_.

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Helices const &	s
	)

References core::scoring::Helices::HH_helix_end, core::scoring::Helices::HH_resnum, core::chemical::element::I, core::conformation::membrane::out, and core::scoring::Helices::total_HH_dimer.

std::ostream& core::scoring::operator<<	(	std::ostream &	ost,
		EMapVector const &	emap
	)

inline

output operator (index;value)

References n_score_types.

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		const Energies &	e
	)

References protocols::comparative_modeling::features::A, core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), core::chemical::element::F, core::scoring::Energies::get_scorefxn_info(), core::chemical::element::I, name_from_score_type(), core::conformation::membrane::out, core::scoring::Energies::residue_total_energies(), core::scoring::ScoreFunctionInfo::scores_present(), core::scoring::Energies::size(), and core::scoring::Energies::total_energies().

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		ScoreFunction const &	sf
	)

inline

References core::conformation::membrane::out, and core::scoring::ScoreFunction::show().

bool core::scoring::operator==	(	ScoreFunctionInfo const &	a,
		ScoreFunctionInfo const &	b
	)

References core::scoring::ScoreFunctionInfo::context_graphs_required_, core::scoring::ScoreFunctionInfo::energy_method_options_, core::scoring::ScoreFunctionInfo::max_atomic_interaction_distance_, core::scoring::ScoreFunctionInfo::max_context_neighbor_cutoff_, n_score_types, num_context_graph_types, and core::scoring::ScoreFunctionInfo::scores_present_.

std::istream & core::scoring::operator>>	(	std::istream &	is,
		ScoreType &	score_type
	)

input operator for ScoreType enum type

read in a string name from a file or std::cin and directly convert it to an ScoreType enum type, for example, std::cin >> ScoreType. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set ScoreType enum type to total_score.

References core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), and total_score.

core::scoring::ScoreFunctionOP core::scoring::parse_score_function	(	utility::tag::TagCOP	tag,
		std::string const &	option_name,
		basic::datacache::DataMap const &	data,
		std::string const &	dflt_key
	)

Look up the score function defined in the <SCOREFXNS> through the given option. Defaults to 'commandline'.

Utility function to find a scorefunction from parser-provided data.

References check_score_function_sanity().

core::scoring::ScoreFunctionOP core::scoring::parse_score_function	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const &	dflt_key
	)

Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Defaults to 'commandline'.

Utility function to find a scorefunction from parser-provided data for the option 'scorefxn'.

References parse_score_function().

std::map< core::Size, core::Real > core::scoring::per_res_rms_at_corresponding_atoms_no_super	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		utility::vector1< bool > const &	mask
	)

Calculate RMSD for each residue in mask, return a map of res to value.

Calculate RMS for each residue in mask, return a map of res to value.

Mask and result corresponds to MOD POSE, not the reference pose!

References core::id::AtomID::atomno(), core::conformation::Residue::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::size(), core::simple_metrics::metrics::sum, and core::pose::Pose::xyz().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate().

bool core::scoring::polymeric_termini_incomplete ( conformation::Residue res )

inline

References core::conformation::Residue::connection_incomplete(), and core::conformation::Residue::n_polymeric_residue_connections().

Referenced by core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), and core::scoring::Ramachandran2B::RamaE_Upper().

std::string const core::scoring::PRE_TALARIS_2013_STANDARD_WTS ( "pre_talaris_2013_standard" )

std::string const core::scoring::REF_2015 ( "ref2015" )

template<class T , class T_Etable >

void core::scoring::residue_fast_pair_energy_attached_H	(	conformation::Residue const &	res1,
		int const	atomno1,
		conformation::Residue const &	res2,
		Size const	atomno2,
		Size const	at1hbegin,
		Size const	at1hend,
		Size const	at2hbegin,
		Size const	at2hend,
		T const &	count_pair,
		T_Etable const &	etable_energy,
		EnergyMap &	emap
	)

inline

class T must define

References core::conformation::Residue::atom(), protocols::antibody::H1, and protocols::antibody::H2.

Referenced by inline_intraresidue_atom_pair_energy(), and inline_residue_atom_pair_energy().

core::Real core::scoring::residue_rmsd_nosuper	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		utility::vector1< core::Size > const &	atom_map,
		bool	skip_hydro
	)

Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Does not superimpose the residues.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::chemical::ResidueType::natoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by automorphic_rmsd().

core::Real core::scoring::residue_rmsd_super	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		utility::vector1< core::Size > const &	atom_map,
		bool	skip_hydro
	)

Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Superimposes the residues (remove rigid-body rotational/translational component of the rmsd.)

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::chemical::ResidueType::natoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by automorphic_rmsd().

core::Real core::scoring::residue_sc_rmsd_no_super	(	core::conformation::ResidueCOP	res1,
		core::conformation::ResidueCOP	res2,
		bool const	fxnal_group_only
	)

utility function to calculate per-residue sidechain rmsd without superposition

Iterates over all non-hydrogen sidechain atoms of two residues and returns their rmsd without superposition.

References core::pose::num_atoms().

Referenced by protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::hbnet::HBNet::monte_carlo_net_clash(), protocols::hbnet::HBNet::net_clash(), protocols::hbnet::HBNet::network_already_stored(), and protocols::hotspot_hashing::residue_sc_rmsd_no_super().

SS_Info const& core::scoring::retrieve_const_ss_info_from_pose ( pose::Pose const & pose )

helper function

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SS_INFO.

Referenced by core::scoring::SecondaryStructurePotential::hspair(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), and core::scoring::SecondaryStructurePotential::sspair().

void core::scoring::retrieve_coordinates	(	const core::pose::Pose &	pose,
		const utility::vector1< core::Size > &	residues,
		FArray2D< core::Real > *	coords
	)

Populates the output parameter with the xyz coordinates of a subset of <pose>'s CA atoms, which are specified in <residues>

References protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

Referenced by CA_gdtmm(), CA_gdttm(), and CA_rmsd().

ChemicalShiftAnisotropyCOP core::scoring::retrieve_CSA_from_pose ( core::pose::Pose const & pose )

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

Referenced by core::scoring::methods::ChemicalShiftAnisotropyEnergy::csa_from_pose(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), and core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing().

ChemicalShiftAnisotropyOP core::scoring::retrieve_CSA_from_pose ( core::pose::Pose & pose )

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

DipolarCouplingCOP core::scoring::retrieve_DC_from_pose ( core::pose::Pose const & pose )

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

Referenced by core::scoring::methods::DipolarCouplingEnergy::dc_from_pose(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), and core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing().

DipolarCouplingOP core::scoring::retrieve_DC_from_pose ( core::pose::Pose & pose )

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

SS_Info& core::scoring::retrieve_nonconst_ss_info_from_pose ( pose::Pose & pose )

helper function

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SS_INFO.

Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().

ResidualDipolarCouplingCOP core::scoring::retrieve_RDC_from_pose ( core::pose::Pose const & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.

Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergy::rdc_from_pose(), and core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().

ResidualDipolarCouplingOP core::scoring::retrieve_RDC_from_pose ( core::pose::Pose & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.

ResidualDipolarCoupling_RohlCOP core::scoring::retrieve_RDC_ROHL_from_pose ( core::pose::Pose const & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.

Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::rdc_from_pose().

ResidualDipolarCoupling_RohlOP core::scoring::retrieve_RDC_ROHL_from_pose ( core::pose::Pose & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.

Real core::scoring::rms_at_all_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map
	)

Calculates RMSD of all atoms in AtomID map, no need for the poses to be the same length.

References core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::pose::Pose::residue(), tr(), and core::pose::Pose::xyz().

Referenced by protocols::fldsgn::MatchResidues::compute_comb().

Real core::scoring::rms_at_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map
	)

Should be more robust to crazy variant type mismatches. Both poses must have the same length.

References rms_at_corresponding_atoms(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::check_screen(), and protocols::stepwise::legacy::modeler::protein::output_silent_struct().

Real core::scoring::rms_at_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		utility::vector1< Size > const &	calc_rms_res
	)

Should be more robust to crazy variant type mismatches. Both poses must have the same length.

References core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

Referenced by rms_at_corresponding_atoms(), and rms_at_corresponding_heavy_atoms().

Real core::scoring::rms_at_corresponding_atoms_no_super	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map
	)

References rms_at_corresponding_atoms_no_super(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), core::simple_metrics::metrics::RMSDMetric::calculate(), protocols::antibody::cdr_backbone_rmsds(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::check_screen(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition(), protocols::rna::AlignmentEnergy::eval_atom_derivative(), protocols::rna::AlignmentEnergy::finalize_total_energy(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose(), and protocols::stepwise::legacy::modeler::protein::output_silent_struct().

Real core::scoring::rms_at_corresponding_atoms_no_super	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		utility::vector1< Size > const &	calc_rms_res
	)

References core::pose::Pose::residue(), core::pose::Pose::size(), core::simple_metrics::metrics::sum, and core::pose::Pose::xyz().

Referenced by rms_at_corresponding_atoms_no_super().

Real core::scoring::rms_at_corresponding_heavy_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose
	)

References rms_at_corresponding_atoms(), and setup_matching_heavy_atoms().

Referenced by protocols::stepwise::modeler::rna::output_data(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

template<class T >

core::Real core::scoring::rmsd_no_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		utility::vector1< core::Size > const &	pose1_residues,
		utility::vector1< core::Size > const &	pose2_residues,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor at given residues.

Calculates rms, NOT allowing rotation/translation – uses current coordinates as-is. The two vectors should be the same length, and taken pairwise should be a mapping. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

The "resno" and "atomno" are calculated based on pose1 (which is what most predicates expect)

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by all_atom_rmsd_nosuper(), all_scatom_rmsd_nosuper(), protocols::ligand_docking::check_RMSD(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), non_peptide_heavy_atom_RMSD(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), and rmsd_no_super_subset().

template<class T >

core::Real core::scoring::rmsd_no_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms, NOT allowing rotation/translation – uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_no_super(pose1, pose2, is_protein_CA);

References rmsd_no_super(), and core::pose::Pose::size().

template<class T >

core::Real core::scoring::rmsd_no_super	(	core::conformation::ResidueCOPs const &	residues1,
		core::conformation::ResidueCOPs const &	residues2,
		T *	predicate
	)

References is_ligand_heavyatom_residues(), and core::pose::num_atoms().

template<class T >

core::Real core::scoring::rmsd_no_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms over a subset of residues, NOT allowing rotation/translation – uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno); the subset is a vector of all the residues, with true for those over which to calculate the rms

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_no_super_subset(pose1, pose2, subset, is_protein_CA);

References rmsd_no_super(), and core::pose::Pose::size().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::best_Kmer_rms(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::docking::calc_Lrmsd(), protocols::loop_modeling::utilities::TrajectoryLogger::calc_rmsd_to_native(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::pose_metric_calculators::compute_rmsd(), protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd(), protocols::antibody::global_loop_rmsd(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

template<class T >

core::Real core::scoring::rmsd_no_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		core::id::SequenceMapping const &	seqmap,
		T *	predicate
	)

like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way...

References rmsd_no_super(), and core::pose::Pose::size().

template<class T >

core::Real core::scoring::rmsd_with_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		utility::vector1< core::Size > const &	pose1_residues,
		utility::vector1< core::Size > const &	pose2_residues,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms, allowing rotation/translation for best fit. The two vectors should be the same length, and taken pairwise should be a mapping. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

The "resno" and "atomno" are calculated based on pose1 (which is what most predicates expect)

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), all_atom_rmsd(), bb_rmsd(), bb_rmsd_including_O(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rpc::JSON_RPC::get_irms(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), nbr_atom_rmsd(), protocols::features::ProteinRMSDFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_with_super(), rmsd_with_super_subset(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

template<class T >

core::Real core::scoring::rmsd_with_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< core::Size > const &	subset_residues,
		T *	predicate
	)

References rmsd_with_super().

template<class T >

core::Real core::scoring::rmsd_with_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms, allowing rotation/translation for best fit. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA);

References rmsd_with_super(), and core::pose::Pose::size().

template<class T >

core::Real core::scoring::rmsd_with_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select a subset atoms for RMS via a predicate function/functor.

Calculates minimal rms, allowing rotation/translation for best fit. Same as above function, but allows a subset of residues over which to superposition to be passed in Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);

References rmsd_with_super(), and core::pose::Pose::size().

Referenced by protocols::symmetry::SymmetricRMSMover::apply(), protocols::docking::calc_CA_Irmsd(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_with_super(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

template<class T >

core::Real core::scoring::rmsd_with_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		core::id::SequenceMapping const &	seqmap,
		T *	predicate
	)

like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way...

References rmsd_with_super(), and core::pose::Pose::size().

std::string const core::scoring::RNA_HIRES_WTS ( "rna/denovo/rna_hires" )

std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS ( "rna/denovo/rna_lores_plus_hires" )

std::string const core::scoring::RNA_LORES_WTS ( "rna/denovo/rna_lores" )

template<class T >

void core::scoring::ROTATE	(	T &	a,
		int	i,
		int	j,
		int	k,
		int	l,
		Real	s,
		Real	tau
	)

Referenced by jacobi(), and jacobi3().

bool core::scoring::same_polarization_group	(	core::conformation::Residue const &	rsd1,
		MultipoleElecResidueInfo const &	mp1,
		core::Size	atm1,
		core::conformation::Residue const &	rsd2,
		core::Size	atm2
	)

inline

References core::scoring::MultipoleElecResidueInfo::const_my_group(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

bool core::scoring::SASAShouldItCount	(	conformation::Residue const &	rsd,
		Size const &	atm
	)

References core::conformation::Residue::atom_name(), and core::conformation::Residue::seqpos().

std::string const core::scoring::SCORE12_PATCH ( "score12" )

std::string const core::scoring::SCORE13 ( "score13" )

std::string const core::scoring::SCORE4_SMOOTH_CART ( "score4_smooth_cart" )

ScoreType core::scoring::score_type_from_name ( std::string const & name )

give a ScoreType string name and return its enum type

Returns the ScoreType titled <name>

example(s): score_type_from_name("fa_sol") See also: ScoreFunction ScoreType Energies Energies.residue_total_energies name_from_score_type

References core::scoring::ScoreTypeManager::score_type_from_name().

Referenced by protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::relax::FastRelax::apply(), protocols::docking::SlideIntoContact::apply(), protocols::loop_grower::LoopGrower::apply(), apply_set_weights(), protocols::relax::FastRelax::batch_apply(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::io::silent::SilentStruct::energies_into_pose(), core::pose::energy_from_pose(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::optimize_weights::IterativeOptEDriver::initialize_free_and_fixed(), protocols::relax::FastRelax::inner_loop_reference_command(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::score_filters::ScoreTypeFilter::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), protocols::helical_bundle::BundleReporterFilter::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), protocols::optimize_weights::OptEData::read_from_file(), protocols::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::optimize_weights::IterativeOptEDriver::score_position_data(), protocols::docking::SlideIntoContact::scorefunction(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), and protocols::ddg::ddGMover::store_energies().

void core::scoring::setup_matching_atoms_with_given_names	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		utility::vector1< std::string > const &	atom_names_to_find,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::has(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by setup_matching_CA_atoms(), and setup_matching_protein_backbone_heavy_atoms().

void core::scoring::setup_matching_CA_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References setup_matching_atoms_with_given_names().

Referenced by protocols::stepwise::legacy::modeler::protein::output_silent_struct().

void core::scoring::setup_matching_heavy_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map(), protocols::stepwise::legacy::modeler::protein::output_silent_struct(), and rms_at_corresponding_heavy_atoms().

void core::scoring::setup_matching_protein_backbone_heavy_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References setup_matching_atoms_with_given_names().

Referenced by protocols::stepwise::legacy::screener::SimpleRMSD_Screener::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map(), and protocols::stepwise::legacy::modeler::protein::output_silent_struct().

std::map< rmsd_atoms, utility::vector1< std::string > > core::scoring::setup_rmsd_atom_names ( )

Returns a map of the rmsd_atom enum and a list of atom names for which this RMSD setting selects for the calculation

References rmsd_all, rmsd_protein_bb_ca, rmsd_protein_bb_heavy, and rmsd_protein_bb_heavy_including_O.

Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::setup_name_mapping().

bool core::scoring::ShouldItCount	(	conformation::Residue const &	rsd,
		Size const &	atm
	)

References core::conformation::Residue::atom_name(), and core::conformation::Residue::seqpos().

void core::scoring::show_detail	(	std::ostream &	out,
		EnergyMap &	energies,
		EnergyMap	weights
	)

References core::chemical::element::F, core::scoring::sasa::LJ, and n_score_types.

std::string const core::scoring::SOFT_REP_DESIGN_WTS ( "soft_rep_design" )

std::string const core::scoring::SOFT_REP_WTS ( "soft_rep" )

std::string const core::scoring::SPLIT_UNFOLDED_BOLTZ ( "SPLIT_UNFOLDED_BOLTZ" )

std::string const core::scoring::SPLIT_UNFOLDED_ELE ( "SPLIT_UNFOLDED_ELE" )

std::string const core::scoring::SPLIT_UNFOLDED_MEAN ( "SPLIT_UNFOLDED_MEAN" )

std::string const core::scoring::SPLIT_UNFOLDED_MEDIAN ( "SPLIT_UNFOLDED_MEDIAN" )

std::string const core::scoring::SPLIT_UNFOLDED_MM ( "SPLIT_UNFOLDED_MM" )

std::string const core::scoring::SPLIT_UNFOLDED_MODE ( "SPLIT_UNFOLDED_MODE" )

std::string const core::scoring::SPLIT_UNFOLDED_PDB ( "SPLIT_UNFOLDED_PDB" )

std::string const core::scoring::SPLIT_UNFOLDED_ROSETTA ( "SPLIT_UNFOLDED_ROSETTA" )

std::string const core::scoring::SPLIT_UNFOLDED_UNIQUE ( "SPLIT_UNFOLDED_UNIQUE" )

std::string const core::scoring::SPLIT_UNFOLDED_USER_DEFINED ( "SPLIT_UNFOLDED_USER_DEFINED" )

Real core::scoring::sqr ( Real x )

inline

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore(), and core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().

void core::scoring::store_CSA_in_pose	(	ChemicalShiftAnisotropyOP	csa_info,
		core::pose::Pose &	pose
	)

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

Referenced by core::scoring::methods::ChemicalShiftAnisotropyEnergy::csa_from_pose().

void core::scoring::store_DC_in_pose	(	DipolarCouplingOP	dc_info,
		core::pose::Pose &	pose
	)

References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().

Referenced by core::scoring::methods::DipolarCouplingEnergy::dc_from_pose().

void core::scoring::store_RDC_in_pose	(	ResidualDipolarCouplingOP	rdc_info,
		core::pose::Pose &	pose
	)

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.

Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy::rdc_from_pose(), protocols::frag_picker::scores::RDCScore::score(), and protocols::abinitio::IterativeBase::score().

void core::scoring::store_RDC_ROHL_in_pose	(	ResidualDipolarCoupling_RohlOP	rdc_info,
		core::pose::Pose &	pose
	)

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.

Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::rdc_from_pose().

Real core::scoring::superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		core::Real const &	rms_calc_offset_val,
		bool const	realign
	)

Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map.

Superimpose mod_pose onto ref_pose using the AtomID mapping, which maps atoms in mod_pose onto atoms in ref_pose. Returns rmsd over alignment.

Note: Atoms in mod_pose whose ids map to bogus atom ids will not be used in the fitting

Usage example: superimpose pose1 onto pose2 by mapping C-alphas of residue 10-30 onto residues 20-40

id::AtomID_Map< id::AtomID > atom_map; id::initialize( atom_map, pose1, id::AtomID::BOGUS_ATOM_ID() ); // maps every atomid to bogus atom

for ( Size i=10; i<=30; ++i ) { id::AtomID const id1( pose1.residue(i).atom_index("CA"), i ); id::AtomID const id2( pose2.residue(i+10).atom_index("CA"), i+10 ); atom_map[ id1 ] = id2; } superimpose_pose( pose1, pose2, atom_map );

The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false).

WARNING: This will give you errors if you try to superimpose a non-symmetric pose onto a symmetric one, even with the correct atom_map. It will not fail, but the superposition will be bad and any subsequent RMSD calculation will be wrong.

References superimpose_pose().

Real core::scoring::superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_map,
		core::Real const &	rms_calc_offset_val = `1.0e-7`,
		bool const	realign = `false`
	)

Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by map< AtomID, AtomID >

The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false).

References core::pose::convert_from_std_map(), core::conformation::symmetry::is_symmetric(), superimpose_pose(), and tr().

Real core::scoring::superimpose_pose	(	pose::Pose &	mod_pose,
		pose::MiniPose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		core::Real const &	rms_calc_offset_val = `1.0e-7`,
		bool const	realign = `false`
	)

Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map.

The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false).

WARNING: this will give you errors if you try to superimpose a non-symmetric pose onto a symmetric one, even with the correct atom_map. It will not fail, but the superposition will be bad and any subsequent RMSD calculation will be wrong.

References core::chemical::ResidueType::natoms(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rms, core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::pose::MiniPose::xyz(), and core::conformation::Residue::xyz().

Referenced by calpha_superimpose_pose(), and superimpose_pose().

template<class T >

core::Real core::scoring::sym_rmsd_with_super_subset	(	core::pose::Pose const &	native_pose,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);.

References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::chemical::element::N, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), rms, core::pose::Pose::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().

static basic::Tracer core::scoring::T ( "core.scoring.Ramachandran2B" )

static

Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::nmr::pre::PREMultiSet::PRE_Curie_prefactor(), core::scoring::Ramachandran2B::read_rama(), and core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives().

std::string const core::scoring::TALARIS_2013 ( "talaris2013" )

std::string const core::scoring::TALARIS_2013_CART ( "talaris2013_cart" )

std::string const core::scoring::TALARIS_2014 ( "talaris2014" )

static basic::Tracer core::scoring::TR ( "core.scoring.HydroxylTorsionPotential" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.AtomVDW" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.PolymerBondedEnergyContainer" )

static

static basic::Tracer core::scoring::tr ( "core.scoring.NeighborList" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.TMscore" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.MembraneTopology" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.RamaPrePro" )

static

static basic::Tracer core::scoring::TR ( "core.scoring.ProQPotential" )

static

static basic::Tracer core::scoring::tr ( "core.scoring.rms_util" )

static

Referenced by automorphic_rmsd(), CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_or_equiv_rmsd(), CA_rmsd(), CA_rmsd_symmetric(), gdtha(), gdtsc(), rms_at_all_corresponding_atoms(), rms_at_corresponding_atoms(), superimpose_pose(), and xyz_gdtmm().

static basic::Tracer core::scoring::TR ( "core.scoring.GenericBondedPotential" )

static

static basic::Tracer core::scoring::TR_it ( "core.scoring.PolymerBondedNeighborIterator" )

static

static basic::Tracer core::scoring::trKillHairpinsIO ( "core.score.SS_Killhairpins_Info" )

static

Referenced by core::scoring::SS_Killhairpins_Info::setup_from_kill_hairpins_file(), and core::scoring::SS_Killhairpins_Info::setup_from_psipred().

std::string const core::scoring::UNFOLDED_MM_STD ( "UNFOLDED_MM_STD" )

std::string const core::scoring::UNFOLDED_RNA ( "UNFOLDED_RNA" )

std::string const core::scoring::UNFOLDED_SCORE12 ( "UNFOLDED_SCORE12" )

std::string const core::scoring::UNFOLDED_SPLIT_MM_STD ( "UNFOLDED_SPLIT_MM_STD" )

std::string const core::scoring::UNFOLDED_SPLIT_TALARIS2013 ( "UNFOLDED_SPLIT_TALARIS2013" )

std::string const core::scoring::UNFOLDED_SPLIT_USER_DEFINED ( "UNFOLDED_SPLIT_USER_DEFINED" )

bool core::scoring::VdWShouldItCount	(	conformation::Residue const &	rsd,
		Size const &	atm
	)

References core::conformation::Residue::atom_name(), and core::conformation::Residue::seqpos().

template<class T >

void core::scoring::vector1_remove	(	utility::vector1< T > &	v,
		T const &	t
	)

inline

private – handles setting the derived data

References protocols::hybridization::t.

Referenced by core::scoring::ScoreFunction::remove_method().

core::Real core::scoring::xyz_gdtmm	(	ObjexxFCL::FArray2D< core::Real >	p1a,
		ObjexxFCL::FArray2D< core::Real >	p2a,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.

core::Real core::scoring::xyz_gdtmm	(	ObjexxFCL::FArray2D< core::Real >	p1a,
		ObjexxFCL::FArray2D< core::Real >	p2a
	)

Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.

core::Real core::scoring::xyz_gdtmm	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a
	)

References xyz_gdtmm().

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), and protocols::hybridization::get_gdtmm().

core::Real core::scoring::xyz_gdtmm	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

References tr().

Referenced by CA_gdtmm(), and xyz_gdtmm().

void core::scoring::xyz_gdttm	(	ObjexxFCL::FArray2D< core::Real >	p1a,
		ObjexxFCL::FArray2D< core::Real >	p2a,
		core::Real &	gdttm_score,
		core::Real &	gdtha_score
	)

void core::scoring::xyz_gdttm	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a,
		core::Real &	gdttm_score,
		core::Real &	gdtha_score
	)

References core::scoring::TMscore::apply(), core::scoring::TMscore::get_GDTHA(), and core::scoring::TMscore::get_GDTTS().

Referenced by protocols::mpi_refinement::add_init_dev_penalty(), and protocols::comparative_modeling::Align_RmsdEvaluator::apply().

int core::scoring::xyz_maxsub	(	ObjexxFCL::FArray2D< core::Real >	p1a,
		ObjexxFCL::FArray2D< core::Real >	p2a,
		int	natoms
	)

int core::scoring::xyz_maxsub	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a,
		int	natoms
	)

Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().

Variable Documentation

std::string const core::scoring::BETA_GENPOT

Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().

std::string const core::scoring::BETA_JULY15

Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().

std::string const core::scoring::BETA_NOV15

Referenced by basename_for_score_function().

std::string const core::scoring::BETA_NOV16

Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().

short const core::scoring::bit_count[]

Initial value:

= { 
0,1,1,2,1,2,2,3, 1,2,2,3,2,3,3,4,   1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,  
1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,   4,5,5,6,5,6,6,7, 5,6,6,7,6,7,7,8,  
}

Referenced by calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::CENTROID_WTS

Referenced by basename_for_score_function(), protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), get_score_function(), get_score_functionName(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::symmetry::SymmetrySlider::setup(), protocols::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::symmetry::SymmetrySlider::SymmetrySlider().

std::string const core::scoring::DNA_INT_WTS

Referenced by basename_for_score_function().

std::string const core::scoring::DNA_INT_WTS_GB

Referenced by basename_for_score_function().

std::string const core::scoring::DOCK_LOW_PATCH

Referenced by basename_for_score_function(), protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), protocols::symmetry::SymmetrySlider::setup(), protocols::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::symmetry::SymmetrySlider::SymmetrySlider().

std::string const core::scoring::DOCK_PATCH

Referenced by basename_for_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol().

std::string const core::scoring::FA_STANDARD_DEFAULT

Referenced by core::scoring::ScoringManager::create_memb_etable_instance(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), and core::scoring::ScoringManager::etable().

std::string const core::scoring::FA_STANDARD_MULTIPOLE

Referenced by core::scoring::ScoringManager::etable().

std::string const core::scoring::FA_STANDARD_SOFT

Referenced by protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), core::scoring::ScoringManager::etable(), and core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn().

int const core::scoring::maskbits = 162

Referenced by calc_per_atom_sasa(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::MEMB_HIGHRES_WTS

Referenced by basename_for_score_function().

std::string const core::scoring::MM_STD_WTS

Referenced by protocols::ncbb::oop::OopCreatorMover::apply(), and basename_for_score_function().

int const core::scoring::num_bytes = 21

Referenced by calc_atom_masks(), calc_per_atom_sasa(), get_num_bytes(), and input_sasa_dats().

int const core::scoring::num_orientations = 162

Referenced by input_sasa_dats().

int const core::scoring::num_overlaps = 100

Referenced by input_sasa_dats().

int const core::scoring::num_phi = 64

Referenced by get_orientation(), and input_sasa_dats().

int const core::scoring::num_theta = 64

Referenced by get_orientation(), and input_sasa_dats().

std::string const core::scoring::PRE_TALARIS_2013_STANDARD_WTS

Referenced by protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::minimization_packing::MinPackMover::apply(), protocols::antibody_legacy::GraftMover::apply(), basename_for_score_function(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::sasa_scores::compute_avge_scores(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::antibody::get_Pack_ScoreFxn(), get_score_functionName(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::antibody::RefineBetaBarrel::init(), protocols::docking::TemperedDocking::init_from_options(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), core::pack::optimize_H_and_notify(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::antibody::LHRepulsiveRampLegacy::set_default(), protocols::symmetric_docking::SymDockProtocol::set_default(), protocols::symmetric_docking::SymSidechainMinMover::set_default_options(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol(), protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes(), and protocols::motifs::IRCollection::try_for_more().

std::string const core::scoring::REF_2015

Referenced by basename_for_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and get_current_default_score_function_name().

std::string const core::scoring::RNA_HIRES_WTS

Referenced by protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), and basename_for_score_function().

std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS

Referenced by basename_for_score_function().

std::string const core::scoring::RNA_LORES_WTS

Referenced by basename_for_score_function(), protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::classify_base_pairs_lores(), core::pose::rna::get_scored_base_stack_list(), and protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo().

std::string const core::scoring::SCORE12_PATCH

Referenced by basename_for_score_function(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and get_score_functionName().

std::string const core::scoring::SCORE13

Referenced by basename_for_score_function().

std::string const core::scoring::SCORE4_SMOOTH_CART

Referenced by protocols::legacy_sewing::LegacyAssemblyMover::apply(), and basename_for_score_function().

std::string const core::scoring::SOFT_REP_DESIGN_WTS

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), basename_for_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and protocols::forge::remodel::RemodelMover::RemodelMover().

std::string const core::scoring::SOFT_REP_WTS

Referenced by basename_for_score_function().

std::string const core::scoring::SPLIT_UNFOLDED_BOLTZ

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_ELE

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_MEAN

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_MEDIAN

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_MM

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_MODE

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_PDB

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_ROSETTA

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_UNIQUE

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance().

std::string const core::scoring::SPLIT_UNFOLDED_USER_DEFINED

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance(), and core::scoring::methods::EnergyMethodOptions::initialize_from_options().

std::string const core::scoring::TALARIS_2013

Referenced by basename_for_score_function(), protocols::boinc::boincOutputFilter(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and core::scoring::ScoreFunctionFactory::validate_talaris().

std::string const core::scoring::TALARIS_2013_CART

Referenced by protocols::legacy_sewing::LegacyAssemblyMover::apply().

std::string const core::scoring::TALARIS_2014

Referenced by basename_for_score_function(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), and core::scoring::ScoreFunctionFactory::validate_talaris().

std::string const core::scoring::UNFOLDED_MM_STD

Referenced by core::scoring::ScoringManager::create_unfolded_state_potential_instance().

std::string const core::scoring::UNFOLDED_RNA

Referenced by core::scoring::ScoringManager::create_unfolded_state_potential_instance().

std::string const core::scoring::UNFOLDED_SCORE12

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), core::scoring::ScoringManager::create_unfolded_state_potential_instance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), and protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies().

std::string const core::scoring::UNFOLDED_SPLIT_MM_STD

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance(), and core::scoring::ScoringManager::create_unfolded_state_potential_instance().

std::string const core::scoring::UNFOLDED_SPLIT_TALARIS2013

Referenced by core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance(), and core::scoring::ScoringManager::create_unfolded_state_potential_instance().

std::string const core::scoring::UNFOLDED_SPLIT_USER_DEFINED

Referenced by core::scoring::ScoringManager::create_unfolded_state_potential_instance(), and core::scoring::methods::EnergyMethodOptions::initialize_from_options().

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