core::scoring::func Namespace Reference

Classes
class	AmberPeriodicFunc
	function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...
class	CharmmPeriodicFunc
	function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...
class	CircularGeneral1D_Func
	Function that allows return of arbitrary FArrays – this time circularized. More...
class	CircularHarmonicFunc
	Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
class	CircularPowerFunc
	Generalization of CircularCircularPowerFunc – other exponents allowed. More...
class	CircularSigmoidalFunc
	Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
class	CircularSplineFunc
class	ConformationXYZ
class	ConstantFunc
	Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation. More...
class	CountViolFunc
class	EtableFunc
	Class for representing arbitrarily defined functions. More...
class	FadeFunc
class	FlatHarmonicFunc
class	FourPointsFunc
	A simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit. More...
class	Func
	Func is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r. More...
class	FuncFactory
class	GaussianChainDoubleFunc
class	GaussianChainFunc
class	GaussianChainGeneralFunc
class	GaussianChainQuadrupleFunc
class	GaussianChainSingleFunc
class	GaussianChainTripleFunc
class	GaussianFunc
	Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation. More...
class	HarmonicFunc
class	IdentityFunc
class	KarplusFunc
	Function that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
class	LinearPenaltyFunction
class	MinMultiHarmonicFunc
class	MixtureFunc
	Derived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information. More...
class	PeriodicFunc
	function of type y = ( k * cos(n * (x - x0) ) ) + C More...
class	ResiduePairXYZ
class	ResidueXYZ
class	ScalarWeightedFunc
class	SigmoidFunc
class	SkipViolFunc
class	SmoothStepFunc
class	SoedingFunc
	Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation. More...
class	SOGFunc
	Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
class	SOGFunc_Impl
	Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
class	SplineFunc
class	SquareWell2Func
class	SquareWellFunc
class	SumFunc
class	TopOutFunc
class	USOGFunc
	Unnormalized, unbounded sum of Gaussians constraint. More...
class	XYZ_Func
	just a simple class that takes an AtomID and returns a Vector (position) More...

Typedefs
typedef utility::pointer::shared_ptr < AmberPeriodicFunc >	AmberPeriodicFuncOP
typedef utility::pointer::shared_ptr < AmberPeriodicFunc const >	AmberPeriodicFuncCOP
typedef utility::pointer::shared_ptr < CircularGeneral1D_Func >	CircularGeneral1D_FuncOP
typedef utility::pointer::shared_ptr < CircularGeneral1D_Func const >	CircularGeneral1D_FuncCOP
typedef utility::pointer::shared_ptr < CircularHarmonicFunc >	CircularHarmonicFuncOP
typedef utility::pointer::shared_ptr < CircularHarmonicFunc const >	CircularHarmonicFuncCOP
typedef utility::pointer::shared_ptr < CircularPowerFunc >	CircularPowerFuncOP
typedef utility::pointer::shared_ptr < CircularPowerFunc const >	CircularPowerFuncCOP
typedef utility::pointer::shared_ptr < CircularSigmoidalFunc >	CircularSigmoidalFuncOP
typedef utility::pointer::shared_ptr < CircularSigmoidalFunc const >	CircularSigmoidalFuncCOP
typedef utility::pointer::shared_ptr < CircularSplineFunc >	CircularSplineFuncOP
typedef utility::pointer::shared_ptr < CircularSplineFunc const >	CircularSplineFuncCOP
typedef utility::pointer::shared_ptr < ConstantFunc >	ConstantFuncOP
typedef utility::pointer::shared_ptr < EtableFunc >	EtableFuncOP
typedef utility::pointer::shared_ptr < FadeFunc >	FadeFuncOP
typedef utility::pointer::shared_ptr < FadeFunc const >	FadeFuncCOP
typedef utility::pointer::shared_ptr < FlatHarmonicFunc >	FlatHarmonicFuncOP
typedef utility::pointer::shared_ptr < FlatHarmonicFunc const >	FlatHarmonicFuncCOP
typedef utility::pointer::shared_ptr < FourPointsFunc >	FourPointsFuncOP
typedef utility::pointer::shared_ptr < FourPointsFunc const >	FourPointsFuncCOP
typedef utility::pointer::shared_ptr < Func >	FuncOP
typedef utility::pointer::shared_ptr < const Func >	FuncCOP
typedef utility::pointer::shared_ptr < GaussianChainDoubleFunc >	GaussianChainDoubleFuncOP
typedef utility::pointer::shared_ptr < GaussianChainDoubleFunc const >	GaussianChainDoubleFuncCOP
typedef utility::pointer::shared_ptr < GaussianChainFunc >	GaussianChainFuncOP
typedef utility::pointer::shared_ptr < GaussianChainFunc const >	GaussianChainFuncCOP
typedef utility::pointer::shared_ptr < GaussianChainGeneralFunc >	GaussianChainGeneralFuncOP
typedef utility::pointer::shared_ptr < GaussianChainGeneralFunc const >	GaussianChainGeneralFuncCOP
typedef utility::pointer::shared_ptr < GaussianChainQuadrupleFunc >	GaussianChainQuadrupleFuncOP
typedef utility::pointer::shared_ptr < GaussianChainQuadrupleFunc const >	GaussianChainQuadrupleFuncCOP
typedef utility::pointer::shared_ptr < GaussianChainSingleFunc >	GaussianChainSingleFuncOP
typedef utility::pointer::shared_ptr < GaussianChainSingleFunc const >	GaussianChainSingleFuncCOP
typedef utility::pointer::shared_ptr < GaussianChainTripleFunc >	GaussianChainTripleFuncOP
typedef utility::pointer::shared_ptr < GaussianChainTripleFunc const >	GaussianChainTripleFuncCOP
typedef utility::pointer::shared_ptr < GaussianFunc >	GaussianFuncOP
typedef utility::pointer::shared_ptr < HarmonicFunc >	HarmonicFuncOP
typedef utility::pointer::shared_ptr < HarmonicFunc const >	HarmonicFuncCOP
typedef utility::pointer::shared_ptr < IdentityFunc >	IdentityFuncOP
typedef utility::pointer::shared_ptr < IdentityFunc const >	IdentityFuncCOP
typedef utility::pointer::shared_ptr < KarplusFunc >	KarplusFuncOP
typedef utility::pointer::shared_ptr < KarplusFunc const >	KarplusFuncCOP
typedef utility::pointer::shared_ptr < MinMultiHarmonicFunc >	MinMultiHarmonicFuncOP
typedef utility::pointer::shared_ptr < MinMultiHarmonicFunc const >	MinMultiHarmonicFuncCOP
typedef utility::pointer::shared_ptr < MixtureFunc >	MixtureFuncOP
typedef utility::pointer::shared_ptr < ScalarWeightedFunc >	ScalarWeightedFuncOP
typedef utility::pointer::shared_ptr < ScalarWeightedFunc const >	ScalarWeightedFuncCOP
typedef utility::pointer::shared_ptr < SigmoidFunc >	SigmoidFuncOP
typedef utility::pointer::shared_ptr < SigmoidFunc const >	SigmoidFuncCOP
typedef utility::pointer::shared_ptr < SmoothStepFunc >	SmoothStepFuncOP
typedef utility::pointer::shared_ptr < SmoothStepFunc const >	SmoothStepFuncCOP
typedef utility::pointer::shared_ptr < SoedingFunc >	SoedingFuncOP
typedef utility::pointer::shared_ptr < SOGFunc >	SOGFuncOP
typedef utility::pointer::shared_ptr < SOGFunc_Impl >	SOGFunc_ImplOP
typedef utility::pointer::shared_ptr < SplineFunc >	SplineFuncOP
typedef utility::pointer::shared_ptr < SplineFunc const >	SplineFuncCOP
typedef utility::vector1 < std::tuple< std::string, platform::Real, platform::Real, platform::Real > >	boundary_fn_type
typedef utility::pointer::shared_ptr < SquareWell2Func >	SquareWell2FuncOP
typedef utility::pointer::shared_ptr < SquareWell2Func const >	SquareWell2FuncCOP
typedef utility::pointer::shared_ptr < SquareWellFunc >	SquareWellFuncOP
typedef utility::pointer::shared_ptr < SquareWellFunc const >	SquareWellFuncCOP
typedef utility::pointer::shared_ptr < SumFunc >	SumFuncOP
typedef utility::pointer::shared_ptr < TopOutFunc >	TopOutFuncOP
typedef utility::pointer::shared_ptr < TopOutFunc const >	TopOutFuncCOP
typedef utility::pointer::shared_ptr < USOGFunc >	USOGFuncOP
typedef utility::pointer::shared_ptr < USOGFunc const >	USOGFuncCOP

Functions
static basic::Tracer	tr ("core.scoring.constraints.Func")
std::ostream &	operator<< (std::ostream &out, Func const &f)
Real	L (Real const &x)
static basic::Tracer	trMinMultiHarmonicFunc ("fragment.picking.scores.MinMultiHarmonicFunc")
core::Real	readValueOrDie (std::istream &in)
	Reads and returns a single floating point value from the specified input stream, aborting if either the failbit or badbit is flipped. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< AmberPeriodicFunc const > core::scoring::func::AmberPeriodicFuncCOP

typedef utility::pointer::shared_ptr< AmberPeriodicFunc > core::scoring::func::AmberPeriodicFuncOP

typedef utility::vector1<std::tuple<std::string, platform::Real, platform::Real, platform::Real> > core::scoring::func::boundary_fn_type

typedef utility::pointer::shared_ptr< CircularGeneral1D_Func const > core::scoring::func::CircularGeneral1D_FuncCOP

typedef utility::pointer::shared_ptr< CircularGeneral1D_Func > core::scoring::func::CircularGeneral1D_FuncOP

typedef utility::pointer::shared_ptr< CircularHarmonicFunc const > core::scoring::func::CircularHarmonicFuncCOP

typedef utility::pointer::shared_ptr< CircularHarmonicFunc > core::scoring::func::CircularHarmonicFuncOP

typedef utility::pointer::shared_ptr< CircularPowerFunc const > core::scoring::func::CircularPowerFuncCOP

typedef utility::pointer::shared_ptr< CircularPowerFunc > core::scoring::func::CircularPowerFuncOP

typedef utility::pointer::shared_ptr< CircularSigmoidalFunc const > core::scoring::func::CircularSigmoidalFuncCOP

typedef utility::pointer::shared_ptr< CircularSigmoidalFunc > core::scoring::func::CircularSigmoidalFuncOP

typedef utility::pointer::shared_ptr< CircularSplineFunc const > core::scoring::func::CircularSplineFuncCOP

typedef utility::pointer::shared_ptr< CircularSplineFunc > core::scoring::func::CircularSplineFuncOP

typedef utility::pointer::shared_ptr< ConstantFunc > core::scoring::func::ConstantFuncOP

typedef utility::pointer::shared_ptr< EtableFunc > core::scoring::func::EtableFuncOP

typedef utility::pointer::shared_ptr< FadeFunc const > core::scoring::func::FadeFuncCOP

typedef utility::pointer::shared_ptr< FadeFunc > core::scoring::func::FadeFuncOP

typedef utility::pointer::shared_ptr< FlatHarmonicFunc const > core::scoring::func::FlatHarmonicFuncCOP

typedef utility::pointer::shared_ptr< FlatHarmonicFunc > core::scoring::func::FlatHarmonicFuncOP

typedef utility::pointer::shared_ptr< FourPointsFunc const > core::scoring::func::FourPointsFuncCOP

typedef utility::pointer::shared_ptr< FourPointsFunc > core::scoring::func::FourPointsFuncOP

typedef utility::pointer::shared_ptr< const Func > core::scoring::func::FuncCOP

typedef utility::pointer::shared_ptr< Func > core::scoring::func::FuncOP

typedef utility::pointer::shared_ptr< GaussianChainDoubleFunc const > core::scoring::func::GaussianChainDoubleFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainDoubleFunc > core::scoring::func::GaussianChainDoubleFuncOP

typedef utility::pointer::shared_ptr< GaussianChainFunc const > core::scoring::func::GaussianChainFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainFunc > core::scoring::func::GaussianChainFuncOP

typedef utility::pointer::shared_ptr< GaussianChainGeneralFunc const > core::scoring::func::GaussianChainGeneralFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainGeneralFunc > core::scoring::func::GaussianChainGeneralFuncOP

typedef utility::pointer::shared_ptr< GaussianChainQuadrupleFunc const > core::scoring::func::GaussianChainQuadrupleFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainQuadrupleFunc > core::scoring::func::GaussianChainQuadrupleFuncOP

typedef utility::pointer::shared_ptr< GaussianChainSingleFunc const > core::scoring::func::GaussianChainSingleFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainSingleFunc > core::scoring::func::GaussianChainSingleFuncOP

typedef utility::pointer::shared_ptr< GaussianChainTripleFunc const > core::scoring::func::GaussianChainTripleFuncCOP

typedef utility::pointer::shared_ptr< GaussianChainTripleFunc > core::scoring::func::GaussianChainTripleFuncOP

typedef utility::pointer::shared_ptr< GaussianFunc > core::scoring::func::GaussianFuncOP

typedef utility::pointer::shared_ptr< HarmonicFunc const > core::scoring::func::HarmonicFuncCOP

typedef utility::pointer::shared_ptr< HarmonicFunc > core::scoring::func::HarmonicFuncOP

typedef utility::pointer::shared_ptr< IdentityFunc const > core::scoring::func::IdentityFuncCOP

typedef utility::pointer::shared_ptr< IdentityFunc > core::scoring::func::IdentityFuncOP

typedef utility::pointer::shared_ptr< KarplusFunc const > core::scoring::func::KarplusFuncCOP

typedef utility::pointer::shared_ptr< KarplusFunc > core::scoring::func::KarplusFuncOP

typedef utility::pointer::shared_ptr< MinMultiHarmonicFunc const > core::scoring::func::MinMultiHarmonicFuncCOP

typedef utility::pointer::shared_ptr< MinMultiHarmonicFunc > core::scoring::func::MinMultiHarmonicFuncOP

typedef utility::pointer::shared_ptr< MixtureFunc > core::scoring::func::MixtureFuncOP

typedef utility::pointer::shared_ptr< ScalarWeightedFunc const > core::scoring::func::ScalarWeightedFuncCOP

typedef utility::pointer::shared_ptr< ScalarWeightedFunc > core::scoring::func::ScalarWeightedFuncOP

typedef utility::pointer::shared_ptr< SigmoidFunc const > core::scoring::func::SigmoidFuncCOP

typedef utility::pointer::shared_ptr< SigmoidFunc > core::scoring::func::SigmoidFuncOP

typedef utility::pointer::shared_ptr< SmoothStepFunc const > core::scoring::func::SmoothStepFuncCOP

typedef utility::pointer::shared_ptr< SmoothStepFunc > core::scoring::func::SmoothStepFuncOP

typedef utility::pointer::shared_ptr< SoedingFunc > core::scoring::func::SoedingFuncOP

typedef utility::pointer::shared_ptr< SOGFunc_Impl > core::scoring::func::SOGFunc_ImplOP

typedef utility::pointer::shared_ptr< SOGFunc > core::scoring::func::SOGFuncOP

typedef utility::pointer::shared_ptr< SplineFunc const > core::scoring::func::SplineFuncCOP

typedef utility::pointer::shared_ptr< SplineFunc > core::scoring::func::SplineFuncOP

typedef utility::pointer::shared_ptr< SquareWell2Func const > core::scoring::func::SquareWell2FuncCOP

typedef utility::pointer::shared_ptr< SquareWell2Func > core::scoring::func::SquareWell2FuncOP

typedef utility::pointer::shared_ptr< SquareWellFunc const > core::scoring::func::SquareWellFuncCOP

typedef utility::pointer::shared_ptr< SquareWellFunc > core::scoring::func::SquareWellFuncOP

typedef utility::pointer::shared_ptr< SumFunc > core::scoring::func::SumFuncOP

typedef utility::pointer::shared_ptr< TopOutFunc const > core::scoring::func::TopOutFuncCOP

typedef utility::pointer::shared_ptr< TopOutFunc > core::scoring::func::TopOutFuncOP

typedef utility::pointer::shared_ptr<USOGFunc const> core::scoring::func::USOGFuncCOP

typedef utility::pointer::shared_ptr<USOGFunc> core::scoring::func::USOGFuncOP

Function Documentation

Real core::scoring::func::L

(

Real const &

x

)

Referenced by core::scoring::func::GaussianChainQuadrupleFunc::dfunc(), and core::scoring::func::GaussianChainQuadrupleFunc::func().

std::ostream & core::scoring::func::operator<<	(	std::ostream &	out,
		Func const &	f
	)

References core::conformation::membrane::out, and core::scoring::func::Func::show().

core::Real core::scoring::func::readValueOrDie

(

std::istream &

in

)

Reads and returns a single floating point value from the specified input stream, aborting if either the failbit or badbit is flipped.

Referenced by core::scoring::func::USOGFunc::read_data().

static basic::Tracer core::scoring::func::tr ( "core.scoring.constraints.Func"  )

static

Referenced by core::scoring::func::Func::read_data().

static basic::Tracer core::scoring::func::trMinMultiHarmonicFunc ( "fragment.picking.scores.MinMultiHarmonicFunc"  )

static

Referenced by core::scoring::func::MinMultiHarmonicFunc::read_data().