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Classes | Typedefs | Functions
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  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  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...
 
class  ResidueXYZ
 
class  ResiduePairXYZ
 
class  ConformationXYZ
 

Typedefs

typedef utility::pointer::shared_ptr< AmberPeriodicFuncAmberPeriodicFuncOP
 
typedef utility::pointer::shared_ptr< AmberPeriodicFunc const > AmberPeriodicFuncCOP
 
typedef utility::pointer::shared_ptr< CircularGeneral1D_FuncCircularGeneral1D_FuncOP
 
typedef utility::pointer::shared_ptr< CircularGeneral1D_Func const > CircularGeneral1D_FuncCOP
 
typedef utility::pointer::shared_ptr< CircularHarmonicFuncCircularHarmonicFuncOP
 
typedef utility::pointer::shared_ptr< CircularHarmonicFunc const > CircularHarmonicFuncCOP
 
typedef utility::pointer::shared_ptr< CircularPowerFuncCircularPowerFuncOP
 
typedef utility::pointer::shared_ptr< CircularPowerFunc const > CircularPowerFuncCOP
 
typedef utility::pointer::shared_ptr< CircularSigmoidalFuncCircularSigmoidalFuncOP
 
typedef utility::pointer::shared_ptr< CircularSigmoidalFunc const > CircularSigmoidalFuncCOP
 
typedef utility::pointer::shared_ptr< CircularSplineFuncCircularSplineFuncOP
 
typedef utility::pointer::shared_ptr< CircularSplineFunc const > CircularSplineFuncCOP
 
typedef utility::pointer::shared_ptr< ConstantFuncConstantFuncOP
 
typedef utility::pointer::shared_ptr< EtableFuncEtableFuncOP
 
typedef utility::pointer::shared_ptr< FadeFuncFadeFuncOP
 
typedef utility::pointer::shared_ptr< FadeFunc const > FadeFuncCOP
 
typedef utility::pointer::shared_ptr< FlatHarmonicFuncFlatHarmonicFuncOP
 
typedef utility::pointer::shared_ptr< FlatHarmonicFunc const > FlatHarmonicFuncCOP
 
typedef utility::pointer::shared_ptr< FourPointsFuncFourPointsFuncOP
 
typedef utility::pointer::shared_ptr< FourPointsFunc const > FourPointsFuncCOP
 
typedef utility::pointer::shared_ptr< FuncFuncOP
 
typedef utility::pointer::shared_ptr< const FuncFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainDoubleFuncGaussianChainDoubleFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainDoubleFunc const > GaussianChainDoubleFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainFuncGaussianChainFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainFunc const > GaussianChainFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainGeneralFuncGaussianChainGeneralFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainGeneralFunc const > GaussianChainGeneralFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainQuadrupleFuncGaussianChainQuadrupleFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainQuadrupleFunc const > GaussianChainQuadrupleFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainSingleFuncGaussianChainSingleFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainSingleFunc const > GaussianChainSingleFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianChainTripleFuncGaussianChainTripleFuncOP
 
typedef utility::pointer::shared_ptr< GaussianChainTripleFunc const > GaussianChainTripleFuncCOP
 
typedef utility::pointer::shared_ptr< GaussianFuncGaussianFuncOP
 
typedef utility::pointer::shared_ptr< HarmonicFuncHarmonicFuncOP
 
typedef utility::pointer::shared_ptr< HarmonicFunc const > HarmonicFuncCOP
 
typedef utility::pointer::shared_ptr< IdentityFuncIdentityFuncOP
 
typedef utility::pointer::shared_ptr< IdentityFunc const > IdentityFuncCOP
 
typedef utility::pointer::shared_ptr< KarplusFuncKarplusFuncOP
 
typedef utility::pointer::shared_ptr< KarplusFunc const > KarplusFuncCOP
 
typedef utility::pointer::shared_ptr< MinMultiHarmonicFuncMinMultiHarmonicFuncOP
 
typedef utility::pointer::shared_ptr< MinMultiHarmonicFunc const > MinMultiHarmonicFuncCOP
 
typedef utility::pointer::shared_ptr< MixtureFuncMixtureFuncOP
 
typedef utility::pointer::shared_ptr< ScalarWeightedFuncScalarWeightedFuncOP
 
typedef utility::pointer::shared_ptr< ScalarWeightedFunc const > ScalarWeightedFuncCOP
 
typedef utility::pointer::shared_ptr< SigmoidFuncSigmoidFuncOP
 
typedef utility::pointer::shared_ptr< SigmoidFunc const > SigmoidFuncCOP
 
typedef utility::pointer::shared_ptr< SmoothStepFuncSmoothStepFuncOP
 
typedef utility::pointer::shared_ptr< SmoothStepFunc const > SmoothStepFuncCOP
 
typedef utility::pointer::shared_ptr< SoedingFuncSoedingFuncOP
 
typedef utility::pointer::shared_ptr< SOGFuncSOGFuncOP
 
typedef utility::pointer::shared_ptr< SOGFunc_ImplSOGFunc_ImplOP
 
typedef utility::pointer::shared_ptr< SplineFuncSplineFuncOP
 
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< SquareWell2FuncSquareWell2FuncOP
 
typedef utility::pointer::shared_ptr< SquareWell2Func const > SquareWell2FuncCOP
 
typedef utility::pointer::shared_ptr< SquareWellFuncSquareWellFuncOP
 
typedef utility::pointer::shared_ptr< SquareWellFunc const > SquareWellFuncCOP
 
typedef utility::pointer::shared_ptr< SumFuncSumFuncOP
 
typedef utility::pointer::shared_ptr< TopOutFuncTopOutFuncOP
 
typedef utility::pointer::shared_ptr< TopOutFunc const > TopOutFuncCOP
 
typedef utility::pointer::shared_ptr< USOGFuncUSOGFuncOP
 
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

◆ AmberPeriodicFuncCOP

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

◆ AmberPeriodicFuncOP

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

◆ boundary_fn_type

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

◆ CircularGeneral1D_FuncCOP

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

◆ CircularGeneral1D_FuncOP

◆ CircularHarmonicFuncCOP

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

◆ CircularHarmonicFuncOP

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

◆ CircularPowerFuncCOP

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

◆ CircularPowerFuncOP

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

◆ CircularSigmoidalFuncCOP

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

◆ CircularSigmoidalFuncOP

◆ CircularSplineFuncCOP

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

◆ CircularSplineFuncOP

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

◆ ConstantFuncOP

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

◆ EtableFuncOP

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

◆ FadeFuncCOP

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

◆ FadeFuncOP

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

◆ FlatHarmonicFuncCOP

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

◆ FlatHarmonicFuncOP

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

◆ FourPointsFuncCOP

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

◆ FourPointsFuncOP

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

◆ FuncCOP

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

◆ FuncOP

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

◆ GaussianChainDoubleFuncCOP

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

◆ GaussianChainDoubleFuncOP

◆ GaussianChainFuncCOP

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

◆ GaussianChainFuncOP

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

◆ GaussianChainGeneralFuncCOP

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

◆ GaussianChainGeneralFuncOP

◆ GaussianChainQuadrupleFuncCOP

◆ GaussianChainQuadrupleFuncOP

◆ GaussianChainSingleFuncCOP

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

◆ GaussianChainSingleFuncOP

◆ GaussianChainTripleFuncCOP

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

◆ GaussianChainTripleFuncOP

◆ GaussianFuncOP

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

◆ HarmonicFuncCOP

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

◆ HarmonicFuncOP

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

◆ IdentityFuncCOP

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

◆ IdentityFuncOP

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

◆ KarplusFuncCOP

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

◆ KarplusFuncOP

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

◆ MinMultiHarmonicFuncCOP

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

◆ MinMultiHarmonicFuncOP

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

◆ MixtureFuncOP

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

◆ ScalarWeightedFuncCOP

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

◆ ScalarWeightedFuncOP

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

◆ SigmoidFuncCOP

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

◆ SigmoidFuncOP

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

◆ SmoothStepFuncCOP

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

◆ SmoothStepFuncOP

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

◆ SoedingFuncOP

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

◆ SOGFunc_ImplOP

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

◆ SOGFuncOP

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

◆ SplineFuncCOP

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

◆ SplineFuncOP

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

◆ SquareWell2FuncCOP

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

◆ SquareWell2FuncOP

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

◆ SquareWellFuncCOP

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

◆ SquareWellFuncOP

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

◆ SumFuncOP

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

◆ TopOutFuncCOP

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

◆ TopOutFuncOP

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

◆ USOGFuncCOP

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

◆ USOGFuncOP

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

Function Documentation

◆ L()

Real core::scoring::func::L ( Real const &  x)

◆ operator<<()

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

◆ readValueOrDie()

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.

References core::conformation::membrane::in.

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

◆ tr()

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

◆ trMinMultiHarmonicFunc()

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