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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  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< 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< 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< 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< GaussianChainSingleFunc const > core::scoring::func::GaussianChainSingleFuncCOP
typedef utility::pointer::shared_ptr< GaussianChainTripleFunc const > core::scoring::func::GaussianChainTripleFuncCOP
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)
std::ostream & core::scoring::func::operator<< ( std::ostream &  out,
Func const &  f 
)
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
static basic::Tracer core::scoring::func::trMinMultiHarmonicFunc ( "fragment.picking.scores.MinMultiHarmonicFunc"  )
static