Rosetta Core  2014.16.56682
Public Member Functions | Friends | List of all members
core::scoring::func::Func Class Referenceabstract

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...

#include <Func.hh>

Public Member Functions

virtual ~Func ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
virtual FuncOP clone () const =0
 
virtual void read_data (std::istream &)
 initialize this Func from the given std::istream. More...
 
virtual Real func (Real const ) const =0
 Returns a value representing this function evaluated at a given point. More...
 
virtual Real dfunc (Real const ) const =0
 Returns a value representing the derivative of this function evaluated at a given point. More...
 
virtual Real estimate_dfunc (Real const r) const
 Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+1e-05). More...
 
virtual Real estimate_dfunc (Real const r, Real const h) const
 Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+h). More...
 
virtual void show (std::ostream &out) const
 Prints out space-delimited columns for r, func, dfunc and dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ). More...
 
virtual void show_definition (std::ostream &out) const
 shows the definition of this function, usually the string type of function and the parameters passed in to the constructor. More...
 
virtual Size show_violations (std::ostream &out, Real r, Size verbose_level, Real threshold=1) const
 show some sort of stringified representation of the violations for this constraint. More...
 

Friends

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

Detailed Description

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.

Constructor & Destructor Documentation

core::scoring::func::Func::~Func ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Member Function Documentation

virtual FuncOP core::scoring::func::Func::clone ( ) const
pure virtual

Implemented in core::scoring::custom_pair_distance::DistanceFunc, core::scoring::disulfides::SG_Dist_Func, core::scoring::disulfides::CB_Angle_Func, core::scoring::disulfides::SGSG_Dihedral_Func, core::scoring::disulfides::CaCbCbCa_Dihedral_Func, core::scoring::disulfides::NCaCaC_Dihedral_Func, core::scoring::disulfides::CBSG_Dihedral_Func, core::scoring::disulfides::CaCbCb_Angle_Func, core::scoring::disulfides::Cen_Distance_Func, core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::disulfides::Cb_Distance_Func, core::scoring::constraints::PeriodicBoundFunc, core::scoring::methods::LK_SigmoidalFunc, core::scoring::func::MixtureFunc, core::scoring::func::FadeFunc, core::scoring::func::USOGFunc, core::scoring::func::SplineFunc, core::scoring::func::EtableFunc, core::scoring::func::SumFunc, core::scoring::func::SOGFunc, core::scoring::constraints::BoundFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::CountViolFunc, core::scoring::func::GaussianFunc, core::scoring::func::GaussianChainFunc, core::scoring::func::SkipViolFunc, core::scoring::func::CircularSigmoidalFunc, core::scoring::func::ConstantFunc, core::scoring::func::CircularGeneral1D_Func, core::scoring::func::CircularHarmonicFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::GaussianChainTripleFunc, core::scoring::func::SquareWell2Func, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::GaussianChainDoubleFunc, core::scoring::func::GaussianChainQuadrupleFunc, core::scoring::func::PeriodicFunc, core::scoring::func::SquareWellFunc, core::scoring::func::GaussianChainSingleFunc, core::scoring::func::KarplusFunc, core::scoring::func::LinearPenaltyFunction, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::SoedingFunc, core::scoring::func::CircularPowerFunc, core::scoring::func::TopOutFunc, core::scoring::func::FlatHarmonicFunc, core::scoring::func::HarmonicFunc, core::scoring::func::IdentityFunc, and core::scoring::func::SigmoidFunc.

virtual Real core::scoring::func::Func::dfunc ( Real  const) const
pure virtual

Returns a value representing the derivative of this function evaluated at a given point.

Implemented in core::scoring::disulfides::SG_Dist_Func, core::scoring::custom_pair_distance::DistanceFunc, core::scoring::disulfides::CB_Angle_Func, core::scoring::disulfides::SGSG_Dihedral_Func, core::scoring::disulfides::CaCbCbCa_Dihedral_Func, core::scoring::disulfides::NCaCaC_Dihedral_Func, core::scoring::disulfides::CBSG_Dihedral_Func, core::scoring::disulfides::CaCbCb_Angle_Func, core::scoring::disulfides::Cen_Distance_Func, core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::disulfides::Cb_Distance_Func, core::scoring::constraints::PeriodicBoundFunc, core::scoring::func::SplineFunc, core::scoring::methods::LK_SigmoidalFunc, core::scoring::func::MixtureFunc, core::scoring::func::FadeFunc, core::scoring::func::USOGFunc, core::scoring::constraints::BoundFunc, core::scoring::func::EtableFunc, core::scoring::func::SOGFunc, core::scoring::func::SumFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::CountViolFunc, core::scoring::func::GaussianFunc, core::scoring::func::ConstantFunc, core::scoring::func::GaussianChainFunc, core::scoring::func::SkipViolFunc, core::scoring::func::SoedingFunc, core::scoring::func::CircularSigmoidalFunc, core::scoring::func::CircularGeneral1D_Func, core::scoring::func::CircularHarmonicFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::GaussianChainTripleFunc, core::scoring::func::SquareWell2Func, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::CircularPowerFunc, core::scoring::func::GaussianChainDoubleFunc, core::scoring::func::GaussianChainQuadrupleFunc, core::scoring::func::PeriodicFunc, core::scoring::func::SquareWellFunc, core::scoring::func::GaussianChainSingleFunc, core::scoring::func::KarplusFunc, core::scoring::func::LinearPenaltyFunction, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::IdentityFunc, core::scoring::func::TopOutFunc, core::scoring::func::FlatHarmonicFunc, core::scoring::func::HarmonicFunc, and core::scoring::func::SigmoidFunc.

Referenced by show().

Real core::scoring::func::Func::estimate_dfunc ( Real const  r) const
virtual

Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+1e-05).

Referenced by show().

Real core::scoring::func::Func::estimate_dfunc ( Real const  r,
Real const  h 
) const
virtual

Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+h).

References func().

virtual Real core::scoring::func::Func::func ( Real  const) const
pure virtual

Returns a value representing this function evaluated at a given point.

Implemented in core::scoring::custom_pair_distance::DistanceFunc, core::scoring::disulfides::SG_Dist_Func, core::scoring::disulfides::CB_Angle_Func, core::scoring::disulfides::SGSG_Dihedral_Func, core::scoring::disulfides::CaCbCbCa_Dihedral_Func, core::scoring::disulfides::NCaCaC_Dihedral_Func, core::scoring::disulfides::CBSG_Dihedral_Func, core::scoring::disulfides::CaCbCb_Angle_Func, core::scoring::disulfides::Cen_Distance_Func, core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::disulfides::Cb_Distance_Func, core::scoring::constraints::PeriodicBoundFunc, core::scoring::func::SplineFunc, core::scoring::methods::LK_SigmoidalFunc, core::scoring::func::MixtureFunc, core::scoring::func::FadeFunc, core::scoring::func::USOGFunc, core::scoring::constraints::BoundFunc, core::scoring::func::EtableFunc, core::scoring::func::SumFunc, core::scoring::func::SOGFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::CountViolFunc, core::scoring::func::GaussianFunc, core::scoring::func::GaussianChainFunc, core::scoring::func::SkipViolFunc, core::scoring::func::CircularSigmoidalFunc, core::scoring::func::ConstantFunc, core::scoring::func::SoedingFunc, core::scoring::func::CircularGeneral1D_Func, core::scoring::func::CircularHarmonicFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::GaussianChainTripleFunc, core::scoring::func::SquareWell2Func, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::GaussianChainDoubleFunc, core::scoring::func::GaussianChainQuadrupleFunc, core::scoring::func::PeriodicFunc, core::scoring::func::SquareWellFunc, core::scoring::func::GaussianChainSingleFunc, core::scoring::func::KarplusFunc, core::scoring::func::LinearPenaltyFunction, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::CircularPowerFunc, core::scoring::func::IdentityFunc, core::scoring::func::TopOutFunc, core::scoring::func::FlatHarmonicFunc, core::scoring::func::HarmonicFunc, and core::scoring::func::SigmoidFunc.

Referenced by estimate_dfunc(), core::scoring::constraints::AmbiguousNMRConstraint::score(), show(), and show_violations().

void core::scoring::func::Func::read_data ( std::istream &  )
virtual

initialize this Func from the given std::istream.

Reimplemented in core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::func::MixtureFunc, core::scoring::constraints::PeriodicBoundFunc, core::scoring::func::SOGFunc, core::scoring::func::SplineFunc, core::scoring::func::GaussianFunc, core::scoring::func::EtableFunc, core::scoring::func::FadeFunc, core::scoring::func::USOGFunc, core::scoring::func::SumFunc, core::scoring::func::ConstantFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::SoedingFunc, core::scoring::func::CountViolFunc, core::scoring::constraints::BoundFunc, core::scoring::func::GaussianChainFunc, core::scoring::func::SkipViolFunc, core::scoring::func::CircularSigmoidalFunc, core::scoring::func::CircularHarmonicFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::GaussianChainTripleFunc, core::scoring::func::SquareWell2Func, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::GaussianChainDoubleFunc, core::scoring::func::GaussianChainQuadrupleFunc, core::scoring::func::PeriodicFunc, core::scoring::func::SquareWellFunc, core::scoring::func::GaussianChainSingleFunc, core::scoring::func::KarplusFunc, core::scoring::func::LinearPenaltyFunction, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::IdentityFunc, core::scoring::func::TopOutFunc, core::scoring::func::FlatHarmonicFunc, core::scoring::func::HarmonicFunc, and core::scoring::func::SigmoidFunc.

References core::scoring::tr.

void core::scoring::func::Func::show ( std::ostream &  out) const
virtual

Prints out space-delimited columns for r, func, dfunc and dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

Reimplemented in core::scoring::func::MixtureFunc.

References dfunc(), core::sequence::end, estimate_dfunc(), func(), and start.

Referenced by core::scoring::func::operator<<().

void core::scoring::func::Func::show_definition ( std::ostream &  out) const
virtual

shows the definition of this function, usually the string type of function and the parameters passed in to the constructor.

Reimplemented in core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::constraints::PeriodicBoundFunc, core::scoring::func::SplineFunc, core::scoring::func::MixtureFunc, core::scoring::func::FadeFunc, core::scoring::func::USOGFunc, core::scoring::constraints::BoundFunc, core::scoring::func::EtableFunc, core::scoring::func::SOGFunc, core::scoring::func::CountViolFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::GaussianFunc, core::scoring::func::SkipViolFunc, core::scoring::func::ConstantFunc, core::scoring::func::GaussianChainFunc, core::scoring::func::SoedingFunc, core::scoring::func::CircularSigmoidalFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::CircularHarmonicFunc, core::scoring::func::GaussianChainTripleFunc, core::scoring::func::SquareWell2Func, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::GaussianChainDoubleFunc, core::scoring::func::GaussianChainQuadrupleFunc, core::scoring::func::PeriodicFunc, core::scoring::func::SquareWellFunc, core::scoring::func::GaussianChainSingleFunc, core::scoring::func::LinearPenaltyFunction, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::KarplusFunc, core::scoring::func::IdentityFunc, core::scoring::func::TopOutFunc, core::scoring::func::SigmoidFunc, core::scoring::func::FlatHarmonicFunc, and core::scoring::func::HarmonicFunc.

Size core::scoring::func::Func::show_violations ( std::ostream &  out,
Real  r,
Size  verbose_level,
Real  threshold = 1 
) const
virtual

show some sort of stringified representation of the violations for this constraint.

Reimplemented in core::scoring::constraints::OffsetPeriodicBoundFunc, core::scoring::constraints::PeriodicBoundFunc, core::scoring::func::SplineFunc, core::scoring::func::FadeFunc, core::scoring::constraints::BoundFunc, core::scoring::func::FlatHarmonicFunc, core::scoring::func::MinMultiHarmonicFunc, core::scoring::func::ScalarWeightedFunc, core::scoring::func::HarmonicFunc, core::scoring::func::CountViolFunc, core::scoring::func::SquareWell2Func, core::scoring::func::LinearPenaltyFunction, core::scoring::func::SquareWellFunc, core::scoring::func::TopOutFunc, core::scoring::func::SkipViolFunc, core::scoring::func::AmberPeriodicFunc, core::scoring::func::CharmmPeriodicFunc, core::scoring::func::PeriodicFunc, core::scoring::func::IdentityFunc, and core::scoring::func::SigmoidFunc.

References func().

Referenced by core::scoring::func::SigmoidFunc::show_violations(), core::scoring::func::IdentityFunc::show_violations(), core::scoring::func::PeriodicFunc::show_violations(), core::scoring::func::CharmmPeriodicFunc::show_violations(), core::scoring::func::AmberPeriodicFunc::show_violations(), core::scoring::func::SquareWellFunc::show_violations(), core::scoring::func::TopOutFunc::show_violations(), core::scoring::func::LinearPenaltyFunction::show_violations(), core::scoring::func::SquareWell2Func::show_violations(), core::scoring::func::HarmonicFunc::show_violations(), core::scoring::func::MinMultiHarmonicFunc::show_violations(), core::scoring::func::FlatHarmonicFunc::show_violations(), core::scoring::func::FadeFunc::show_violations(), and core::scoring::func::SplineFunc::show_violations().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const Func &  f 
)
friend
The documentation for this class was generated from the following files:
Generated on Mon Apr 21 2014 16:27:15 for Rosetta Core by   doxygen 1.8.7