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core::scoring::constraints::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>

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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.

Definition at line 31 of file Func.hh.

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 38 of file Func.cc.

Member Function Documentation

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

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

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

Referenced by show().

Real core::scoring::constraints::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).

Definition at line 47 of file Func.cc.

Referenced by core::scoring::constraints::SoedingFunc::dfunc(), and show().

Real core::scoring::constraints::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).

Definition at line 52 of file Func.cc.

References func().

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

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

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

initialize this Func from the given std::istream.

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

Definition at line 41 of file Func.cc.

References core::scoring::constraints::tr().

void core::scoring::constraints::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::constraints::MixtureFunc.

Definition at line 56 of file Func.cc.

References protocols::comparative_modeling::features::A, dfunc(), core::sequence::end, estimate_dfunc(), func(), and protocols::loops::start.

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

void core::scoring::constraints::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::constraints::SplineFunc, core::scoring::constraints::MixtureFunc, core::scoring::constraints::FadeFunc, core::scoring::constraints::USOGFunc, core::scoring::constraints::BoundFunc, core::scoring::constraints::EtableFunc, core::scoring::constraints::SOGFunc, core::scoring::constraints::CountViolFunc, core::scoring::constraints::ScalarWeightedFunc, core::scoring::constraints::GaussianFunc, core::scoring::constraints::SkipViolFunc, core::scoring::constraints::ConstantFunc, core::scoring::constraints::SoedingFunc, core::scoring::constraints::CircularSigmoidalFunc, core::scoring::constraints::AmberPeriodicFunc, core::scoring::constraints::CircularHarmonicFunc, core::scoring::constraints::SquareWell2Func, core::scoring::constraints::CharmmPeriodicFunc, core::scoring::constraints::PeriodicFunc, core::scoring::constraints::SquareWellFunc, core::scoring::constraints::LinearPenaltyFunction, core::scoring::constraints::MinMultiHarmonicFunc, core::scoring::constraints::KarplusFunc, core::scoring::constraints::IdentityFunc, core::scoring::constraints::TopOutFunc, core::scoring::constraints::SigmoidFunc, core::scoring::constraints::FlatHarmonicFunc, and core::scoring::constraints::HarmonicFunc.

Definition at line 77 of file Func.cc.

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

Definition at line 81 of file Func.cc.

References func().

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

Friends And Related Function Documentation

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

Definition at line 87 of file Func.cc.

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:28:22 for Rosetta 3.5 by   doxygen 1.8.4