Rosetta 3.4
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core::scoring::constraints::Func Class Reference

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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List of all members.

Public Member Functions

virtual FuncOP clone () const =0
virtual void read_data (std::istream &)
 initialize this Func from the given std::istream.
virtual Real func (Real const ) const =0
 Returns a value representing this function evaluated at a given point.
virtual Real dfunc (Real const ) const =0
 Returns a value representing the derivative of this function evaluated at a given point.
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).
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).
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 ).
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.
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.

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.


Member Function Documentation

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

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

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

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).

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).

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

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

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

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

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

void core::scoring::constraints::Func::show_definition ( std::ostream &  out) const [virtual]
Size core::scoring::constraints::Func::show_violations ( std::ostream &  out,
Real  r,
Size  verbose_level,
Real  threshold = 1 
) const [virtual]

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:
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