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...

#include <MixtureFunc.hh>

Inheritance diagram for core::scoring::func::MixtureFunc:

[legend]

Public Member Functions
	MixtureFunc (Real const anchor, Real const gaussian_param, Real const exp_param, Real const mixture_param, Real const bg_mean, Real const bg_sd)

FuncOP	clone () const
	returns a clone of this MixtureFunc More...

virtual bool	operator== (Func const &other) const
	Equality operator. Looks for strict equality. Floating-point comparison is the rule rather than the exception. More...

virtual bool	same_type_as_me (Func const &other) const
	Does the input Func, "other", have the same type as me? Necessary for the equality operator to function correctly. All derived Func classes must implement this function. More...

Real	func (Real const x) const
	Returns the value of this MixtureFunc evaluated at distance x. More...

Real	dfunc (Real const x) const
	Returns the value of the first derivative of this MixtureFunc at distance x. More...

virtual void	show_definition (std::ostream &out) const
	show the definitio of this MixtureFunc to the specified output stream. More...

Real	dfunc_component (Real const x, Real &g, Real &h, Real &g_prime, Real &h_prime) const
	Function that's used for debugging. Given x, this calculates g(x), h(x), g'(x) and h'(x). More...

Real	calc_kl_divergence () const
	Calculates the K-L divergence between the inferred and background distributions. More...

virtual void	show (std::ostream &out) const
	Prints this MixtureFunc to the given ostream. More...

void	read_data (std::istream &in)
	The parameters are: More...

Real	func_ (Real x) const
	Returns the value of this MixtureFunc evaluated at distance x. More...

Public Member Functions inherited from core::scoring::func::Func
virtual	~Func ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

bool	operator!= (Func const &other) const
	inequality operator – simply the negation of the (virtual) equality operator 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 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...

Private Member Functions
void	verify_parameters_ ()

Private Attributes
Real	rmax_

Real	fmax_

Real	anchor_

Real	gaussian_param_

Real	exp_param_

Real	mixture_param_

Real	bg_mean_

Real	bg_sd_

Friends
std::ostream &	operator<< (std::ostream &out, const MixtureFunc &f)
	Calls show( out ) on this MixtureFunc. More...

Detailed Description

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.

Constructor & Destructor Documentation

core::scoring::func::MixtureFunc::MixtureFunc	(	Real const	anchor,
		Real const	gaussian_param,
		Real const	exp_param,
		Real const	mixture_param,
		Real const	bg_mean,
		Real const	bg_sd
	)

inline

Constructor for MixtureFunc. Arguments to the constructor are:

anchor: parameter representing the value at which this function is anchored, represents the mean of the Gaussian distribution and the highest point of the exponential distribution.
gaussian_param: parameter for Gaussian portion of g(r), representing the standard deviation of a Gaussian distribution around anchor.
exp_param: parameter for Exponential portion of g(r), representing the rate at which the exponential distribution drops off from anchor.
mixture_param: parameter describing the mixture of the Gaussian and Exponential functions that make up g(r).
bg_mean: parameter representing the mean of h(r).
bg_sd: parameter representing the standard deviation of h(r).

References anchor_, and verify_parameters_().

Referenced by clone().

Member Function Documentation

Real core::scoring::func::MixtureFunc::calc_kl_divergence ( ) const

Calculates the K-L divergence between the inferred and background distributions.

References core::sequence::end, and protocols::loops::start.

FuncOP core::scoring::func::MixtureFunc::clone ( ) const

inlinevirtual

returns a clone of this MixtureFunc

Implements core::scoring::func::Func.

References MixtureFunc().

Real core::scoring::func::MixtureFunc::dfunc ( Real const x ) const

virtual

Returns the value of the first derivative of this MixtureFunc at distance x.

Implements core::scoring::func::Func.

Real core::scoring::func::MixtureFunc::dfunc_component	(	Real const	x,
		Real &	g,
		Real &	h,
		Real &	g_prime,
		Real &	h_prime
	)		const

Function that's used for debugging. Given x, this calculates g(x), h(x), g'(x) and h'(x).

References core::scoring::constraints::dexponential(), core::scoring::constraints::dgaussian(), core::scoring::constraints::exponential_deriv(), and core::scoring::constraints::gaussian_deriv().

Real core::scoring::func::MixtureFunc::func ( Real const x ) const

virtual

Returns the value of this MixtureFunc evaluated at distance x.

Implements core::scoring::func::Func.

References protocols::hybridization::score.

Real core::scoring::func::MixtureFunc::func_ ( Real x ) const

Returns the value of this MixtureFunc evaluated at distance x.

private

References core::scoring::constraints::dexponential(), core::scoring::constraints::dgaussian(), and protocols::hybridization::score.

bool core::scoring::func::MixtureFunc::operator== ( Func const & other ) const

virtual

Equality operator. Looks for strict equality. Floating-point comparison is the rule rather than the exception.

Implements core::scoring::func::Func.

References anchor_, bg_mean_, bg_sd_, exp_param_, fmax_, gaussian_param_, mixture_param_, rmax_, and core::scoring::func::Func::same_type_as_me().

void core::scoring::func::MixtureFunc::read_data ( std::istream & in )

virtual

The parameters are:

Initializes this MixtureFunc from the given istream. An example of the type of string from which the istream should be constructed is: "MIXTUREFUNC 6.9734 3.598 0.222 0.872 19.396 7.643". The interpretation is to create initialize this MixtureFunc object with the following parameters:

anchor 6.9734
gaussian_param 3.598
exp_param 0.222
mixture_param 0.872
bg_mean 19.396
bg_sd 7.643

Reimplemented from core::scoring::func::Func.

bool core::scoring::func::MixtureFunc::same_type_as_me ( Func const & other ) const

virtual

Does the input Func, "other", have the same type as me? Necessary for the equality operator to function correctly. All derived Func classes must implement this function.

Implements core::scoring::func::Func.

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

virtual

Prints this MixtureFunc to the given ostream.

Reimplemented from core::scoring::func::Func.

References protocols::comparative_modeling::features::A, core::sequence::end, core::chemical::element::F, core::chemical::element::I, and protocols::loops::start.

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

virtual

show the definitio of this MixtureFunc to the specified output stream.

Reimplemented from core::scoring::func::Func.

void core::scoring::func::MixtureFunc::verify_parameters_ ( )

private

Referenced by MixtureFunc().

Friends And Related Function Documentation

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

friend

Calls show( out ) on this MixtureFunc.

Member Data Documentation

Real core::scoring::func::MixtureFunc::anchor_

private

Referenced by MixtureFunc(), and operator==().

Real core::scoring::func::MixtureFunc::bg_mean_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::bg_sd_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::exp_param_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::fmax_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::gaussian_param_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::mixture_param_

private

Referenced by operator==().

Real core::scoring::func::MixtureFunc::rmax_

private

Referenced by operator==().

The documentation for this class was generated from the following files:

src/core/scoring/func/MixtureFunc.hh
src/core/scoring/func/MixtureFunc.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation