#include <FadeInterval.hh>

Inheritance diagram for core::scoring::hbonds::FadeInterval:

Collaboration diagram for core::scoring::hbonds::FadeInterval:

Public Member Functions
virtual	~FadeInterval ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	FadeInterval ()
	Constructor. More...

	FadeInterval (Real const min0, Real const fmin, Real const fmax, Real const max0, bool const smooth=false)

	FadeInterval (std::string const &name, Real const min0, Real const fmin, Real const fmax, Real const max0, bool const smooth=false)

void	value_deriv (Real const x, double &val, double &deriv) const

double	value (Real const x) const

std::string	get_name () const

Real	get_min0 () const

Real	get_fmin () const

Real	get_fmax () const

Real	get_max0 () const

bool	get_smooth () const

void	show (std::ostream &out) const

Private Attributes
std::string const	name_

Real const	min0_

Real const	fmin_

Real const	fmax_

Real const	max0_

double const	dfade_min_

double const	dfade_max_

bool const	smooth_

Friends
bool	operator== (FadeInterval const &a, FadeInterval const &b)

bool	operator!= (FadeInterval const &a, FadeInterval const &b)

std::ostream &	operator<< (std::ostream &out, FadeInterval const &fade_interval)

Detailed Description

Classic FadeInterval.

stores an "fading interval" [a b c d] with a <= b <= c <= d and computes the fraction of containment for x, which is defined to be 0 if x is outside of (a,d), 1 if x is inside of [b,c], and a linear ramp otherwise. ___/--—___ i.e. (x-a)/(b-a) for x in (a,b), and (d-x)/(d-c) for x in (c,d) This is used to ensure that hbond scoring as a sum Er + ExH + ExD goes to zero at the edges.

Notes about discontinuities: if x equals a, b, c, or d then deriv = 0 if x == a == b then value = 0 if x == c == d and a < c then value = 1 if x == c == d and a == c then value = 0 In particular if a == b == c == d then for all x, value == deriv == 0

Smooth FadeInteval

Rather than using a piecewise linear fading function, use a piecewise sigmoid function to have a continuous derivative.

Look for a canonical sigmoid function f(x) such that, f(0) = 1 f(1) = 0 // goes through the the knots f'(0) = 0 f'(1) = 0 // is horizontal at the knots a continuous differative f(x-.5)-.5 is odd // symmetric

I claim, f(x) = 2x^3 - 3x^2 + 1, satisfies these constraints: f(0) = 2(0)^3 - 3(x)^2 + 1 = 1 f(1) = 2(1)^3 - 3(1)^2 + 1 = 2 - 3 + 1 = 0

f'(x) = 6x^2 - 6x = 6x(x-1) f'(0) = 6(0)(0-1) = 0 f'(1) = 6(1)(1-1) = 0

a function g(x) is odd if g(-x) = -g(x) f((-x)-.5)-.5 = 2(-x-.5)^3 - 3(-x-.5)^2 + 1 - .5 = -2x^3 - 6x^2 - 4.5x - .5 -(f(x-.5)-.5) = -2(x-.5)^3 + 3(x-.5)^2 - 1 + .5 = -2x^3 - 6x^2 - 4.5x - .5

Given the knots –a-b—c-d– transform f(x) to fill a-b and c-d to connect the linear regions.

a-b region: let z(x) = (x-a)/(b-a) and z'(x) = 1/(b-a) use g(x) = 1-f(-z(x)) = -2z^3 + 3z^2 and g'(x) = -6z(z-1)*z'(x) c-d region: let z(x) = (x-c)/(d-c) and z'(x) = 1/(d-c) use g(x) = f(z) = 2z^3 - 3z^2 + 1 and g'(x) = 6z(z-1)*z'(x)

Definition at line 92 of file FadeInterval.hh.

Constructor & Destructor Documentation

core::scoring::hbonds::FadeInterval::~FadeInterval ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 30 of file FadeInterval.cc.

core::scoring::hbonds::FadeInterval::FadeInterval ( )

Constructor.

Definition at line 39 of file FadeInterval.cc.

core::scoring::hbonds::FadeInterval::FadeInterval	(	Real const	min0,
		Real const	fmin,
		Real const	fmax,
		Real const	max0,
		bool const	smooth = `false`
	)

Definition at line 50 of file FadeInterval.cc.

core::scoring::hbonds::FadeInterval::FadeInterval	(	std::string const &	name,
		Real const	min0,
		Real const	fmin,
		Real const	fmax,
		Real const	max0,
		bool const	smooth = `false`
	)

Definition at line 68 of file FadeInterval.cc.

Member Function Documentation

Real core::scoring::hbonds::FadeInterval::get_fmax ( ) const

Definition at line 160 of file FadeInterval.cc.

References fmax_.

Real core::scoring::hbonds::FadeInterval::get_fmin ( ) const

Definition at line 154 of file FadeInterval.cc.

References fmin_.

Real core::scoring::hbonds::FadeInterval::get_max0 ( ) const

Definition at line 166 of file FadeInterval.cc.

References max0_.

Real core::scoring::hbonds::FadeInterval::get_min0 ( ) const

Definition at line 148 of file FadeInterval.cc.

References min0_.

string core::scoring::hbonds::FadeInterval::get_name ( ) const

Definition at line 142 of file FadeInterval.cc.

References name_.

bool core::scoring::hbonds::FadeInterval::get_smooth ( ) const

Definition at line 172 of file FadeInterval.cc.

References smooth_.

void core::scoring::hbonds::FadeInterval::show ( std::ostream & out) const

Definition at line 208 of file FadeInterval.cc.

References fmax_, fmin_, max0_, min0_, name_, and smooth_.

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

double core::scoring::hbonds::FadeInterval::value ( Real const x) const

Definition at line 117 of file FadeInterval.cc.

References dfade_max_, dfade_min_, fmax_, fmin_, max0_, min0_, and smooth_.

void core::scoring::hbonds::FadeInterval::value_deriv	(	Real const	x,
		double &	val,
		double &	deriv
	)		const

Definition at line 88 of file FadeInterval.cc.

References dfade_max_, dfade_min_, fmax_, fmin_, max0_, min0_, and smooth_.

Friends And Related Function Documentation

bool operator!=	(	FadeInterval const &	a,
		FadeInterval const &	b
	)

friend

Definition at line 191 of file FadeInterval.cc.

std::ostream& operator<<	(	std::ostream &	out,
		FadeInterval const &	fade_interval
	)

friend

Definition at line 199 of file FadeInterval.cc.

bool operator==	(	FadeInterval const &	a,
		FadeInterval const &	b
	)

friend

Definition at line 178 of file FadeInterval.cc.

Member Data Documentation

double const core::scoring::hbonds::FadeInterval::dfade_max_

private

Definition at line 168 of file FadeInterval.hh.

Referenced by value(), and value_deriv().

double const core::scoring::hbonds::FadeInterval::dfade_min_

private

Definition at line 167 of file FadeInterval.hh.

Referenced by value(), and value_deriv().

Real const core::scoring::hbonds::FadeInterval::fmax_

private

Definition at line 165 of file FadeInterval.hh.

Referenced by get_fmax(), core::scoring::hbonds::operator==(), show(), value(), and value_deriv().

Real const core::scoring::hbonds::FadeInterval::fmin_

private

Definition at line 164 of file FadeInterval.hh.

Referenced by get_fmin(), core::scoring::hbonds::operator==(), show(), value(), and value_deriv().

Real const core::scoring::hbonds::FadeInterval::max0_

private

Definition at line 166 of file FadeInterval.hh.

Referenced by get_max0(), core::scoring::hbonds::operator==(), show(), value(), and value_deriv().

Real const core::scoring::hbonds::FadeInterval::min0_

private

Definition at line 163 of file FadeInterval.hh.

Referenced by get_min0(), core::scoring::hbonds::operator==(), show(), value(), and value_deriv().

std::string const core::scoring::hbonds::FadeInterval::name_

private

Definition at line 162 of file FadeInterval.hh.

Referenced by get_name(), and show().

bool const core::scoring::hbonds::FadeInterval::smooth_

private

Definition at line 169 of file FadeInterval.hh.

Referenced by get_smooth(), core::scoring::hbonds::operator==(), show(), value(), and value_deriv().

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

src/core/scoring/hbonds/FadeInterval.hh
src/core/scoring/hbonds/FadeInterval.cc

Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation