IMP::core::Harmonic Class Reference

Harmonic function (symmetric about the mean) More...

#include <IMP/core/Harmonic.h>

Inheritance diagram for IMP::core::Harmonic:

Detailed Description

Harmonic function (symmetric about the mean)

This is a simple score modeling an harmonic oscillator. The score is 0.5 * k * x * x, where k is the 'force constant' and x is the distance from the mean.

See Also

TruncatedHarmonic

HarmonicUpperBound

HarmonicLowerBound

Definition at line 24 of file core/Harmonic.h.

Public Member Functions
	Harmonic (Float mean, Float k)
virtual double	evaluate (double feature) const
	Calculate score with respect to the given feature. More...
virtual DerivativePair	evaluate_with_derivative (double feature) const
	Calculate score and derivative with respect to the given feature. More...
Float	get_k () const
	Return the spring constant. More...
Float	get_mean () const
	Return the mean of this function. More...
virtual std::string	get_type_name () const
virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...
void	set_k (Float k)
	Set the spring constant. More...
void	set_mean (Float mean)
	Set the mean of this function. More...
Public Member Functions inherited from IMP::kernel::UnaryFunction
	UnaryFunction (std::string name="UnaryFunction%1%")
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Static Public Member Functions
static Float	get_k_from_standard_deviation (Float sd, Float t=297.15)
	Return the k to use for a given Gaussian standard deviation. More...

Additional Inherited Members
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::core::Harmonic::Harmonic	(	Float	mean,
		Float	k
	)

Create with the given mean and the spring constant k

Definition at line 27 of file core/Harmonic.h.

Member Function Documentation

virtual double IMP::core::Harmonic::evaluate ( double  feature ) const

virtual

Calculate score with respect to the given feature.

Parameters

[in]

feature

Value of feature being tested.

Returns

Score

Reimplemented from IMP::kernel::UnaryFunction.

Reimplemented in IMP::core::HarmonicLowerBound, and IMP::core::HarmonicUpperBound.

Definition at line 34 of file core/Harmonic.h.

virtual DerivativePair IMP::core::Harmonic::evaluate_with_derivative ( double  feature ) const

virtual

Calculate score and derivative with respect to the given feature.

Parameters

[in]

feature

Value of feature being tested.

Returns

a FloatPair containing the score and its partial derivative with respect to the given feaure.

Reimplemented from IMP::kernel::UnaryFunction.

Reimplemented in IMP::core::HarmonicLowerBound, and IMP::core::HarmonicUpperBound.

Definition at line 29 of file core/Harmonic.h.

Float IMP::core::Harmonic::get_k

(

)

const

Return the spring constant.

Definition at line 44 of file core/Harmonic.h.

static Float IMP::core::Harmonic::get_k_from_standard_deviation ( Float  sd, Float  t = 297.15  )

static

Return the k to use for a given Gaussian standard deviation.

Given the standard deviation of a Gaussian distribution, get the force constant of the harmonic score function that yields that same distribution. For temperature in Kelvin, this assumes the score function is energy in kcal/mol, and thus returns a force constant in kcal/mol/A/A.

Parameters

[in]	sd	Gaussian standard deviation, in angstroms
[in]	t	System temperature, in Kelvin

Returns

Force constant

Definition at line 62 of file core/Harmonic.h.

Float IMP::core::Harmonic::get_mean

(

)

const

Return the mean of this function.

Definition at line 41 of file core/Harmonic.h.

virtual ::IMP::base::VersionInfo IMP::core::Harmonic::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Reimplemented in IMP::core::HarmonicLowerBound, and IMP::core::HarmonicUpperBound.

Definition at line 38 of file core/Harmonic.h.

void IMP::core::Harmonic::set_k

(

Float

k

)

Set the spring constant.

Definition at line 50 of file core/Harmonic.h.

void IMP::core::Harmonic::set_mean

(

Float

mean

)

Set the mean of this function.

Definition at line 47 of file core/Harmonic.h.

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

• core/Harmonic.h