IMP::core::Harmonic Class Reference

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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

Examples: charmm forcefield verbose, simplex, rigid brownian dynamics, tasks, multiscale, imp restraints in modeller, pair restraint, domino approach, load protein restrain bonds

Inheritance diagram for IMP::core::Harmonic:

List of all members.

Public Member Functions
	Harmonic (Float mean, Float k)
Float	get_k () const
Float	get_mean () const
void	set_k (Float k)
	Set the spring constant.
void	set_mean (Float mean)
	Set the mean of this function.
Public Member Functions inherited from IMP::UnaryFunction
virtual double	evaluate (double feature) const
	Calculate score with respect to the given feature.
virtual DerivativePair	evaluate_with_derivative (double feature) const
	Calculate score and derivative with respect to the given feature.
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object.
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 Harmonic *	get_from (IMP::base::Object *o)
static Float	get_k_from_standard_deviation (Float sd, Float t=297.15)
	Return the k to use for a given Gaussian standard deviation.

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Constructor & Destructor Documentation

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

Create with the given mean and the spring constant k

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Member Function Documentation

Float IMP::core::Harmonic::get_k

(

)

const

Returns:

the spring constant

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

Float IMP::core::Harmonic::get_mean

(

)

const

Returns:

the mean of this function

void IMP::core::Harmonic::set_k

(

Float

k

)

Set the spring constant.

void IMP::core::Harmonic::set_mean

(

Float

mean

)

Set the mean of this function.

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

• Harmonic.h