IMP::misc::FreelyJointedChain Class Reference

Score on end-to-end distance of freely jointed chain. More...

#include <IMP/misc/FreelyJointedChain.h>

Inheritance diagram for IMP::misc::FreelyJointedChain:

Detailed Description

Score on end-to-end distance of freely jointed chain.

A flexible linker can be represented by the freely jointed chain model as a polymer under a Gaussian random walk. The end-to-end distance \( z \) then follows the distribution

\[p(z | \beta) = 4 \pi z^2 (\frac{\beta}{\pi})^{3/2)} \exp{(-\beta z^2)},\]

where \( \beta = \frac{3}{2 N b^2} \), \( N \) is the number of links, and \( b \) is the average length of a single link. The score reaches its minimum value when \( z = \frac{1}{\sqrt{\beta}} \).

See KA Dill, S Bromberg. Molecular Driving Forces. 2nd Edition. 2010. Eqs 33.26, 33.27.

Note

While the Gaussian approximation breaks down when \(z > N b\), the score naturally increases as a harmonic restraint with force constant \(2 \beta\).

The resulting score blows up as the \( z \) approaches 0. Therefore, in this implementation, when \( z = .01 z_{min} \), where \( z_{min} \) is the value of \( z \) where the score is minimized, then the score increases linearly as \( z \) decreases.

See Also

WormLikeChain

core::Harmonic

Definition at line 41 of file FreelyJointedChain.h.

Public Member Functions
	FreelyJointedChain (int link_num, double link_length)
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...
double	get_average_distance () const
	Get the average distance from the surface. More...
double	get_distance_at_minimum () const
	Get the distance at which the score is at its minimum value. More...
double	get_link_length () const
	Get length of each chain link. More...
int	get_link_number () const
	Get number of links in chain. More...
virtual std::string	get_type_name () const
virtual ::IMP::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...
void	set_link_length (double b)
	Set the length of each chain link. More...
void	set_link_number (int N)
	Set the number of links in chain. More...
Public Member Functions inherited from IMP::UnaryFunction
	UnaryFunction (std::string name="UnaryFunction%1%")
Public Member Functions inherited from IMP::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)

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

Member Function Documentation

virtual double IMP::misc::FreelyJointedChain::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::UnaryFunction.

Definition at line 73 of file FreelyJointedChain.h.

virtual DerivativePair IMP::misc::FreelyJointedChain::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 DerivativePair containing the score and its partial derivative with respect to the given feature.

Reimplemented from IMP::UnaryFunction.

Definition at line 60 of file FreelyJointedChain.h.

double IMP::misc::FreelyJointedChain::get_average_distance

(

)

const

Get the average distance from the surface.

Definition at line 105 of file FreelyJointedChain.h.

double IMP::misc::FreelyJointedChain::get_distance_at_minimum

(

)

const

Get the distance at which the score is at its minimum value.

Definition at line 100 of file FreelyJointedChain.h.

double IMP::misc::FreelyJointedChain::get_link_length

(

)

const

Get length of each chain link.

Definition at line 83 of file FreelyJointedChain.h.

int IMP::misc::FreelyJointedChain::get_link_number

(

)

const

Get number of links in chain.

Definition at line 80 of file FreelyJointedChain.h.

virtual ::IMP::VersionInfo IMP::misc::FreelyJointedChain::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 77 of file FreelyJointedChain.h.

void IMP::misc::FreelyJointedChain::set_link_length

(

double

b

)

Set the length of each chain link.

Definition at line 93 of file FreelyJointedChain.h.

void IMP::misc::FreelyJointedChain::set_link_number

(

int

N

)

Set the number of links in chain.

Definition at line 86 of file FreelyJointedChain.h.

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

• FreelyJointedChain.h