IMP::misc::WormLikeChain Class Reference

Worm-like-chain energy for polymer chains. More...

#include <IMP/misc/WormLikeChain.h>

Inheritance diagram for IMP::misc::WormLikeChain:

Detailed Description

Worm-like-chain energy for polymer chains.

This function implements one polymer force/extension curve. It is a physical energy and all the inputs are in angstroms and the outputs in kcal/mol (/angstrom).

Note

The actual worm like chain force blows up as the extension approaches the maximum. Since that makes optimization problematic, we just linearly extend the force after 99% of maximum.

Definition at line 27 of file WormLikeChain.h.

Public Member Functions
	WormLikeChain (Float l_max, Float lp)
	Define the energy term. More...
void	do_show (std::ostream &out) const
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...
virtual std::string	get_type_name () const override
virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. 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 ()

Constructor & Destructor Documentation

IMP::misc::WormLikeChain::WormLikeChain	(	Float	l_max,
		Float	lp
	)

Define the energy term.

Parameters

[in]	l_max	maximum length of the chain in angstroms
[in]	lp	persistence length in angstroms

Definition at line 33 of file WormLikeChain.h.

Member Function Documentation

virtual double IMP::misc::WormLikeChain::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.

virtual DerivativePair IMP::misc::WormLikeChain::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.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 42 of file WormLikeChain.h.

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

• WormLikeChain.h