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IMP Reference Guide  develop.5de2a9ba5d,2024/02/24
The Integrative Modeling Platform
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_maxmaximum length of the chain in angstroms
[in]lppersistence 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]featureValue 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]featureValue 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.


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