Detailed Description

Smooth interaction scores by switching the derivatives (force switch).

This function leaves the scores unaffected for distances below or equal to min_distance, returns zero for distances above max_distance, and between the two thresholds smoothes the score such that its first derivatives drop linearly, i.e. the score is simply multiplied by

\[ \begin{cases} 1 & d \leq d_{min} \ \frac{(d_{max} - d)^2 (d_{max} + 2d - 3d_{min})} {(d_{max} - d_{min})^3} & d_{min} < d \leq d_{max} \ 0 & d > d_{max} \end{cases} \]

where \(d\) is the distance, and \(d_{min}\) and \(d_{max}\) are the thresholds set in the ForceSwitch constructor.

This behavior is roughly equivalent to CHARMM's force switch nonbonded interaction smoothing (which is also the smoothing mechanism used by MODELLER).

See Also: CoulombPairScore

Definition at line 72 of file smoothing_functions.h.

Public Member Functions
	ForceSwitch (double min_distance, double max_distance)

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...

double	operator() (double score, double distance) const
	Smooth the score at a given distance. More...

DerivativePair	operator() (double score, double deriv, double distance) const
	Smooth the score and its first derivative at a given distance. More...

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 ::IMP::VersionInfo IMP::atom::ForceSwitch::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 119 of file smoothing_functions.h.

double IMP::atom::ForceSwitch::operator()	(	double	score,
		double	distance
	)		const

virtual

Smooth the score at a given distance.

Returns: the smoothed score.

Implements IMP::atom::SmoothingFunction.

Definition at line 107 of file smoothing_functions.h.

DerivativePair IMP::atom::ForceSwitch::operator()	(	double	score,
		double	deriv,
		double	distance
	)		const

virtual

Smooth the score and its first derivative at a given distance.

Returns: a DerivativePair containing the smoothed score and its first derivative.

Implements IMP::atom::SmoothingFunction.

Definition at line 112 of file smoothing_functions.h.

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

smoothing_functions.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation