BALL::ScoringFunction Class Reference

#include <BALL/SCORING/COMMON/scoringFunction.h>

Inheritance diagram for BALL::ScoringFunction:

Classes
struct	Default
struct	Option

Public Member Functions
	ScoringFunction ()
	ScoringFunction (const ScoringFunction &sf)
	ScoringFunction (Molecule &receptor, Molecule &ligand)
	ScoringFunction (Molecule &receptor, Molecule &ligand, const Options &options)
virtual	~ScoringFunction ()
virtual void	clear ()
ScoringFunction &	operator= (const ScoringFunction &sf)
bool	setup ()
bool	setup (Molecule &receptor, Molecule &ligand)
bool	setup (Molecule &receptor, Molecule &ligand, const Options &options)
virtual bool	specificSetup () throw (Exception::TooManyErrors)
void	setMaximumNumberOfErrors (Size nr)
Size	getMaximumNumberOfErrors () const
void	setFirstMolecule (Molecule &molecule1)
Molecule *	getFirstMolecule () const
void	setSecondMolecule (Molecule &molecule2)
Molecule *	getSecondMolecule () const
void	setReceptor (Molecule &receptor)
Molecule *	getReceptor () const
void	setLigand (Molecule &ligand)
Molecule *	getLigand () const
void	setIntercept (double intercept)
double	getIntercept () const
void	setBaseFunction (ScoringBaseFunction &base_function)
	Set the instance of BaseFunction for the scoring function.
ScoringBaseFunction *	getBaseFunction () const
void	insertComponent (ScoringComponent *component, float coefficient=1.0f)
void	removeComponent (const ScoringComponent *component)
void	removeComponent (const String &name)
void	setCoefficient (const ScoringComponent *component, float coefficient)
void	setCoefficient (const String &name, float coefficient)
bool	getCoefficient (const ScoringComponent *component, float &coefficient) const
bool	getCoefficient (const String &name, float &coefficient) const
ScoringComponent *	getComponent (const String &name) const
	Return a pointer to a component in the components vector.
ScoringComponent *	getComponent (const Size index) const
	Return a pointer to a component in the components vector.
double	calculateScore ()
const HashSet< const Atom * > &	getUnassignedAtoms () const
HashSet< const Atom * > &	getUnassignedAtoms ()

Public Attributes
Options	options

Protected Attributes
Molecule *	molecule1_
Molecule *	molecule2_
String	name_
double	score_
double	intercept_
ScoringBaseFunction *	base_function_
std::vector< std::pair < ScoringComponent *, float > >	components_
HashSet< const Atom * >	unassigned_atoms_
Size	max_number_of_errors_
Size	number_of_errors_

Detailed Description

Definition at line 20 of file scoringFunction.h.

Constructor & Destructor Documentation

BALL::ScoringFunction::ScoringFunction

(

)

BALL::ScoringFunction::ScoringFunction

(

const ScoringFunction &

sf

)

BALL::ScoringFunction::ScoringFunction	(	Molecule &	receptor,
		Molecule &	ligand
	)

BALL::ScoringFunction::ScoringFunction	(	Molecule &	receptor,
		Molecule &	ligand,
		const Options &	options
	)

virtual BALL::ScoringFunction::~ScoringFunction ( )

virtual

Member Function Documentation

double BALL::ScoringFunction::calculateScore

(

)

virtual void BALL::ScoringFunction::clear ( )

virtual

Reimplemented in BALL::SLICKEnergy, and BALL::SLICKScore.

ScoringBaseFunction* BALL::ScoringFunction::getBaseFunction

(

)

const

Return a pointer to the instance of BaseFunction used by this scoring function.

bool BALL::ScoringFunction::getCoefficient	(	const ScoringComponent *	component,
		float &	coefficient
	)		const

Get the coefficient of a component. If there was no matching component, return false, ow return true.

bool BALL::ScoringFunction::getCoefficient	(	const String &	name,
		float &	coefficient
	)		const

Get the coefficient of a component. If there was no matching component, return false, ow return true.

ScoringComponent* BALL::ScoringFunction::getComponent

(

const String &

name

)

const

Return a pointer to a component in the components vector.

ScoringComponent* BALL::ScoringFunction::getComponent

(

const Size

index

)

const

Return a pointer to a component in the components vector.

Molecule* BALL::ScoringFunction::getFirstMolecule

(

)

const

double BALL::ScoringFunction::getIntercept

(

)

const

Molecule* BALL::ScoringFunction::getLigand

(

)

const

Return the ligand of the complex (which is just the same as molecule2_).

Size BALL::ScoringFunction::getMaximumNumberOfErrors

(

)

const

Molecule* BALL::ScoringFunction::getReceptor

(

)

const

Return the receptor of the complex (which is just the same as molecule1_).

Molecule* BALL::ScoringFunction::getSecondMolecule

(

)

const

const HashSet<const Atom*>& BALL::ScoringFunction::getUnassignedAtoms

(

)

const

HashSet<const Atom*>& BALL::ScoringFunction::getUnassignedAtoms

(

)

void BALL::ScoringFunction::insertComponent	(	ScoringComponent *	component,
		float	coefficient = 1.0f
	)

ScoringFunction& BALL::ScoringFunction::operator=

(

const ScoringFunction &

sf

)

void BALL::ScoringFunction::removeComponent

(

const ScoringComponent *

component

)

Remove a component from the component list of this scoring function and delete it from memory. If there was no matching component, do nothing. Note that the user will get no feedback if there was no component removed.

void BALL::ScoringFunction::removeComponent

(

const String &

name

)

Remove a component from the component list of this scoring function and delete it from memory. If there was no matching component, do nothing. Note that the user will get no feedback if there was no component removed. Only the first occurrence of a name in the component list will be removed.

void BALL::ScoringFunction::setBaseFunction

(

ScoringBaseFunction &

base_function

)

Set the instance of BaseFunction for the scoring function.

void BALL::ScoringFunction::setCoefficient	(	const ScoringComponent *	component,
		float	coefficient
	)

Set the coefficient of a component. If there was no matching component, do nothing. Note that the user will get no feedback if there was no coefficient set.

void BALL::ScoringFunction::setCoefficient	(	const String &	name,
		float	coefficient
	)

Set the coefficient of a named component. If there was no matching component, do nothing. Note that the user will get no feedback if there was no coefficient set. Only the first occurrence of a name in the component list will be changed.

void BALL::ScoringFunction::setFirstMolecule

(

Molecule &

molecule1

)

void BALL::ScoringFunction::setIntercept

(

double

intercept

)

void BALL::ScoringFunction::setLigand

(

Molecule &

ligand

)

Set the ligand of the complex (which is just the same as molecule2_).

void BALL::ScoringFunction::setMaximumNumberOfErrors

(

Size

nr

)

void BALL::ScoringFunction::setReceptor

(

Molecule &

receptor

)

Set the receptor of the complex (which is just the same as molecule1_).

void BALL::ScoringFunction::setSecondMolecule

(

Molecule &

molecule2

)

bool BALL::ScoringFunction::setup

(

)

bool BALL::ScoringFunction::setup	(	Molecule &	receptor,
		Molecule &	ligand
	)

bool BALL::ScoringFunction::setup	(	Molecule &	receptor,
		Molecule &	ligand,
		const Options &	options
	)

virtual bool BALL::ScoringFunction::specificSetup ( ) throw (Exception::TooManyErrors)

virtual

Reimplemented in BALL::SLICKEnergy, and BALL::SLICKScore.

Member Data Documentation

ScoringBaseFunction* BALL::ScoringFunction::base_function_

protected

Definition at line 259 of file scoringFunction.h.

std::vector< std::pair<ScoringComponent*, float> > BALL::ScoringFunction::components_

protected

Definition at line 265 of file scoringFunction.h.

double BALL::ScoringFunction::intercept_

protected

Definition at line 255 of file scoringFunction.h.

Size BALL::ScoringFunction::max_number_of_errors_

protected

Definition at line 271 of file scoringFunction.h.

Molecule* BALL::ScoringFunction::molecule1_

protected

Definition at line 241 of file scoringFunction.h.

Molecule* BALL::ScoringFunction::molecule2_

protected

Definition at line 246 of file scoringFunction.h.

String BALL::ScoringFunction::name_

protected

Definition at line 249 of file scoringFunction.h.

Size BALL::ScoringFunction::number_of_errors_

protected

Definition at line 274 of file scoringFunction.h.

Options BALL::ScoringFunction::options

Definition at line 233 of file scoringFunction.h.

double BALL::ScoringFunction::score_

protected

Definition at line 252 of file scoringFunction.h.

HashSet<const Atom*> BALL::ScoringFunction::unassigned_atoms_

protected

Definition at line 268 of file scoringFunction.h.