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_

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 String &	name,
		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 ScoringComponent *	component,
		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 Size index ) const

Return a pointer to a component in the components vector.

ScoringComponent* BALL::ScoringFunction::getComponent ( const String & name ) 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

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

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

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

ScoringFunction& BALL::ScoringFunction::operator= ( const ScoringFunction & sf )

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::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::setBaseFunction ( ScoringBaseFunction & base_function )

Set the instance of BaseFunction for the scoring function.

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::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::setFirstMolecule ( Molecule & molecule1 )