BALL::ScoringComponent Class Reference

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

Inheritance diagram for BALL::ScoringComponent:

Public Member Functions
	ScoringComponent ()
	ScoringComponent (const ScoringComponent &sc)
	ScoringComponent (ScoringFunction &sf)
void	selectBaseFunction (String function)
virtual	~ScoringComponent ()
virtual void	clear ()
virtual bool	setup ()
virtual void	setupLigand ()
ScoringFunction *	getScoringFunction () const
void	setScoringFunction (ScoringFunction &sf)
String	getName () const
void	setName (const String &name)
const String &	getTypeName ()
double	getRawScore () const
double	getScaledScore () const
virtual void	update (const vector< std::pair< Atom *, Atom * > > &pair_vector)
virtual double	updateScore ()
virtual void	setLigandIntraMolecular (bool b)
bool	isLigandIntraMolecular ()
bool	isGridable ()
bool	isAtomPairwise ()
void	setCoefficient (const double &coeff)
const double &	getCoefficient ()
void	setNormalizationParameters (double stddev, double mean)
void	getNormalizationParameters (double &stddev, double &mean)
bool	isEnabled ()
void	enable ()
void	disable ()

Protected Member Functions
double	scaleScore (double score) const

Protected Attributes
bool	ligand_intra_molecular_
bool	gridable_
bool	atom_pairwise_
ScoringFunction *	scoring_function_
ScoringBaseFunction *	base_function_
double	score_
double	coefficient_
double	stddev_
double	mean_
bool	enabled_
String	type_name_

Detailed Description

Definition at line 20 of file scoringComponent.h.

Constructor & Destructor Documentation

BALL::ScoringComponent::ScoringComponent

(

)

BALL::ScoringComponent::ScoringComponent

(

const ScoringComponent &

sc

)

BALL::ScoringComponent::ScoringComponent

(

ScoringFunction &

sf

)

virtual BALL::ScoringComponent::~ScoringComponent ( )

virtual

Member Function Documentation

virtual void BALL::ScoringComponent::clear ( )

virtual

Reimplemented in BALL::CHPISlick, BALL::PolarSolvation, BALL::CHPI, BALL::NonpolarSolvation, BALL::HydrogenBondSlick, BALL::HydrogenBond, BALL::VanDerWaalsSlick, BALL::CharmmNonBonded, BALL::Lipophilic, BALL::AmberNonBonded, BALL::PLP, BALL::MMFF94NonBonded, BALL::BuriedPolar, BALL::AromaticRingStacking, and BALL::Polarity.

void BALL::ScoringComponent::disable

(

)

void BALL::ScoringComponent::enable

(

)

const double& BALL::ScoringComponent::getCoefficient

(

)

String BALL::ScoringComponent::getName

(

)

const

void BALL::ScoringComponent::getNormalizationParameters	(	double &	stddev,
		double &	mean
	)

double BALL::ScoringComponent::getRawScore

(

)

const

double BALL::ScoringComponent::getScaledScore

(

)

const

ScoringFunction* BALL::ScoringComponent::getScoringFunction

(

)

const

const String& BALL::ScoringComponent::getTypeName

(

)

bool BALL::ScoringComponent::isAtomPairwise

(

)

Does this component calculate the score based on atom-atom pairs?

bool BALL::ScoringComponent::isEnabled

(

)

bool BALL::ScoringComponent::isGridable

(

)

Can the scores of this ScoringFunction be precomputed for a grid?

bool BALL::ScoringComponent::isLigandIntraMolecular

(

)

Is this ScoringComponent to be used to calculate an intra-molecular score for the ligand ?

double BALL::ScoringComponent::scaleScore ( double  score ) const

protected

Multiplies the score_ with coefficient_ and, if necessary, does transformation and backtransformation.

void BALL::ScoringComponent::selectBaseFunction

(

String

function

)

select the base function (necessary only if the specific ScoringComponent uses it). Possible choices are 'fermi' and 'linear'.

void BALL::ScoringComponent::setCoefficient

(

const double &

coeff

)

virtual void BALL::ScoringComponent::setLigandIntraMolecular ( bool  b )

virtual

Reimplemented in BALL::RotationalEntropy.

void BALL::ScoringComponent::setName

(

const String &

name

)

void BALL::ScoringComponent::setNormalizationParameters	(	double	stddev,
		double	mean
	)

void BALL::ScoringComponent::setScoringFunction

(

ScoringFunction &

sf

)

virtual bool BALL::ScoringComponent::setup ( )

virtual

Reimplemented in BALL::CHPISlick, BALL::PolarSolvation, BALL::CHPI, BALL::NonpolarSolvation, BALL::HydrogenBondSlick, BALL::HydrogenBond, BALL::CharmmTorsion, BALL::CharmmNonBonded, BALL::AmberTorsion, BALL::VanDerWaalsSlick, BALL::Lipophilic, BALL::AmberNonBonded, BALL::MMFF94StretchBend, BALL::MMFF94NonBonded, BALL::MMFF94Torsion, BALL::CharmmImproperTorsion, BALL::BuriedPolar, BALL::ForceFieldComponent, BALL::Polarity, BALL::MMFF94OutOfPlaneBend, BALL::AmberBend, BALL::AmberStretch, BALL::CharmmBend, and BALL::CharmmStretch.

virtual void BALL::ScoringComponent::setupLigand ( )

virtual

Function that needs to be called once for every new ligand.
The default implementation of this base class does nothing and should be overloaded by derived classes if necessary.

Reimplemented in BALL::CHPI, BALL::HydrogenBond, BALL::Lipophilic, BALL::BuriedPolar, BALL::Polarity, BALL::AromaticRingStacking, and BALL::PB.

virtual void BALL::ScoringComponent::update ( const vector< std::pair< Atom *, Atom * > > &  pair_vector )

virtual

Update this ScoringComponent using the given atom-pairs.
This function should be overloaded by all ScoringComponents

Reimplemented in BALL::CHPISlick, BALL::PolarSolvation, BALL::CHPI, BALL::NonpolarSolvation, BALL::HydrogenBond, BALL::HydrogenBondSlick, BALL::AmberNonBonded, BALL::VanDerWaalsSlick, BALL::BuriedPolar, BALL::PLP, BALL::Polarity, BALL::AromaticRingStacking, BALL::Electrostatic, BALL::RotationalEntropy, BALL::VanDerWaals, BALL::BurialDepth, and BALL::PB.

virtual double BALL::ScoringComponent::updateScore ( )

virtual

Calculate the score for this component (for all interactions that have been set by the last call of update()) and return the score.
The coefficient assigned by the user to this component should be taken into account for the calculation, so that the weighted score is returned.

Reimplemented in BALL::CHPISlick, BALL::PolarSolvation, BALL::CHPI, BALL::NonpolarSolvation, BALL::HydrogenBondSlick, BALL::HydrogenBond, BALL::ForceFieldComponent, BALL::Lipophilic, BALL::VanDerWaalsSlick, BALL::BuriedPolar, BALL::Polarity, BALL::AromaticRingStacking, BALL::Electrostatic, BALL::VanDerWaals, BALL::BurialDepth, BALL::PB, BALL::Solvation, BALL::FragmentationalSolvation, and BALL::RotationalEntropy.

Member Data Documentation

bool BALL::ScoringComponent::atom_pairwise_

protected

Does this component calculate the score based on atom-atom pairs?

Definition at line 106 of file scoringComponent.h.

ScoringBaseFunction* BALL::ScoringComponent::base_function_

protected

Definition at line 110 of file scoringComponent.h.

double BALL::ScoringComponent::coefficient_

protected

Definition at line 114 of file scoringComponent.h.

bool BALL::ScoringComponent::enabled_

protected

Determines whether this ScoringComponent is enabled and should be used when ScoringFunction::update()/updateScore() is called.

Definition at line 127 of file scoringComponent.h.

bool BALL::ScoringComponent::gridable_

protected

Can the scores of this ScoringFunction be precomputed for a grid?

Definition at line 101 of file scoringComponent.h.

bool BALL::ScoringComponent::ligand_intra_molecular_

protected

Is this ScoringComponent to be used to calculate an intra-molecular score for the ligand?

Definition at line 96 of file scoringComponent.h.

double BALL::ScoringComponent::mean_

protected

Definition at line 117 of file scoringComponent.h.

double BALL::ScoringComponent::score_

protected

Definition at line 112 of file scoringComponent.h.

ScoringFunction* BALL::ScoringComponent::scoring_function_

protected

Definition at line 108 of file scoringComponent.h.

double BALL::ScoringComponent::stddev_

protected

Definition at line 116 of file scoringComponent.h.

String BALL::ScoringComponent::type_name_

protected

An abreviation for the type of this ScoringComponent, i.e.: 'ES', 'vdW', 'fragSolv', 'nRot', 'HB'.
This type-name cannot be changed dynmically and is used to differentiate between the differnt types of ScoringComponents as is necessary e.g. for PharmacophoreConstraints.

Definition at line 135 of file scoringComponent.h.