BALL::HydrogenBond Class Reference

#include <BALL/SCORING/COMPONENTS/hydrogenBond.h>

Inheritance diagram for BALL::HydrogenBond:

Classes
struct	Option
struct	Default

Public Types
enum	Mode { LIGAND_HYDROGENS , RECEPTOR_HYDROGENS , ALL_HYDROGENS }

Public Member Functions
Constructors and Destructors
	HydrogenBond (Mode mode) throw ()
	HydrogenBond (ScoringFunction &sf, Mode mode) throw ()
	HydrogenBond (ScoringComponent &sc, Mode mode) throw ()
	HydrogenBond (const HydrogenBond &fhb) throw ()
virtual	~HydrogenBond () throw ()
Assignment
const HydrogenBond &	operator= (const HydrogenBond &fhb) throw ()
virtual void	clear () throw ()
Predicates.
bool	operator== (const HydrogenBond &fhb) const throw ()
Setup Methods
virtual bool	setup ()
void	setupLigand ()
void	enableChargeEvaluation (bool b)
Public Member Functions inherited from BALL::ScoringComponent
	ScoringComponent ()
	ScoringComponent (const ScoringComponent &sc)
	ScoringComponent (ScoringFunction &sf)
void	selectBaseFunction (String function)
virtual	~ScoringComponent ()
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	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 ()

Accessors
virtual double	updateScore ()
void	update (const vector< std::pair< Atom *, Atom * > > &pair_vector)

Additional Inherited Members
Protected Member Functions inherited from BALL::ScoringComponent
double	scaleScore (double score) const
Protected Attributes inherited from BALL::ScoringComponent
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

Fresno Hydrogen Bond component.

Definition at line 17 of file hydrogenBond.h.

Member Enumeration Documentation

Mode

enum BALL::HydrogenBond::Mode

Enumerator
LIGAND_HYDROGENS
RECEPTOR_HYDROGENS
ALL_HYDROGENS

Definition at line 84 of file hydrogenBond.h.

Constructor & Destructor Documentation

HydrogenBond() [1/4]

BALL::HydrogenBond::HydrogenBond	(	Mode	mode	)
throw	(	)

Default constructor.

HydrogenBond() [2/4]

BALL::HydrogenBond::HydrogenBond	(	ScoringFunction &	sf,
		Mode	mode )
throw	(	)

Constructor.

HydrogenBond() [3/4]

BALL::HydrogenBond::HydrogenBond	(	ScoringComponent &	sc,
		Mode	mode )
throw	(	)

Constructor.

HydrogenBond() [4/4]

BALL::HydrogenBond::HydrogenBond	(	const HydrogenBond &	fhb	)
throw	(	)

Copy constructor

~HydrogenBond()

virtual BALL::HydrogenBond::~HydrogenBond ( ) throw (  )

virtual

Destructor.

Member Function Documentation

clear()

virtual void BALL::HydrogenBond::clear ( ) throw (  )

virtual

Clear method.

Reimplemented from BALL::ScoringComponent.

enableChargeEvaluation()

void BALL::HydrogenBond::enableChargeEvaluation

(

bool

b

)

If charge-evaluation is enabled, hydrogen bonds with large charge difference between hydrogen bond acceptor and hydrogen will receive a better score than those with a small difference.
By default, this is disabled.

operator=()

const HydrogenBond & BALL::HydrogenBond::operator=	(	const HydrogenBond &	fhb	)
throw	(	)

Assignment.

operator==()

bool BALL::HydrogenBond::operator==	(	const HydrogenBond &	fhb	)	const
throw	(	)

setup()

virtual bool BALL::HydrogenBond::setup ( )

virtual

Setup method.

Reimplemented from BALL::ScoringComponent.

setupLigand()

void BALL::HydrogenBond::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 from BALL::ScoringComponent.

update()

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

virtual

Update possible_hydrogen_bonds_ from the given AtomPairVector.
If intermolecular H-bonds are to be evaluated, the first atom of each pair must be a ligand atom and the second one a receptor atom. This is automatically done this way by ScoringFunction::createNonbondedPairVector().

Reimplemented from BALL::ScoringComponent.

updateScore()

virtual double BALL::HydrogenBond::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 from BALL::ScoringComponent.