BALL::PLP Class Reference

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

Inheritance diagram for BALL::PLP:

Classes
struct	NonBondedPairData

Public Member Functions
	PLP () throw ()
	Default constructor.
	PLP (ForceField &force_field) throw ()
	Constructor.
	PLP (const PLP &MMFF94_non_bonded) throw ()
	Copy constructor.
virtual	~PLP () throw ()
	Destructor.
const PLP &	operator= (const PLP &anb) throw ()
	Assignment operator.
void	setRotatableBonds (std::vector< Bond * > &bonds)
void	update (const std::vector< std::pair< Atom *, Atom * > > &atom_vector)
virtual void	clear () throw ()
	Clear method.
bool	operator== (const PLP &anb) throw ()
	Equality operator.
bool	setup (Options &options)
virtual double	updateEnergy () throw ()
	Calculates and returns the component's energy.
virtual void	updateForces () throw ()
	Calculates and returns the component's forces.
virtual void	update ()
double	getVDWEnergy () const
double	getESEnergy () const
Public Member Functions inherited from BALL::ForceFieldComponent
	ForceFieldComponent ()
	ForceFieldComponent (ForceField &force_field)
	ForceFieldComponent (const ForceFieldComponent &force_field_component)
virtual	~ForceFieldComponent ()
virtual bool	setup ()
ForceField *	getForceField () const
void	setForceField (ForceField &force_field)
void	setName (const String &name)
String	getName () const
bool	isEnabled () const
void	setEnabled (bool state)
virtual double	getEnergy () const
double	updateScore ()
Public Member Functions inherited from BALL::ScoringComponent
	ScoringComponent ()
	ScoringComponent (const ScoringComponent &sc)
	ScoringComponent (ScoringFunction &sf)
void	selectBaseFunction (String function)
virtual	~ScoringComponent ()
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	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 ()

Static Public Member Functions
static Size	getAtomType (const Atom *atom)

Static Protected Member Functions
static bool	isNSp3 (const Atom *at)
static bool	isSp3 (const Atom *at)

Protected Attributes
double	es_energy_
double	vdw_energy_
ForceField *	force_field_
double	energy_
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_

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

Detailed Description

Piecewise Linear Potential

Definition at line 18 of file PLP.h.

Constructor & Destructor Documentation

PLP() [1/3]

BALL::PLP::PLP	(		)
throw	(	)

Default constructor.

PLP() [2/3]

BALL::PLP::PLP	(	ForceField &	force_field	)
throw	(	)

Constructor.

PLP() [3/3]

BALL::PLP::PLP	(	const PLP &	MMFF94_non_bonded	)
throw	(	)

Copy constructor.

~PLP()

virtual BALL::PLP::~PLP ( ) throw (  )

virtual

Destructor.

Member Function Documentation

clear()

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

virtual

Clear method.

Reimplemented from BALL::ScoringComponent.

getAtomType()

Size BALL::PLP::getAtomType ( const Atom * atom )

static

Returns the Gehlhaar Atom-Type (0, 1, 2 or 3) for the given atom.
0 : steric
1 : donor
2 : acceptor
3 : both
4 : metal

getESEnergy()

double BALL::PLP::getESEnergy

(

)

const

getVDWEnergy()

double BALL::PLP::getVDWEnergy

(

)

const

isNSp3()

bool BALL::PLP::isNSp3 ( const Atom * at )

staticprotected

isSp3()

bool BALL::PLP::isSp3 ( const Atom * at )

staticprotected

operator=()

const PLP & BALL::PLP::operator=	(	const PLP &	anb	)
throw	(	)

Assignment operator.

operator==()

bool BALL::PLP::operator==	(	const PLP &	anb	)
throw	(	)

Equality operator.

setRotatableBonds()

void BALL::PLP::setRotatableBonds

(

std::vector< Bond * > &

bonds

)

Set the rotatable bonds. This is necessary in order to be able to compute GHTorsion-Energies.
Note that setting the rotatable bonds must of course be done anew for each new ligand !!

setup()

bool BALL::PLP::setup

(

Options &

options

)

Setup this component according to the given options.

update() [1/2]

virtual void BALL::PLP::update ( )

virtual

Update the pair list. This method is called by the force field whenever ForceField::update is called. It is used to recalculate the nonbonded pair list.

Exceptions

BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

update() [2/2]

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

virtual

Update this component using only the given atom-pairs

Reimplemented from BALL::ScoringComponent.

updateEnergy()

virtual double BALL::PLP::updateEnergy ( ) throw (  )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

updateForces()

virtual void BALL::PLP::updateForces ( ) throw (  )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

es_energy_

double BALL::PLP::es_energy_

protected

Definition at line 115 of file PLP.h.

vdw_energy_

double BALL::PLP::vdw_energy_

protected

Definition at line 118 of file PLP.h.