BALL::MMFF94NonBonded Class Reference

#include <BALL/MOLMEC/MMFF94/MMFF94NonBonded.h>

Inheritance diagram for BALL::MMFF94NonBonded:

Classes
struct	NonBondedPairData

Public Member Functions
	MMFF94NonBonded ()
	Default constructor.
	MMFF94NonBonded (ForceField &force_field)
	Constructor.
	MMFF94NonBonded (const MMFF94NonBonded &MMFF94_non_bonded)
	Copy constructor.
virtual	~MMFF94NonBonded ()
	Destructor.
const MMFF94NonBonded &	operator= (const MMFF94NonBonded &anb)
	Assignment operator.
virtual void	clear ()
	Clear method.
bool	operator== (const MMFF94NonBonded &anb)
	Equality operator.
virtual bool	setup ()
virtual double	updateEnergy ()
	Calculates and returns the component's energy.
virtual void	updateForces ()
	Calculates and returns the component's forces.
virtual void	update ()
virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()
	Computes the most efficient way to calculate the non-bonded atom pairs.
const ForceField::PairVector &	getAtomPairs () const
const vector< NonBondedPairData > &	getNonBondedData () const
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 ()
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	update (const vector< std::pair< Atom *, Atom * > > &pair_vector)
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 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

MMFF94 NonBonded (VdW + Electrostatic) component

Definition at line 31 of file MMFF94NonBonded.h.

Constructor & Destructor Documentation

MMFF94NonBonded() [1/3]

BALL::MMFF94NonBonded::MMFF94NonBonded

(

)

Default constructor.

MMFF94NonBonded() [2/3]

BALL::MMFF94NonBonded::MMFF94NonBonded

(

ForceField &

force_field

)

Constructor.

MMFF94NonBonded() [3/3]

BALL::MMFF94NonBonded::MMFF94NonBonded

(

const MMFF94NonBonded &

MMFF94_non_bonded

)

Copy constructor.

~MMFF94NonBonded()

virtual BALL::MMFF94NonBonded::~MMFF94NonBonded ( )

virtual

Destructor.

Member Function Documentation

clear()

virtual void BALL::MMFF94NonBonded::clear ( )

virtual

Clear method.

Reimplemented from BALL::ScoringComponent.

determineMethodOfAtomPairGeneration()

virtual MolmecSupport::PairListAlgorithmType BALL::MMFF94NonBonded::determineMethodOfAtomPairGeneration ( )

virtual

Computes the most efficient way to calculate the non-bonded atom pairs.

getAtomPairs()

const ForceField::PairVector & BALL::MMFF94NonBonded::getAtomPairs ( ) const

inline

Definition at line 114 of file MMFF94NonBonded.h.

getESEnergy()

double BALL::MMFF94NonBonded::getESEnergy

(

)

const

getNonBondedData()

const vector< NonBondedPairData > & BALL::MMFF94NonBonded::getNonBondedData ( ) const

inline

Definition at line 117 of file MMFF94NonBonded.h.

getVDWEnergy()

double BALL::MMFF94NonBonded::getVDWEnergy

(

)

const

operator=()

const MMFF94NonBonded & BALL::MMFF94NonBonded::operator=

(

const MMFF94NonBonded &

anb

)

Assignment operator.

operator==()

bool BALL::MMFF94NonBonded::operator==

(

const MMFF94NonBonded &

anb

)

Equality operator.

setup()

virtual bool BALL::MMFF94NonBonded::setup ( )

virtual

Setup method.

Exceptions

BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

update()

virtual void BALL::MMFF94NonBonded::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.

updateEnergy()

virtual double BALL::MMFF94NonBonded::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

updateForces()

virtual void BALL::MMFF94NonBonded::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

es_energy_

double BALL::MMFF94NonBonded::es_energy_

protected

Definition at line 128 of file MMFF94NonBonded.h.

vdw_energy_

double BALL::MMFF94NonBonded::vdw_energy_

protected

Definition at line 131 of file MMFF94NonBonded.h.