#include <BALL/MOLMEC/AMBER/amberNonBonded.h>

Inheritance diagram for BALL::AmberNonBonded:

Public Member Functions
Constructors and Destructors <br>
	AmberNonBonded ()

	AmberNonBonded (ForceField &force_field)

	AmberNonBonded (const AmberNonBonded &amber_non_bonded)

virtual	~AmberNonBonded ()

const AmberNonBonded &	operator= (const AmberNonBonded &anb)

virtual void	clear ()

bool	operator== (const AmberNonBonded &anb)

Setup Methods
virtual bool	setup ()

bool	setup (Options &options, ForceFieldParameters &par)

Accessors
virtual double	updateEnergy ()

virtual void	updateForces ()

virtual void	update ()

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

virtual double	getElectrostaticEnergy () const

virtual double	getVdwEnergy () 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	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 Attributes
static const double	ELECTROSTATIC_FACTOR

Neighbourhood and Parameter calculations
double	electrostatic_energy_

double	vdw_energy_

virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()

virtual void	buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom , Atom > > &atom_vector, const LennardJones &lennard_jones, const Potential1210 &hydrogen_bond)

void	enableStoreInteractions (bool b=true)

void	setAdvancedElectrostatic (AdvancedElectrostatic *advES)

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

Protected Attributes inherited from BALL::ForceFieldComponent
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_

Detailed Description

Amber NonBonded (VdW + Electrostatic) component

Definition at line 38 of file amberNonBonded.h.

Constructor & Destructor Documentation

◆ AmberNonBonded() [1/3]

BALL::AmberNonBonded::AmberNonBonded ( )

Default constructor.

◆ AmberNonBonded() [2/3]

BALL::AmberNonBonded::AmberNonBonded ( ForceField & force_field )

Constructor.

◆ AmberNonBonded() [3/3]

BALL::AmberNonBonded::AmberNonBonded ( const AmberNonBonded & amber_non_bonded )

Copy constructor

◆ ~AmberNonBonded()

virtual BALL::AmberNonBonded::~AmberNonBonded ( )

virtual

Destructor.

Member Function Documentation

◆ buildVectorOfNonBondedAtomPairs()

virtual void BALL::AmberNonBonded::buildVectorOfNonBondedAtomPairs	(	const std::vector< std::pair< Atom , Atom > > &	atom_vector,
		const LennardJones &	lennard_jones,
		const Potential1210 &	hydrogen_bond
	)

virtual

Build a vector of non-bonded atom pairs with the vdw parameters

Exceptions

BALL::Exception::TooManyErrors

◆ clear()

virtual void BALL::AmberNonBonded::clear ( )

virtual

Clear method

Reimplemented from BALL::ScoringComponent.

◆ determineMethodOfAtomPairGeneration()

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

virtual

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

◆ enableStoreInteractions()

void BALL::AmberNonBonded::enableStoreInteractions ( bool b = true )

◆ getElectrostaticEnergy()

virtual double BALL::AmberNonBonded::getElectrostaticEnergy ( ) const

virtual

Return the electrostatic energy.

◆ getVdwEnergy()

virtual double BALL::AmberNonBonded::getVdwEnergy ( ) const

virtual

Return the Van-der-Waals energy.

◆ operator=()

const AmberNonBonded& BALL::AmberNonBonded::operator= ( const AmberNonBonded & anb )

Assignment Assignment operator

◆ operator==()

bool BALL::AmberNonBonded::operator== ( const AmberNonBonded & anb )

Predicates Equality operator

◆ setAdvancedElectrostatic()

void BALL::AmberNonBonded::setAdvancedElectrostatic ( AdvancedElectrostatic * advES )

◆ setup() [1/2]

virtual bool BALL::AmberNonBonded::setup ( )

virtual

Setup method.

Exceptions

BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

◆ setup() [2/2]

bool BALL::AmberNonBonded::setup	(	Options &	options,
		ForceFieldParameters &	par
	)

Setup this component according to the given options and store the ForceFieldParameters in par

◆ update() [1/2]

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

virtual

Update this component using the given atom-pairs only

Reimplemented from BALL::ScoringComponent.

◆ updateEnergy()

virtual double BALL::AmberNonBonded::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

◆ updateForces()

virtual void BALL::AmberNonBonded::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

◆ electrostatic_energy_

double BALL::AmberNonBonded::electrostatic_energy_

protected

Definition at line 186 of file amberNonBonded.h.

◆ ELECTROSTATIC_FACTOR

const double BALL::AmberNonBonded::ELECTROSTATIC_FACTOR

static

Definition at line 47 of file amberNonBonded.h.

◆ vdw_energy_

double BALL::AmberNonBonded::vdw_energy_

protected

Definition at line 190 of file amberNonBonded.h.

Public Member Functions

Static Public Attributes

Neighbourhood and Parameter calculations

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AmberNonBonded() [1/3]

◆ AmberNonBonded() [2/3]

◆ AmberNonBonded() [3/3]

◆ ~AmberNonBonded()

Member Function Documentation

◆ buildVectorOfNonBondedAtomPairs()

◆ clear()

◆ determineMethodOfAtomPairGeneration()

◆ enableStoreInteractions()

◆ getElectrostaticEnergy()

◆ getVdwEnergy()

◆ operator=()

◆ operator==()

◆ setAdvancedElectrostatic()

◆ setup() [1/2]

◆ setup() [2/2]

◆ update() [1/2]

◆ update() [2/2]

◆ updateEnergy()

◆ updateForces()

Member Data Documentation

◆ electrostatic_energy_

◆ ELECTROSTATIC_FACTOR

◆ vdw_energy_