BALL::AmberNonBonded Class Reference

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

Inheritance diagram for BALL::AmberNonBonded:

Public Member Functions
Constructors and Destructors
	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
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.