BALL::CharmmNonBonded Class Reference

#include <BALL/MOLMEC/CHARMM/charmmNonBonded.h>

Inheritance diagram for BALL::CharmmNonBonded:

Public Member Functions
Constructors and Destructors
	CharmmNonBonded ()
	CharmmNonBonded (ForceField &force_field)
	CharmmNonBonded (const CharmmNonBonded &charmm_non_bonded)
virtual	~CharmmNonBonded ()
Assignment
const CharmmNonBonded &	operator= (const CharmmNonBonded &charmm_non_bonded)
virtual void	clear ()
Predicates
bool	operator== (const CharmmNonBonded &charmm_non_bonded)
Setup Methods
virtual bool	setup ()
Accessors
virtual double	updateEnergy ()
virtual void	updateForces ()
virtual double	getElectrostaticEnergy () const
virtual double	getVdwEnergy () const
virtual double	getSolvationEnergy () 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
virtual void	update ()
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 ()

Neighbourhood and Parameter calculations
double	electrostatic_energy_
double	vdw_energy_
double	solvation_energy_
virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()
virtual void	buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom *, Atom * > > &atom_vector)

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

Charmm NonBonded component. This force field component implements the non-bonded interactions in the CHARMM force field: van-der-Waals interaction, electrostatics, and solvation (in EEF1 only).

Definition at line 45 of file charmmNonBonded.h.

Constructor & Destructor Documentation

CharmmNonBonded() [1/3]

BALL::CharmmNonBonded::CharmmNonBonded

(

)

Default constructor.

CharmmNonBonded() [2/3]

BALL::CharmmNonBonded::CharmmNonBonded

(

ForceField &

force_field

)

Constructor.

CharmmNonBonded() [3/3]

BALL::CharmmNonBonded::CharmmNonBonded

(

const CharmmNonBonded &

charmm_non_bonded

)

Copy constructor

~CharmmNonBonded()

virtual BALL::CharmmNonBonded::~CharmmNonBonded ( )

virtual

Destructor.

Member Function Documentation

buildVectorOfNonBondedAtomPairs()

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

virtual

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

Exceptions

BALL::Exception::TooManyErrors

clear()

virtual void BALL::CharmmNonBonded::clear ( )

virtual

Clear method

Reimplemented from BALL::ScoringComponent.

determineMethodOfAtomPairGeneration()

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

virtual

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

getElectrostaticEnergy()

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

virtual

Return the electrostatic energy.

getSolvationEnergy()

virtual double BALL::CharmmNonBonded::getSolvationEnergy ( ) const

virtual

Return the solvation energy.

getVdwEnergy()

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

virtual

Return the Van-der-Waals energy.

operator=()

const CharmmNonBonded & BALL::CharmmNonBonded::operator=

(

const CharmmNonBonded &

charmm_non_bonded

)

Assignment operator

operator==()

bool BALL::CharmmNonBonded::operator==

(

const CharmmNonBonded &

charmm_non_bonded

)

Equality operator

setup()

virtual bool BALL::CharmmNonBonded::setup ( )

virtual

Setup method.

Exceptions

BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

updateEnergy()

virtual double BALL::CharmmNonBonded::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

updateForces()

virtual void BALL::CharmmNonBonded::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

electrostatic_energy_

double BALL::CharmmNonBonded::electrostatic_energy_

protected

Definition at line 172 of file charmmNonBonded.h.

solvation_energy_

double BALL::CharmmNonBonded::solvation_energy_

protected

Definition at line 180 of file charmmNonBonded.h.

vdw_energy_

double BALL::CharmmNonBonded::vdw_energy_

protected

Definition at line 176 of file charmmNonBonded.h.