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 () throw (Exception::TooManyErrors)
Accessors
virtual double	updateEnergy ()
virtual void	updateForces ()
virtual double	getElectrostaticEnergy () const
virtual double	getVdwEnergy () const
virtual double	getSolvationEnergy () const
Neighbourhood and Parameter calculations
virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()
virtual void	buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom *, Atom * > > &atom_vector) throw (Exception::TooManyErrors)
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 () throw (Exception::TooManyErrors)
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	electrostatic_energy_
double	vdw_energy_
double	solvation_energy_
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_

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

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

BALL::CharmmNonBonded::CharmmNonBonded

(

)

Default constructor.

BALL::CharmmNonBonded::CharmmNonBonded

(

ForceField &

force_field

)

Constructor.

BALL::CharmmNonBonded::CharmmNonBonded

(

const CharmmNonBonded &

charmm_non_bonded

)

Copy constructor

virtual BALL::CharmmNonBonded::~CharmmNonBonded ( )

virtual

Destructor.

Member Function Documentation

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

virtual

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

virtual void BALL::CharmmNonBonded::clear ( )

virtual

Clear method

Reimplemented from BALL::ScoringComponent.

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

virtual

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

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

virtual

Return the electrostatic energy.

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

virtual

Return the solvation energy.

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

virtual

Return the Van-der-Waals energy.

const CharmmNonBonded& BALL::CharmmNonBonded::operator=

(

const CharmmNonBonded &

charmm_non_bonded

)

Assignment operator

bool BALL::CharmmNonBonded::operator==

(

const CharmmNonBonded &

charmm_non_bonded

)

Equality operator

virtual bool BALL::CharmmNonBonded::setup ( ) throw ( Exception::TooManyErrors )

virtual

Setup method.

Reimplemented from BALL::ForceFieldComponent.

virtual double BALL::CharmmNonBonded::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

virtual void BALL::CharmmNonBonded::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

double BALL::CharmmNonBonded::electrostatic_energy_

protected

Definition at line 172 of file charmmNonBonded.h.

double BALL::CharmmNonBonded::solvation_energy_

protected

Definition at line 180 of file charmmNonBonded.h.

double BALL::CharmmNonBonded::vdw_energy_

protected

Definition at line 176 of file charmmNonBonded.h.