BALL::VanDerWaalsSlick Class Reference

#include <BALL/SCORING/COMPONENTS/vanDerWaalsSlick.h>

Inheritance diagram for BALL::VanDerWaalsSlick:

Classes
struct	Default
struct	Option

Public Types
enum	CalculationMethod { CALCULATION__FULL_LJ_POTENTIAL , CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE , CALCULATION__SOFTENED_LJ_POTENTIAL_LOG }

Public Member Functions
	VanDerWaalsSlick ()
	VanDerWaalsSlick (ScoringFunction &sf)
	VanDerWaalsSlick (ScoringComponent &sc)
virtual	~VanDerWaalsSlick ()
virtual void	clear ()
virtual bool	setup ()
void	update (const vector< std::pair< Atom *, Atom * > > &)
virtual 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 ()

Protected Attributes
std::vector< LennardJones::Data >	non_bonded_
std::vector< bool >	is_hydrogen_bond_
Size	number_of_1_4_
Size	number_of_h_bonds_
LennardJones	lennard_jones_
Potential1210	hydrogen_bond_
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

SLICK van-der-Waals Component based on AmberNonBonded \ {\bf Definition:} \URL{BALL/SCORING/COMPONENTS/vanDerWaalsSlick.h}

Definition at line 18 of file vanDerWaalsSlick.h.

Member Enumeration Documentation

CalculationMethod

enum BALL::VanDerWaalsSlick::CalculationMethod

Enumerator
CALCULATION__FULL_LJ_POTENTIAL	Full Lennard-Jones 6-12 potential.
CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE	Softened Lennard-Jones 6-12 potential (simple cut)
CALCULATION__SOFTENED_LJ_POTENTIAL_LOG	Log-Softened Lennard-Jones 6-12 potential.

Definition at line 23 of file vanDerWaalsSlick.h.

Constructor & Destructor Documentation

VanDerWaalsSlick() [1/3]

BALL::VanDerWaalsSlick::VanDerWaalsSlick

(

)

VanDerWaalsSlick() [2/3]

BALL::VanDerWaalsSlick::VanDerWaalsSlick

(

ScoringFunction &

sf

)

VanDerWaalsSlick() [3/3]

BALL::VanDerWaalsSlick::VanDerWaalsSlick

(

ScoringComponent &

sc

)

~VanDerWaalsSlick()

virtual BALL::VanDerWaalsSlick::~VanDerWaalsSlick ( )

virtual

Member Function Documentation

clear()

virtual void BALL::VanDerWaalsSlick::clear ( )

virtual

Reimplemented from BALL::ScoringComponent.

setup()

virtual bool BALL::VanDerWaalsSlick::setup ( )

virtual

Setup method

Reimplemented from BALL::ScoringComponent.

update()

void BALL::VanDerWaalsSlick::update ( const vector< std::pair< Atom *, Atom * > > &  pair_vector )

virtual

Update this ScoringComponent using the given atom-pairs.
This function should be overloaded by all ScoringComponents

Reimplemented from BALL::ScoringComponent.

updateScore()

virtual double BALL::VanDerWaalsSlick::updateScore ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ScoringComponent.

Member Data Documentation

hydrogen_bond_

Potential1210 BALL::VanDerWaalsSlick::hydrogen_bond_

protected

Definition at line 132 of file vanDerWaalsSlick.h.

is_hydrogen_bond_

std::vector<bool> BALL::VanDerWaalsSlick::is_hydrogen_bond_

protected

Definition at line 126 of file vanDerWaalsSlick.h.

lennard_jones_

LennardJones BALL::VanDerWaalsSlick::lennard_jones_

protected

Definition at line 131 of file vanDerWaalsSlick.h.

non_bonded_

std::vector<LennardJones::Data> BALL::VanDerWaalsSlick::non_bonded_

protected

Definition at line 123 of file vanDerWaalsSlick.h.

number_of_1_4_

Size BALL::VanDerWaalsSlick::number_of_1_4_

protected

Definition at line 128 of file vanDerWaalsSlick.h.

number_of_h_bonds_

Size BALL::VanDerWaalsSlick::number_of_h_bonds_

protected

Definition at line 129 of file vanDerWaalsSlick.h.