BALL::VanDerWaals Class Reference

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

Inheritance diagram for BALL::VanDerWaals:

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
	VanDerWaals ()
	VanDerWaals (ScoringFunction &sf)
	VanDerWaals (ScoringComponent &sc)
virtual	~VanDerWaals ()
virtual void	clear ()
virtual bool	setup ()
virtual double	calculateScore ()
Public Member Functions inherited from BALL::ScoringComponent
	ScoringComponent ()
	ScoringComponent (const ScoringComponent &sc)
	ScoringComponent (ScoringFunction &sf)
virtual	~ScoringComponent ()
ScoringFunction *	getScoringFunction () const
void	setScoringFunction (ScoringFunction &sf)
String	getName () const
void	setName (const String &name)
virtual double	getScore () const

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
ScoringFunction *	scoring_function_
double	score_

Private Member Functions
double	calculateVDWEnergy_ (const AtomVector &atom_vector)
Size	createNonBondedList_ (const ForceField::PairVector &atom_pair_vector)

Private Attributes
System	vdw_system_
Molecule *	vdw_receptor_
Molecule *	vdw_ligand_
Size	calculation_method_
float	cut_on_vdw_
float	cut_off_vdw_
float	scaling_vdw_1_4_
float	softening_limit_
Size	verbosity_

Detailed Description

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

Definition at line 18 of file vanDerWaals.h.

Member Enumeration Documentation

enum BALL::VanDerWaals::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 25 of file vanDerWaals.h.

Constructor & Destructor Documentation

BALL::VanDerWaals::VanDerWaals

(

)

BALL::VanDerWaals::VanDerWaals

(

ScoringFunction &

sf

)

BALL::VanDerWaals::VanDerWaals

(

ScoringComponent &

sc

)

virtual BALL::VanDerWaals::~VanDerWaals ( )

virtual

Member Function Documentation

virtual double BALL::VanDerWaals::calculateScore ( )

virtual

Reimplemented from BALL::ScoringComponent.

double BALL::VanDerWaals::calculateVDWEnergy_ ( const AtomVector &  atom_vector )

private

virtual void BALL::VanDerWaals::clear ( )

virtual

Reimplemented from BALL::ScoringComponent.

Size BALL::VanDerWaals::createNonBondedList_ ( const ForceField::PairVector &  atom_pair_vector )

private

virtual bool BALL::VanDerWaals::setup ( )

virtual

Reimplemented from BALL::ScoringComponent.

Member Data Documentation

Size BALL::VanDerWaals::calculation_method_

private

Definition at line 145 of file vanDerWaals.h.

float BALL::VanDerWaals::cut_off_vdw_

private

Definition at line 151 of file vanDerWaals.h.

float BALL::VanDerWaals::cut_on_vdw_

private

Definition at line 148 of file vanDerWaals.h.

Potential1210 BALL::VanDerWaals::hydrogen_bond_

protected

Definition at line 130 of file vanDerWaals.h.

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

protected

Definition at line 124 of file vanDerWaals.h.

LennardJones BALL::VanDerWaals::lennard_jones_

protected

Definition at line 129 of file vanDerWaals.h.

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

protected

Definition at line 121 of file vanDerWaals.h.

Size BALL::VanDerWaals::number_of_1_4_

protected

Definition at line 126 of file vanDerWaals.h.

Size BALL::VanDerWaals::number_of_h_bonds_

protected

Definition at line 127 of file vanDerWaals.h.

float BALL::VanDerWaals::scaling_vdw_1_4_

private

Definition at line 154 of file vanDerWaals.h.

float BALL::VanDerWaals::softening_limit_

private

Definition at line 157 of file vanDerWaals.h.

Molecule* BALL::VanDerWaals::vdw_ligand_

private

Definition at line 142 of file vanDerWaals.h.

Molecule* BALL::VanDerWaals::vdw_receptor_

private

Definition at line 139 of file vanDerWaals.h.

System BALL::VanDerWaals::vdw_system_

private

Definition at line 136 of file vanDerWaals.h.

Size BALL::VanDerWaals::verbosity_

private

Definition at line 168 of file vanDerWaals.h.