BALL::PolarSolvation Class Reference

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

Inheritance diagram for BALL::PolarSolvation:

List of all members.

Classes
struct	Default
struct	Option
Public Types
enum	CalculationMethod {   CALCULATION__FRESNO, CALCULATION__FULL_SLICK, CALCULATION__FULL_CYCLE, CALCULATION__FULL_CYCLE_FOCUSED,   CALCULATION__COULOMB, CALCULATION__EEF1 }
enum	AveragingMethod { AVERAGING__NONE, AVERAGING__STATIC, AVERAGING__RANDOM_FACTOR, AVERAGING__RANDOM }
Public Member Functions
Constructors and Destructors
	PolarSolvation ()
	PolarSolvation (ScoringFunction &sf)
	PolarSolvation (const PolarSolvation &fhb)
virtual	~PolarSolvation ()
Assignment
const PolarSolvation &	operator= (const PolarSolvation &fr)
virtual void	clear ()
Predicates.
bool	operator== (const PolarSolvation &fr) const
Setup Methods
virtual bool	setup ()
Accessors
virtual double	calculateScore ()
Private Member Functions
bool	computeEnergyDifference_ (System &system, float &energy)
bool	computeESEnergy_ (System &system, float &energy)
float	computeESInteractionEnergy_ (const Molecule &molecule, const HashMap< const Atom *, float > &p_hash)
bool	computeFullCycle_ (System &system, Molecule &protein, Molecule &ligand, float &energy)
Vector3	permuteComponentSigns_ (Vector3 vector, Size permutation)
Size	uniteAtoms_ (Molecule &molecule)
Private Attributes
Molecule	desolv_protein_
Molecule	desolv_ligand_
Size	calculation_method_
Size	averaging_
bool	unite_atoms_
Size	verbosity_
FDPB	fdpb_
GeneralizedBornModel	gbm_
bool	use_gb_
float	spacing_
float	bulk_water_dc_
float	vacuum_dc_

---

Detailed Description

SLICK polar solvation component \ { Definition:} {BALL/SCORING/COMPONENTS/polarSolvation.h}

---

Member Enumeration Documentation

enum BALL::PolarSolvation::AveragingMethod

Averaging methods for model 0 and 3

Enumerator:

AVERAGING__NONE	No averaging will be done.
AVERAGING__STATIC	The grid of the PB solver will be translated a bit in every direction by a fixed length.
AVERAGING__RANDOM_FACTOR	The grid of the PB solver will be translated a bit in every direction by a randomly chosen length (not yet implemented).
AVERAGING__RANDOM	The grid of the PB solver will be translated a bit in every direction by different randomly chosen length (not yet implemented).

enum BALL::PolarSolvation::CalculationMethod

Enumerator:

CALCULATION__FRESNO
CALCULATION__FULL_SLICK
CALCULATION__FULL_CYCLE
CALCULATION__FULL_CYCLE_FOCUSED
CALCULATION__COULOMB
CALCULATION__EEF1

---

Constructor & Destructor Documentation

BALL::PolarSolvation::PolarSolvation

(

)

Default constructor.

BALL::PolarSolvation::PolarSolvation

(

ScoringFunction &

sf

)

Constructor.

BALL::PolarSolvation::PolarSolvation

(

const PolarSolvation &

fhb

)

Copy constructor

virtual BALL::PolarSolvation::~PolarSolvation

(

)

[virtual]

Destructor.

---

Member Function Documentation

virtual double BALL::PolarSolvation::calculateScore

(

)

[virtual]

Calculates and returns the component's energy.

Reimplemented from BALL::ScoringComponent.

virtual void BALL::PolarSolvation::clear

(

)

[virtual]

Clear method.

Reimplemented from BALL::ScoringComponent.

bool BALL::PolarSolvation::computeEnergyDifference_	(	System &	system,
		float &	energy
	)			[private]

bool BALL::PolarSolvation::computeESEnergy_	(	System &	system,
		float &	energy
	)			[private]

float BALL::PolarSolvation::computeESInteractionEnergy_	(	const Molecule &	molecule,
		const HashMap< const Atom *, float > &	p_hash
	)			[private]

bool BALL::PolarSolvation::computeFullCycle_	(	System &	system,
		Molecule &	protein,
		Molecule &	ligand,
		float &	energy
	)			[private]

const PolarSolvation& BALL::PolarSolvation::operator=

(

const PolarSolvation &

fr

)

Assignment.

bool BALL::PolarSolvation::operator==

(

const PolarSolvation &

fr

)

const

Vector3 BALL::PolarSolvation::permuteComponentSigns_	(	Vector3	vector,
		Size	permutation
	)			[private]

virtual bool BALL::PolarSolvation::setup

(

)

[virtual]

Setup method.

Reimplemented from BALL::ScoringComponent.

Size BALL::PolarSolvation::uniteAtoms_

(

Molecule &

molecule

)

[private]

---

Member Data Documentation

Size BALL::PolarSolvation::averaging_ [private]

float BALL::PolarSolvation::bulk_water_dc_ [private]

Size BALL::PolarSolvation::calculation_method_ [private]

Molecule BALL::PolarSolvation::desolv_ligand_ [private]

Molecule BALL::PolarSolvation::desolv_protein_ [private]

FDPB BALL::PolarSolvation::fdpb_ [private]

GeneralizedBornModel BALL::PolarSolvation::gbm_ [private]

float BALL::PolarSolvation::spacing_ [private]

bool BALL::PolarSolvation::unite_atoms_ [private]

bool BALL::PolarSolvation::use_gb_ [private]

float BALL::PolarSolvation::vacuum_dc_ [private]

Size BALL::PolarSolvation::verbosity_ [private]