BALL::PolarSolvation Class Reference

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

Inheritance diagram for BALL::PolarSolvation:

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 ()
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

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_

Additional Inherited Members
Protected Attributes inherited from BALL::ScoringComponent
ScoringFunction *	scoring_function_
double	score_

Detailed Description

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

Definition at line 17 of file 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).

Definition at line 56 of file polarSolvation.h.

enum BALL::PolarSolvation::CalculationMethod

Enumerator
CALCULATION__FRESNO
CALCULATION__FULL_SLICK
CALCULATION__FULL_CYCLE
CALCULATION__FULL_CYCLE_FOCUSED
CALCULATION__COULOMB
CALCULATION__EEF1

Definition at line 25 of file polarSolvation.h.

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

Definition at line 266 of file polarSolvation.h.

float BALL::PolarSolvation::bulk_water_dc_

private

Definition at line 294 of file polarSolvation.h.

Size BALL::PolarSolvation::calculation_method_

private

Definition at line 262 of file polarSolvation.h.

Molecule BALL::PolarSolvation::desolv_ligand_

private

Definition at line 258 of file polarSolvation.h.

Molecule BALL::PolarSolvation::desolv_protein_

private

Definition at line 254 of file polarSolvation.h.

FDPB BALL::PolarSolvation::fdpb_

private

Definition at line 278 of file polarSolvation.h.

GeneralizedBornModel BALL::PolarSolvation::gbm_

private

Definition at line 282 of file polarSolvation.h.

float BALL::PolarSolvation::spacing_

private

Definition at line 290 of file polarSolvation.h.

bool BALL::PolarSolvation::unite_atoms_

private

Definition at line 270 of file polarSolvation.h.

bool BALL::PolarSolvation::use_gb_

private

Definition at line 286 of file polarSolvation.h.

float BALL::PolarSolvation::vacuum_dc_

private

Definition at line 298 of file polarSolvation.h.

Size BALL::PolarSolvation::verbosity_

private

Definition at line 274 of file polarSolvation.h.