BALL  1.4.1
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BALL::PolarSolvation Class Reference

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

Inheritance diagram for BALL::PolarSolvation:
BALL::ScoringComponent

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 PolarSolvationoperator= (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 ()
ScoringFunctiongetScoringFunction () 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
ScoringFunctionscoring_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

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.

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.