BALL  1.5.0
Protected Attributes | List of all members
BALL::CharmmNonBonded Class Reference

#include <BALL/MOLMEC/CHARMM/charmmNonBonded.h>

Inheritance diagram for BALL::CharmmNonBonded:
BALL::ForceFieldComponent BALL::ScoringComponent

Public Member Functions

Constructors and Destructors
 CharmmNonBonded ()
 
 CharmmNonBonded (ForceField &force_field)
 
 CharmmNonBonded (const CharmmNonBonded &charmm_non_bonded)
 
virtual ~CharmmNonBonded ()
 
Assignment
const CharmmNonBondedoperator= (const CharmmNonBonded &charmm_non_bonded)
 
virtual void clear ()
 
Predicates
bool operator== (const CharmmNonBonded &charmm_non_bonded)
 
Setup Methods
virtual bool setup ()
 
Accessors
virtual double updateEnergy ()
 
virtual void updateForces ()
 
virtual double getElectrostaticEnergy () const
 
virtual double getVdwEnergy () const
 
virtual double getSolvationEnergy () const
 
Neighbourhood and Parameter calculations
virtual MolmecSupport::PairListAlgorithmType determineMethodOfAtomPairGeneration ()
 
virtual void buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom *, Atom *> > &atom_vector)
 
- Public Member Functions inherited from BALL::ForceFieldComponent
 ForceFieldComponent ()
 
 ForceFieldComponent (ForceField &force_field)
 
 ForceFieldComponent (const ForceFieldComponent &force_field_component)
 
virtual ~ForceFieldComponent ()
 
ForceFieldgetForceField () const
 
void setForceField (ForceField &force_field)
 
void setName (const String &name)
 
String getName () const
 
bool isEnabled () const
 
void setEnabled (bool state)
 
virtual double getEnergy () const
 
virtual void update ()
 
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 ()
 
ScoringFunctiongetScoringFunction () const
 
void setScoringFunction (ScoringFunction &sf)
 
String getName () const
 
void setName (const String &name)
 
const StringgetTypeName ()
 
double getRawScore () const
 
double getScaledScore () const
 
virtual void update (const vector< std::pair< Atom *, Atom *> > &pair_vector)
 
virtual void setLigandIntraMolecular (bool b)
 
bool isLigandIntraMolecular ()
 
bool isGridable ()
 
bool isAtomPairwise ()
 
void setCoefficient (const double &coeff)
 
const doublegetCoefficient ()
 
void setNormalizationParameters (double stddev, double mean)
 
void getNormalizationParameters (double &stddev, double &mean)
 
bool isEnabled ()
 
void enable ()
 
void disable ()
 

Protected Attributes

double electrostatic_energy_
 
double vdw_energy_
 
double solvation_energy_
 
- Protected Attributes inherited from BALL::ForceFieldComponent
ForceFieldforce_field_
 
double energy_
 
- Protected Attributes inherited from BALL::ScoringComponent
bool ligand_intra_molecular_
 
bool gridable_
 
bool atom_pairwise_
 
ScoringFunctionscoring_function_
 
ScoringBaseFunctionbase_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

Charmm NonBonded component. This force field component implements the non-bonded interactions in the CHARMM force field: van-der-Waals interaction, electrostatics, and solvation (in EEF1 only).

Definition at line 45 of file charmmNonBonded.h.

Constructor & Destructor Documentation

◆ CharmmNonBonded() [1/3]

BALL::CharmmNonBonded::CharmmNonBonded ( )

Default constructor.

◆ CharmmNonBonded() [2/3]

BALL::CharmmNonBonded::CharmmNonBonded ( ForceField force_field)

Constructor.

◆ CharmmNonBonded() [3/3]

BALL::CharmmNonBonded::CharmmNonBonded ( const CharmmNonBonded charmm_non_bonded)

Copy constructor

◆ ~CharmmNonBonded()

virtual BALL::CharmmNonBonded::~CharmmNonBonded ( )
virtual

Destructor.

Member Function Documentation

◆ buildVectorOfNonBondedAtomPairs()

virtual void BALL::CharmmNonBonded::buildVectorOfNonBondedAtomPairs ( const std::vector< std::pair< Atom *, Atom *> > &  atom_vector)
virtual

Build a vector of non-bonded atom pairs with the vdw parameters

Exceptions
BALL::Exception::TooManyErrors

◆ clear()

virtual void BALL::CharmmNonBonded::clear ( )
virtual

Clear method

Reimplemented from BALL::ScoringComponent.

◆ determineMethodOfAtomPairGeneration()

virtual MolmecSupport::PairListAlgorithmType BALL::CharmmNonBonded::determineMethodOfAtomPairGeneration ( )
virtual

Computes the most efficient way to calculate the non-bonded atom pairs

◆ getElectrostaticEnergy()

virtual double BALL::CharmmNonBonded::getElectrostaticEnergy ( ) const
virtual

Return the electrostatic energy.

◆ getSolvationEnergy()

virtual double BALL::CharmmNonBonded::getSolvationEnergy ( ) const
virtual

Return the solvation energy.

◆ getVdwEnergy()

virtual double BALL::CharmmNonBonded::getVdwEnergy ( ) const
virtual

Return the Van-der-Waals energy.

◆ operator=()

const CharmmNonBonded& BALL::CharmmNonBonded::operator= ( const CharmmNonBonded charmm_non_bonded)

Assignment operator

◆ operator==()

bool BALL::CharmmNonBonded::operator== ( const CharmmNonBonded charmm_non_bonded)

Equality operator

◆ setup()

virtual bool BALL::CharmmNonBonded::setup ( )
virtual

Setup method.

Exceptions
BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

◆ updateEnergy()

virtual double BALL::CharmmNonBonded::updateEnergy ( )
virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

◆ updateForces()

virtual void BALL::CharmmNonBonded::updateForces ( )
virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

◆ electrostatic_energy_

double BALL::CharmmNonBonded::electrostatic_energy_
protected

Definition at line 172 of file charmmNonBonded.h.

◆ solvation_energy_

double BALL::CharmmNonBonded::solvation_energy_
protected

Definition at line 180 of file charmmNonBonded.h.

◆ vdw_energy_

double BALL::CharmmNonBonded::vdw_energy_
protected

Definition at line 176 of file charmmNonBonded.h.