BALL  1.4.1
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BALL::VanDerWaals Class Reference

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

Inheritance diagram for BALL::VanDerWaals:
BALL::ScoringComponent

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 ()
ScoringFunctiongetScoringFunction () const
void setScoringFunction (ScoringFunction &sf)
String getName () const
void setName (const String &name)
virtual double getScore () const

Protected Attributes

std::vector< LennardJones::Datanon_bonded_
std::vector< boolis_hydrogen_bond_
Size number_of_1_4_
Size number_of_h_bonds_
LennardJones lennard_jones_
Potential1210 hydrogen_bond_
- Protected Attributes inherited from BALL::ScoringComponent
ScoringFunctionscoring_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_
Moleculevdw_receptor_
Moleculevdw_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

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.