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vanDerWaalsSlick.h
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// $Id: vanDerWaals.h,v 1.3 2006/05/21 17:35:26 anker Exp $
// Molecular Mechanics: SLICK force field, modified van-der-Waals term
#ifndef BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
#define BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
#include <BALL/SCORING/COMMON/scoringComponent.h>
#include <BALL/MOLMEC/AMBER/amberNonBonded.h>
#include <BALL/MOLMEC/PARAMETER/lennardJones.h>
#include <BALL/MOLMEC/COMMON/atomVector.h>
#include <BALL/MOLMEC/COMMON/forceField.h>
namespace BALL
{
class BALL_EXPORT VanDerWaalsSlick : public ScoringComponent
{
public:
enum CalculationMethod
{
CALCULATION__FULL_LJ_POTENTIAL,
CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE,
CALCULATION__SOFTENED_LJ_POTENTIAL_LOG
};
struct BALL_EXPORT Option
{
static const String VERBOSITY;
static const String VDW_METHOD;
static const String VDW_CUT_ON;
static const String VDW_CUT_OFF;
static const String VDW_SOFTENING_LIMIT;
static const String LENNARD_JONES_FILE;
};
struct Default
{
static const Size VERBOSITY;
static const Size VDW_METHOD;
static const float VDW_CUT_ON;
static const float VDW_CUT_OFF;
static const float VDW_SOFTENING_LIMIT;
static const String LENNARD_JONES_FILE;
};
VanDerWaalsSlick()
;
VanDerWaalsSlick(ScoringFunction& sf)
;
VanDerWaalsSlick(ScoringComponent& sc)
;
virtual ~VanDerWaalsSlick()
;
virtual void clear()
;
virtual bool setup();
void update(const vector<std::pair<Atom*, Atom*> >& /* pair_vector */);
virtual double updateScore();
protected:
//_
std::vector<LennardJones::Data> non_bonded_;
//_
std::vector<bool> is_hydrogen_bond_;
Size number_of_1_4_;
Size number_of_h_bonds_;
LennardJones lennard_jones_;
Potential1210 hydrogen_bond_;
private:
//_
System vdw_system_;
//_
Molecule* vdw_receptor_;
//_
Molecule* vdw_ligand_;
//_
Size calculation_method_;
//_
float cut_on_vdw_;
//_
float cut_off_vdw_;
//_
float scaling_vdw_1_4_;
//_
float softening_limit_;
//_
double calculateVDWEnergy_(const AtomVector& atom_vector)
;
//_
Size createNonBondedList_(const ForceField::PairVector& atom_pair_vector)
;
//_ Verbosity of the code
Size verbosity_;
};
}
#endif // BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
amberNonBonded.h
atomVector.h
BALL::AtomVector
Definition atomVector.h:31
BALL::ForceField::PairVector
std::vector< std::pair< Atom *, Atom * > > PairVector
Definition forceField.h:99
BALL::LennardJones
Definition lennardJones.h:44
BALL::Molecule
Definition molecule.h:31
BALL::Potential1210
Definition potential1210.h:27
BALL::ScoringComponent::ScoringComponent
ScoringComponent()
BALL::ScoringFunction
Definition scoringFunction.h:29
BALL::String
Definition string.h:57
BALL::System
Definition KERNEL/system.h:40
BALL::VanDerWaalsSlick::update
void update(const vector< std::pair< Atom *, Atom * > > &)
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick()
BALL::VanDerWaalsSlick::setup
virtual bool setup()
BALL::VanDerWaalsSlick::number_of_h_bonds_
Size number_of_h_bonds_
Definition vanDerWaalsSlick.h:129
BALL::VanDerWaalsSlick::non_bonded_
std::vector< LennardJones::Data > non_bonded_
Definition vanDerWaalsSlick.h:123
BALL::VanDerWaalsSlick::clear
virtual void clear()
BALL::VanDerWaalsSlick::is_hydrogen_bond_
std::vector< bool > is_hydrogen_bond_
Definition vanDerWaalsSlick.h:126
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick(ScoringFunction &sf)
BALL::VanDerWaalsSlick::CalculationMethod
CalculationMethod
Definition vanDerWaalsSlick.h:24
BALL::VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG
@ CALCULATION__SOFTENED_LJ_POTENTIAL_LOG
Log-Softened Lennard-Jones 6-12 potential.
Definition vanDerWaalsSlick.h:32
BALL::VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE
@ CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE
Softened Lennard-Jones 6-12 potential (simple cut).
Definition vanDerWaalsSlick.h:29
BALL::VanDerWaalsSlick::CALCULATION__FULL_LJ_POTENTIAL
@ CALCULATION__FULL_LJ_POTENTIAL
Full Lennard-Jones 6-12 potential.
Definition vanDerWaalsSlick.h:26
BALL::VanDerWaalsSlick::number_of_1_4_
Size number_of_1_4_
Definition vanDerWaalsSlick.h:128
BALL::VanDerWaalsSlick::lennard_jones_
LennardJones lennard_jones_
Definition vanDerWaalsSlick.h:131
BALL::VanDerWaalsSlick::~VanDerWaalsSlick
virtual ~VanDerWaalsSlick()
BALL::VanDerWaalsSlick::hydrogen_bond_
Potential1210 hydrogen_bond_
Definition vanDerWaalsSlick.h:132
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick(ScoringComponent &sc)
BALL::VanDerWaalsSlick::updateScore
virtual double updateScore()
forceField.h
lennardJones.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
scoringComponent.h
BALL::VanDerWaalsSlick::Default
Definition vanDerWaalsSlick.h:63
BALL::VanDerWaalsSlick::Default::VDW_CUT_OFF
static const float VDW_CUT_OFF
Definition vanDerWaalsSlick.h:75
BALL::VanDerWaalsSlick::Default::LENNARD_JONES_FILE
static const String LENNARD_JONES_FILE
Definition vanDerWaalsSlick.h:81
BALL::VanDerWaalsSlick::Default::VDW_METHOD
static const Size VDW_METHOD
Definition vanDerWaalsSlick.h:69
BALL::VanDerWaalsSlick::Default::VDW_CUT_ON
static const float VDW_CUT_ON
Definition vanDerWaalsSlick.h:72
BALL::VanDerWaalsSlick::Default::VDW_SOFTENING_LIMIT
static const float VDW_SOFTENING_LIMIT
Definition vanDerWaalsSlick.h:78
BALL::VanDerWaalsSlick::Default::VERBOSITY
static const Size VERBOSITY
Definition vanDerWaalsSlick.h:66
BALL::VanDerWaalsSlick::Option
Definition vanDerWaalsSlick.h:39
BALL::VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT
static const String VDW_SOFTENING_LIMIT
Definition vanDerWaalsSlick.h:54
BALL::VanDerWaalsSlick::Option::VDW_CUT_ON
static const String VDW_CUT_ON
Definition vanDerWaalsSlick.h:48
BALL::VanDerWaalsSlick::Option::VDW_CUT_OFF
static const String VDW_CUT_OFF
Definition vanDerWaalsSlick.h:51
BALL::VanDerWaalsSlick::Option::VERBOSITY
static const String VERBOSITY
Definition vanDerWaalsSlick.h:42
BALL::VanDerWaalsSlick::Option::LENNARD_JONES_FILE
static const String LENNARD_JONES_FILE
Definition vanDerWaalsSlick.h:57
BALL::VanDerWaalsSlick::Option::VDW_METHOD
static const String VDW_METHOD
Definition vanDerWaalsSlick.h:45