vanDerWaals.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_VANDERWAALS_H
#define BALL_SCORING_COMPONENTS_VANDERWAALS_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 VanDerWaals
    : public ScoringComponent
  {

    public:

    enum CalculationMethod
    {
      CALCULATION__FULL_LJ_POTENTIAL,

      CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE,

      CALCULATION__SOFTENED_LJ_POTENTIAL_LOG

    };


    struct 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;

    };



    VanDerWaals()
      ;

    VanDerWaals(ScoringFunction& sf)
      ;

    VanDerWaals(ScoringComponent& sc)
      ;

    virtual ~VanDerWaals()
      ;

    virtual void clear()
      ;

    virtual bool setup()
      ;

    virtual double calculateScore()
      ;


    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_VANDERWAALS_H