buriedPolar.h

// $Id: buriedPolar.h,v 1.3 2006/05/21 17:38:39 anker Exp $
// Molecular Mechanics: Fresno force field, lipophilic component

#ifndef BALL_SCORING_COMPONENTS_FRESNOBURIEDPOLAR_H
#define BALL_SCORING_COMPONENTS_FRESNOBURIEDPOLAR_H

#include <BALL/SCORING/COMMON/scoringComponent.h>

namespace BALL
{

  class BuriedPolar
    : public ScoringComponent
  {

    public:

    struct Option
    {

      static const char* BP_R1_OFFSET;

      static const char* BP_R2_OFFSET;

      static const char* CREATE_INTERACTIONS_FILE;

      static const char* VERBOSITY;

    };

    struct Default
    {

      static const float BP_R1_OFFSET;

      static const float BP_R2_OFFSET;

      static const bool CREATE_INTERACTIONS_FILE;

      static const Size VERBOSITY;

    };




    BuriedPolar()
      ;

    BuriedPolar(ScoringFunction& sf)
      ;

    BuriedPolar(const BuriedPolar& bp)
      ;

    virtual ~BuriedPolar()
      ;



    const BuriedPolar& operator = (const BuriedPolar& bp)
      ;

    virtual void clear()
      ;



    bool operator == (const BuriedPolar& bp) const
      ;



    virtual bool setup()
      ;



    virtual double calculateScore()
      ;


    private:

    /*_
    */
    std::vector< std::pair<const Atom*, const Atom*> > possible_buried_polar_interactions_;

    /*_
    */
    double factor_;

    /*_ This length will be added to the sum of the van-der-Waals radii for
        obtaining the lower bound of the scoring function.
    */
    double r1_offset_;

    /*_ The upper bound for the scoring function is obtained by adding a
        constant to the lower bound.
    */
    double r2_offset_;

    // The following two variables are only necessary if the buried polar
    // component is meant to assign its own radii. They are unused at the
    // moment.

    Molecule* bp_receptor_;

    Molecule* bp_ligand_;

    bool write_interactions_file_;

    Size verbosity_;

  };

} // namespace BALL

#endif // BALL_SCORING_COMPONENTS_FRESNOBURIEDPOLAR_H

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