scoringFunction.h

Go to the documentation of this file.

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: scoringFunction.h,v 1.2 2006/05/21 18:15:28 anker Exp $

#ifndef BALL_SCORING_COMMON_SCORINGFUNCTION_H
#define BALL_SCORING_COMMON_SCORINGFUNCTION_H

#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/options.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/SCORING/COMMON/baseFunction.h>
#include <BALL/SCORING/COMMON/scoringComponent.h>

namespace BALL
{

  class ScoringComponent;

  class ScoringFunction
  {

    public:

    struct Option
    {

      static const char* VERBOSITY;

      static const char* BASE_FUNCTION_TYPE;

    };


    struct Default
    {

      static const Size VERBOSITY;

      static const Size BASE_FUNCTION_TYPE;

    };

    ScoringFunction()
      ;

    ScoringFunction(const ScoringFunction& sf)
      ;

    ScoringFunction(Molecule& receptor, Molecule& ligand)
      ;

    ScoringFunction(Molecule& receptor, Molecule& ligand,
        const Options& options)
      ;

    virtual ~ScoringFunction()
      ;

    virtual void clear()
      ;

    ScoringFunction& operator = (const ScoringFunction& sf)
      ;

    bool setup()
      ;

    bool setup(Molecule& receptor, Molecule& ligand)
      ;

    bool setup(Molecule& receptor, Molecule& ligand, const Options& options)
      ;

    virtual bool specificSetup()
      throw(Exception::TooManyErrors);

    void setMaximumNumberOfErrors(Size nr)
      ;

    Size getMaximumNumberOfErrors() const
      ;

    void setFirstMolecule(Molecule& molecule1) 
      ;

    Molecule* getFirstMolecule() const
      ;

    void setSecondMolecule(Molecule& molecule2) 
      ;

    Molecule* getSecondMolecule() const
      ;

    void setReceptor(Molecule& receptor) 
      ;

    Molecule* getReceptor() const
      ;

    void setLigand(Molecule& ligand) 
      ;

    Molecule* getLigand() const
      ;

    void setIntercept(double intercept)
      ;

    double getIntercept() const
      ;

    void setBaseFunction(ScoringBaseFunction& base_function)
      ;

    ScoringBaseFunction* getBaseFunction() const
      ;

    void insertComponent(ScoringComponent* component, float coefficient = 1.0f)
      ;

    void removeComponent(const ScoringComponent* component)
      ;

    void removeComponent(const String& name)
      ;

    void setCoefficient(const ScoringComponent* component, float coefficient)
      ;

    void setCoefficient(const String& name, float coefficient)
      ;

    bool getCoefficient(const ScoringComponent* component,
        float& coefficient) const
      ;

    bool getCoefficient(const String& name, float& coefficient) const
      ;

    ScoringComponent* getComponent(const String& name) const
      ;

    ScoringComponent* getComponent(const Size index) const
      ;

    double calculateScore()
      ;

    const HashSet<const Atom*>& getUnassignedAtoms() const
      ;

    HashSet<const Atom*>& getUnassignedAtoms()
      ;

    Options options;


    protected:

    /*_ The first molecule of the complex, being the receptor in
        receptor/ligand complexes
      */
    Molecule* molecule1_;

    /*_ The second molecule of the complex, being the ligand in
        receptor/ligand complexes
      */
    Molecule* molecule2_;

    //_ The name of the scoring function
    String name_;

    //_ The overall score of the scoring function
    double score_;

    //_ The intercept necessary for calculating the score
    double intercept_;

    /*_ The base funcion for scoring simple terms
    */
    ScoringBaseFunction* base_function_;

    /*_ A list of components comprising the scoring function, along with
        the coefficients for each term necessary for calculating the final
        score.
    */
    std::vector< std::pair<ScoringComponent*, float> > components_;

    //_ Atoms, for which the setup of the force field fails
    HashSet<const Atom*> unassigned_atoms_;

    //_ Max number of unassigned atoms
    Size max_number_of_errors_;

    //_ Actual number of countde errors
    Size number_of_errors_;


  };

} // namespace BALL

#endif // BALL_SCORING_COMMON_SCORINGFUNCTION_H

---