evolutionaryDocking.h

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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Jan Fuhrmann, Marcel Schumann $
// ----------------------------------------------------

#ifndef BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H
#define BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H

#ifndef BALL_DATATYPE_REGULARDATA3D_H
#include <BALL/DATATYPE/regularData3D.h>
#endif

#ifndef BALL_KERNEL_SYSTEM_H
#include <BALL/KERNEL/system.h>
#endif

#ifndef BALL_DOCKING_COMMON_DOCKINGALGORITHM_H
#include <BALL/DOCKING/COMMON/dockingAlgorithm.h>
#endif

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

namespace BALL
{
  class GeneticAlgorithm;

  class DockProblem;


  class BALL_EXPORT EvolutionaryDocking : public DockingAlgorithm
    {
    public:

     struct Option
      {
  static const String MAX_ITERATIONS;
  static const String POPULATION_NUMBER;
  static const String INITIAL_POPULATION;
  static const String POPULATION;
  static const String SURVIVORS;
  static const String MUTATION_RATE;
  static const String MUTATION_SAVE;
  static const String CONV_ITERATIONS;
  static const String CONV_VALUE;
  static const String CONV_START;
  static const String BEST_NUM;
  static const char* SCORING_TYPE;
      };

      struct Default
      {
  static const int MAX_ITERATIONS;
  static const int POPULATION_NUMBER;
  static const int INITIAL_POPULATION;
  static const int POPULATION;
  static const int SURVIVORS;
  static const double MUTATION_RATE;
  static const int MUTATION_SAVE;
  static const int CONV_ITERATIONS;
  static const double CONV_VALUE;
  static const int CONV_START;
  static const int BEST_NUM;
  static const String SCORING_TYPE;
      };


  EvolutionaryDocking(System &system1, System &system2, Options& new_options);

  EvolutionaryDocking(System& receptor, System& ligand, string config_file);

      ~EvolutionaryDocking();

      virtual void setup(System& ligand, BALL::ScoringFunction* sf, Options& new_options);

      virtual void setup(System& ligand, BALL::ScoringFunction* sf);

      void setup(System& receptor, System& ligand, Options& new_options);

      void start();

      double dockLigand(AtomContainer& ligand, bool verbose = 0);

      float getProgress() const;

      bool redraw();

      Vector3& getReferenceLigandCenter();

   //   ConformationSet getConformationSet(Index total_number = 0);

      static void getDefaultOptions(Options& options);


    protected:

     // virtual const AtomContainer& getIntermediateResult_()
  //throw();

      void destroy_();

      void applyBestConformation();

      GeneticAlgorithm* ga_;

      DockProblem* dp_;

      Vector3 reference_center_;

    };
}

#endif /* BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H */