/usr/include/BALL/DOCKING/GENETICDOCK/evolutionaryDocking.h is in libball1.4-dev 1.4.3~beta1-3.
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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 EvolutionaryDocking
This class is derived from class DockingAlgorithm.
small ligand docking algorithm via a genetic Algorithm.
*/
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);
/** destructor
*/
~EvolutionaryDocking();
/** The setup routines.
*/
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);
/** Start the main loop of the algorithm.
*/
void start();
/** docks the given ligand and returns the score for the best conformation */
double dockLigand(AtomContainer& ligand, bool verbose = 0);
/** return the overall docking progress as a percentage
*/
float getProgress() const;
/** true if new ligand position has to be drawn
*/
bool redraw();
Vector3& getReferenceLigandCenter();
/** return ranked conformations.
*/
// ConformationSet getConformationSet(Index total_number = 0);
/** stores the default options of this algorithms in the given Option object */
static void getDefaultOptions(Options& options);
protected:
// virtual const AtomContainer& getIntermediateResult_()
//throw();
/** Free all allocated memory and destroys the options and results
*/
void destroy_();
void applyBestConformation();
/** optimization method
*/
GeneticAlgorithm* ga_;
/** mapping class for docking
*/
DockProblem* dp_;
/** the geometrical center of the reference ligand */
Vector3 reference_center_;
};
}
#endif /* BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H */
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