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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 BALL_DEPRECATED 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 */
BALL_DEPRECATED
#define BALL_DEPRECATED
Definition COMMON/global.h:64
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
system.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::DockProblem
Definition dockProblem.h:36
BALL::DockingAlgorithm::DockingAlgorithm
DockingAlgorithm()
BALL::DockingAlgorithm::options
Options options
Definition dockingAlgorithm.h:67
BALL::EvolutionaryDocking::redraw
bool redraw()
BALL::EvolutionaryDocking::getDefaultOptions
static void getDefaultOptions(Options &options)
BALL::EvolutionaryDocking::setup
virtual void setup(System &ligand, BALL::ScoringFunction *sf)
BALL::EvolutionaryDocking::applyBestConformation
void applyBestConformation()
BALL::EvolutionaryDocking::setup
virtual void setup(System &ligand, BALL::ScoringFunction *sf, Options &new_options)
BALL::EvolutionaryDocking::dp_
DockProblem * dp_
Definition evolutionaryDocking.h:129
BALL::EvolutionaryDocking::destroy_
void destroy_()
BALL::EvolutionaryDocking::EvolutionaryDocking
EvolutionaryDocking(System &receptor, System &ligand, string config_file)
BALL::EvolutionaryDocking::~EvolutionaryDocking
~EvolutionaryDocking()
BALL::EvolutionaryDocking::reference_center_
Vector3 reference_center_
Definition evolutionaryDocking.h:132
BALL::EvolutionaryDocking::getReferenceLigandCenter
Vector3 & getReferenceLigandCenter()
BALL::EvolutionaryDocking::ga_
GeneticAlgorithm * ga_
Definition evolutionaryDocking.h:125
BALL::EvolutionaryDocking::start
void start()
BALL::EvolutionaryDocking::setup
void setup(System &receptor, System &ligand, Options &new_options)
BALL::EvolutionaryDocking::getProgress
float getProgress() const
BALL::EvolutionaryDocking::dockLigand
double dockLigand(AtomContainer &ligand, bool verbose=0)
BALL::EvolutionaryDocking::EvolutionaryDocking
EvolutionaryDocking(System &system1, System &system2, Options &new_options)
BALL::GeneticAlgorithm
Definition geneticAlgorithm.h:24
BALL::Options
Definition options.h:48
BALL::ScoringFunction
Definition scoringFunction.h:29
BALL::String
Definition string.h:57
BALL::System
Definition KERNEL/system.h:40
dockingAlgorithm.h
BALL
Definition constants.h:13
BALL::Vector3
TVector3< float > Vector3
Definition vector3.h:1084
regularData3D.h
scoringFunction.h
BALL::EvolutionaryDocking::Default
Definition evolutionaryDocking.h:55
BALL::EvolutionaryDocking::Default::MUTATION_RATE
static const double MUTATION_RATE
Definition evolutionaryDocking.h:61
BALL::EvolutionaryDocking::Default::BEST_NUM
static const int BEST_NUM
Definition evolutionaryDocking.h:66
BALL::EvolutionaryDocking::Default::SURVIVORS
static const int SURVIVORS
Definition evolutionaryDocking.h:60
BALL::EvolutionaryDocking::Default::CONV_VALUE
static const double CONV_VALUE
Definition evolutionaryDocking.h:64
BALL::EvolutionaryDocking::Default::POPULATION_NUMBER
static const int POPULATION_NUMBER
Definition evolutionaryDocking.h:57
BALL::EvolutionaryDocking::Default::MUTATION_SAVE
static const int MUTATION_SAVE
Definition evolutionaryDocking.h:62
BALL::EvolutionaryDocking::Default::SCORING_TYPE
static const String SCORING_TYPE
Definition evolutionaryDocking.h:67
BALL::EvolutionaryDocking::Default::INITIAL_POPULATION
static const int INITIAL_POPULATION
Definition evolutionaryDocking.h:58
BALL::EvolutionaryDocking::Default::CONV_START
static const int CONV_START
Definition evolutionaryDocking.h:65
BALL::EvolutionaryDocking::Default::MAX_ITERATIONS
static const int MAX_ITERATIONS
Definition evolutionaryDocking.h:56
BALL::EvolutionaryDocking::Default::POPULATION
static const int POPULATION
Definition evolutionaryDocking.h:59
BALL::EvolutionaryDocking::Default::CONV_ITERATIONS
static const int CONV_ITERATIONS
Definition evolutionaryDocking.h:63
BALL::EvolutionaryDocking::Option
Definition evolutionaryDocking.h:39
BALL::EvolutionaryDocking::Option::CONV_ITERATIONS
static const String CONV_ITERATIONS
Definition evolutionaryDocking.h:47
BALL::EvolutionaryDocking::Option::BEST_NUM
static const String BEST_NUM
Definition evolutionaryDocking.h:50
BALL::EvolutionaryDocking::Option::MUTATION_SAVE
static const String MUTATION_SAVE
Definition evolutionaryDocking.h:46
BALL::EvolutionaryDocking::Option::POPULATION
static const String POPULATION
Definition evolutionaryDocking.h:43
BALL::EvolutionaryDocking::Option::SURVIVORS
static const String SURVIVORS
Definition evolutionaryDocking.h:44
BALL::EvolutionaryDocking::Option::CONV_VALUE
static const String CONV_VALUE
Definition evolutionaryDocking.h:48
BALL::EvolutionaryDocking::Option::POPULATION_NUMBER
static const String POPULATION_NUMBER
Definition evolutionaryDocking.h:41
BALL::EvolutionaryDocking::Option::MAX_ITERATIONS
static const String MAX_ITERATIONS
Definition evolutionaryDocking.h:40
BALL::EvolutionaryDocking::Option::SCORING_TYPE
static const char * SCORING_TYPE
Definition evolutionaryDocking.h:51
BALL::EvolutionaryDocking::Option::MUTATION_RATE
static const String MUTATION_RATE
Definition evolutionaryDocking.h:45
BALL::EvolutionaryDocking::Option::CONV_START
static const String CONV_START
Definition evolutionaryDocking.h:49
BALL::EvolutionaryDocking::Option::INITIAL_POPULATION
static const String INITIAL_POPULATION
Definition evolutionaryDocking.h:42