BALL  1.5.0
evolutionaryDocking.h
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1 // ----------------------------------------------------
2 // $Maintainer: Marcel Schumann $
3 // $Authors: Jan Fuhrmann, Marcel Schumann $
4 // ----------------------------------------------------
5 
6 #ifndef BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H
7 #define BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H
8 
9 #ifndef BALL_DATATYPE_REGULARDATA3D_H
11 #endif
12 
13 #ifndef BALL_KERNEL_SYSTEM_H
14 # include <BALL/KERNEL/system.h>
15 #endif
16 
17 #ifndef BALL_DOCKING_COMMON_DOCKINGALGORITHM_H
19 #endif
20 
22 
23 namespace BALL
24 {
25  class GeneticAlgorithm;
26 
27  class DockProblem;
28 
35  {
36  public:
37 
38  struct Option
39  {
40  static const String MAX_ITERATIONS;
41  static const String POPULATION_NUMBER;
42  static const String INITIAL_POPULATION;
43  static const String POPULATION;
44  static const String SURVIVORS;
45  static const String MUTATION_RATE;
46  static const String MUTATION_SAVE;
47  static const String CONV_ITERATIONS;
48  static const String CONV_VALUE;
49  static const String CONV_START;
50  static const String BEST_NUM;
51  static const char *SCORING_TYPE;
52  };
53 
54  struct Default
55  {
56  static const int MAX_ITERATIONS;
57  static const int POPULATION_NUMBER;
58  static const int INITIAL_POPULATION;
59  static const int POPULATION;
60  static const int SURVIVORS;
61  static const double MUTATION_RATE;
62  static const int MUTATION_SAVE;
63  static const int CONV_ITERATIONS;
64  static const double CONV_VALUE;
65  static const int CONV_START;
66  static const int BEST_NUM;
67  static const String SCORING_TYPE;
68  };
69 
70 
71  EvolutionaryDocking(System& system1, System& system2, Options& new_options);
72 
73  EvolutionaryDocking(System& receptor, System& ligand, string config_file);
74 
78 
81  virtual void setup(System & ligand, BALL::ScoringFunction * sf, Options & new_options);
82 
83  virtual void setup(System & ligand, BALL::ScoringFunction * sf);
84 
85  void setup(System & receptor, System & ligand, Options & new_options);
86 
89  void start();
90 
92  double dockLigand(AtomContainer &ligand, bool verbose = 0);
93 
96  float getProgress() const;
97 
100  bool redraw();
101 
103 
106  // ConformationSet getConformationSet(Index total_number = 0);
107 
109  static void getDefaultOptions(Options & options);
110 
111 
112  protected:
113 
114  // virtual const AtomContainer& getIntermediateResult_()
115  //throw();
116 
119  void destroy_();
120 
122 
126 
130 
133 
134  };
135 }
136 
137 #endif /* BALL_DOCKING_GENETICDOCK_EVOLUTIONARYDOCKING_H */
BALL::EvolutionaryDocking::Option::POPULATION_NUMBER
static const String POPULATION_NUMBER
Definition: evolutionaryDocking.h:41
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
BALL::EvolutionaryDocking::Default::CONV_START
static const int CONV_START
Definition: evolutionaryDocking.h:65
BALL::EvolutionaryDocking::Option::MUTATION_SAVE
static const String MUTATION_SAVE
Definition: evolutionaryDocking.h:46
BALL::EvolutionaryDocking::setup
virtual void setup(System &ligand, BALL::ScoringFunction *sf)
dockingAlgorithm.h
BALL::Options
Definition: options.h:48
BALL::EvolutionaryDocking::applyBestConformation
void applyBestConformation()
BALL::EvolutionaryDocking::EvolutionaryDocking
EvolutionaryDocking(System &system1, System &system2, Options &new_options)
BALL::EvolutionaryDocking::Option::CONV_START
static const String CONV_START
Definition: evolutionaryDocking.h:49
BALL::EvolutionaryDocking::~EvolutionaryDocking
~EvolutionaryDocking()
BALL::EvolutionaryDocking::Option
Definition: evolutionaryDocking.h:39
BALL::AtomContainer
Definition: atomContainer.h:32
BALL::System
Definition: KERNEL/system.h:40
BALL::EvolutionaryDocking::setup
void setup(System &receptor, System &ligand, Options &new_options)
BALL::EvolutionaryDocking::Option::CONV_ITERATIONS
static const String CONV_ITERATIONS
Definition: evolutionaryDocking.h:47
BALL::EvolutionaryDocking::getReferenceLigandCenter
Vector3 & getReferenceLigandCenter()
BALL::EvolutionaryDocking::Default::POPULATION_NUMBER
static const int POPULATION_NUMBER
Definition: evolutionaryDocking.h:57
BALL::EvolutionaryDocking::setup
virtual void setup(System &ligand, BALL::ScoringFunction *sf, Options &new_options)
BALL::EvolutionaryDocking::redraw
bool redraw()
BALL::String
Definition: string.h:57
BALL::EvolutionaryDocking::Option::SCORING_TYPE
static const char * SCORING_TYPE
Definition: evolutionaryDocking.h:51
BALL
Definition: constants.h:13
BALL::EvolutionaryDocking::Default::MAX_ITERATIONS
static const int MAX_ITERATIONS
Definition: evolutionaryDocking.h:56
BALL::EvolutionaryDocking
Definition: evolutionaryDocking.h:35
BALL::EvolutionaryDocking::Option::SURVIVORS
static const String SURVIVORS
Definition: evolutionaryDocking.h:44
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::MUTATION_SAVE
static const int MUTATION_SAVE
Definition: evolutionaryDocking.h:62
BALL::EvolutionaryDocking::Default
Definition: evolutionaryDocking.h:55
BALL::DockingAlgorithm
Definition: dockingAlgorithm.h:46
BALL::EvolutionaryDocking::start
void start()
BALL::TVector3< float >
BALL::DockProblem
Definition: dockProblem.h:36
BALL::EvolutionaryDocking::Default::SCORING_TYPE
static const String SCORING_TYPE
Definition: evolutionaryDocking.h:67
BALL::EvolutionaryDocking::Option::INITIAL_POPULATION
static const String INITIAL_POPULATION
Definition: evolutionaryDocking.h:42
BALL::EvolutionaryDocking::Option::BEST_NUM
static const String BEST_NUM
Definition: evolutionaryDocking.h:50
BALL::EvolutionaryDocking::reference_center_
Vector3 reference_center_
Definition: evolutionaryDocking.h:132
BALL::EvolutionaryDocking::ga_
GeneticAlgorithm * ga_
Definition: evolutionaryDocking.h:125
BALL::EvolutionaryDocking::Default::BEST_NUM
static const int BEST_NUM
Definition: evolutionaryDocking.h:66
BALL::EvolutionaryDocking::Default::MUTATION_RATE
static const double MUTATION_RATE
Definition: evolutionaryDocking.h:61
BALL::EvolutionaryDocking::EvolutionaryDocking
EvolutionaryDocking(System &receptor, System &ligand, string config_file)
BALL::EvolutionaryDocking::dockLigand
double dockLigand(AtomContainer &ligand, bool verbose=0)
scoringFunction.h
BALL::EvolutionaryDocking::Option::MUTATION_RATE
static const String MUTATION_RATE
Definition: evolutionaryDocking.h:45
BALL::EvolutionaryDocking::Option::CONV_VALUE
static const String CONV_VALUE
Definition: evolutionaryDocking.h:48
BALL::EvolutionaryDocking::Option::MAX_ITERATIONS
static const String MAX_ITERATIONS
Definition: evolutionaryDocking.h:40
TEST::verbose
int verbose
Definition: classTest.h:18
BALL::EvolutionaryDocking::Default::POPULATION
static const int POPULATION
Definition: evolutionaryDocking.h:59
system.h
BALL::EvolutionaryDocking::Default::CONV_ITERATIONS
static const int CONV_ITERATIONS
Definition: evolutionaryDocking.h:63
BALL::GeneticAlgorithm
Definition: geneticAlgorithm.h:24
BALL::EvolutionaryDocking::getProgress
float getProgress() const
regularData3D.h
BALL::EvolutionaryDocking::dp_
DockProblem * dp_
Definition: evolutionaryDocking.h:129
BALL::EvolutionaryDocking::Default::INITIAL_POPULATION
static const int INITIAL_POPULATION
Definition: evolutionaryDocking.h:58
BALL::EvolutionaryDocking::getDefaultOptions
static void getDefaultOptions(Options &options)
BALL::EvolutionaryDocking::Option::POPULATION
static const String POPULATION
Definition: evolutionaryDocking.h:43
BALL::EvolutionaryDocking::destroy_
void destroy_()
BALL_DEPRECATED
#define BALL_DEPRECATED
Definition: COMMON/global.h:64
BALL::ScoringFunction
Definition: scoringFunction.h:29