BALL 1.5.0
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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
23namespace BALL
24{
25 class GeneticAlgorithm;
26
27 class DockProblem;
28
35 {
36 public:
37
38 struct Option
39 {
40 static const String MAX_ITERATIONS;
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 */
static void getDefaultOptions(Options &options)
virtual void setup(System &ligand, BALL::ScoringFunction *sf)
virtual void setup(System &ligand, BALL::ScoringFunction *sf, Options &new_options)
EvolutionaryDocking(System &receptor, System &ligand, string config_file)
Vector3 & getReferenceLigandCenter()
void setup(System &receptor, System &ligand, Options &new_options)
double dockLigand(AtomContainer &ligand, bool verbose=0)
EvolutionaryDocking(System &system1, System &system2, Options &new_options)
#define BALL_DEPRECATED
#define BALL_EXPORT