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ReactionRateCalculation.hh
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1 #ifndef GGL_CHEM_REACTIONRATECALCULATION_HH_
2 #define GGL_CHEM_REACTIONRATECALCULATION_HH_
3 
4 #include "ggl/chem/Reaction.hh"
5 
6 #include <ggl/Rule.hh>
7 
8 
9 namespace ggl {
10  namespace chem {
11 
12  ////////////////////////////////////////////////////////////////////////////
13 
14  /*! @brief Interface reaction rate calculation
15  *
16  * Abstract super class for reaction rate calculations.
17  *
18  * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
19  *
20  */
21  class ReactionRateCalculation
22  {
23  public:
24 
25  //! default construction
26  ReactionRateCalculation() {}
27 
28  //! default destruction
29  virtual ~ReactionRateCalculation() {}
30 
31  /*! Calculates the reaction rate for a given Reaction.
32  *
33  * @param reaction the Reaction object to calculate the rate for
34  * @return the according reaction rate
35  */
36  virtual
37  double
38  getRate( const Reaction & reaction ) const = 0;
39 
40  /*! Announces whether the reaction rate calculation needs the explicit
41  * transition state present within the reaction information or not.
42  *
43  * @return true iff the reaction calculation needs the presence of an
44  * explicit transition state, false otherwise (no transition
45  * state needed)
46  */
47  virtual
48  bool
49  needTransitionState( void ) const = 0;
50  };
51 
52  ////////////////////////////////////////////////////////////////////////////
53 
54 
55  /*! A reaction rate calculator that does not calculate a rate but returns
56  * a fixed reaction rate independently from the given reaction.
57  *
58  * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
59  *
60  */
61  class RRC_Fixed : public ReactionRateCalculation
62  {
63  protected:
64 
65  //! the fixed rate to return for all reactions
66  const double fixRate;
67 
68  public:
69 
70  /*! Constructs a new reaction rate calculator that yields always the
71  * same fixed reaction rate given.
72  *
73  * @param fixRate the fixed rate to be assigned to all reactions
74  */
75  RRC_Fixed(const double fixRate );
76 
77  //! default destruction
78  virtual ~RRC_Fixed();
79 
80  /*! Returns a fixed transition rate for all reactions.
81  *
82  * @param reaction the Reaction object to calculate the rate for; but
83  * doesnt matter because fixed rate returned!
84  * @return the fixed reaction rate
85  */
86  virtual
87  double
88  getRate( const Reaction & reaction ) const;
89 
90  /*! No transition state needed, such that this returns always false!
91  *
92  * @return false because no transition state needed for a fixed
93  * reaction rate
94  */
95  virtual
96  bool
97  needTransitionState( void ) const;
98  };
99 
100 
101  ////////////////////////////////////////////////////////////////////////////
102 
103 
104  /*! A reaction rate calculator that does not calculate a rate (returns
105  * always "nan") but enforces, that the reactions transition state is
106  * calculated.
107  *
108  * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
109  *
110  */
111  class RRC_TState : public ReactionRateCalculation
112  {
113  public:
114 
115  /*! Constructs a new reaction rate calculator that yields always the
116  * same reaction rate ("nan") but enforces the creation of the
117  * reactions transition state.
118  */
119  RRC_TState();
120 
121  //! default destruction
122  virtual ~RRC_TState();
123 
124  /*! Returns a "nan" transition rate for all reactions.
125  *
126  * @param reaction the Reaction object to calculate the rate for; but
127  * doesnt matter because "nan" returned!
128  * @return "nan"
129  */
130  virtual
131  double
132  getRate( const Reaction & reaction ) const;
133 
134  /*! YES, a transition state is needed!
135  *
136  * @return true, because that's the class for! ;)
137  */
138  virtual
139  bool
140  needTransitionState( void ) const;
141  };
142 
143 
144  ////////////////////////////////////////////////////////////////////////////
145 
146  } // namespace chem
147 } // namespace ggl
148 
149 #endif /*REACTIONRATECALCULATION_HH_*/
150