IMP  2.0.0
The Integrative Modeling Platform
core/Harmonic.h
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1 /**
2  * \file IMP/core/Harmonic.h \brief Harmonic function.
3  *
4  * Copyright 2007-2013 IMP Inventors. All rights reserved.
5  */
6 
7 #ifndef IMPCORE_HARMONIC_H
8 #define IMPCORE_HARMONIC_H
9 
10 #include <IMP/core/core_config.h>
11 #include <IMP/UnaryFunction.h>
13 #include <IMP/utility.h>
14 
15 IMPCORE_BEGIN_NAMESPACE
16 
17 //! %Harmonic function (symmetric about the mean)
18 /** This is a simple score modeling an harmonic oscillator. The score is
19  0.5 * k * x * x, where k is the 'force constant' and x is the distance
20  from the mean.
21  \see TruncatedHarmonic
22  \see HarmonicUpperBound
23  \see HarmonicLowerBound
24  */
25 class Harmonic : public UnaryFunction
26 {
27 public:
28  /** Create with the given mean and the spring constant k */
29  Harmonic(Float mean, Float k) : mean_(mean), k_(k) {}
30 
31  virtual DerivativePair evaluate_with_derivative(double feature) const {
32  return DerivativePair(0.5 * k_ * square(feature-mean_),
33  k_*(feature - mean_));
34  }
35 
36  virtual double evaluate(double feature) const {
37  return 0.5 * k_ * square(feature-mean_);
38  }
39 
41 
42  //! \return the mean of this function
43  Float get_mean() const {
44  return mean_;
45  }
46 
47  //! \return the spring constant
48  Float get_k() const {
49  return k_;
50  }
51 
52  //! Set the mean of this function
53  void set_mean(Float mean) {
54  mean_ = mean;
55  }
56 
57  //! Set the spring constant
58  void set_k(Float k) {
59  k_ = k;
60  }
61 
62 
63  //! Return the k to use for a given Gaussian standard deviation.
64  /** Given the standard deviation of a Gaussian distribution, get
65  the force constant of the harmonic score function that yields that
66  same distribution. For temperature in Kelvin, this assumes the score
67  function is energy in kcal/mol, and thus returns a force constant in
68  kcal/mol/A/A.
69  \param[in] sd Gaussian standard deviation, in angstroms
70  \param[in] t System temperature, in Kelvin
71  \return Force constant
72  */
74  // Gas constant in kcal/mol K
75  const static Float R = 8.31441 / 4186.8;
76  return R * t / square(sd);
77  }
78 
79 private:
80  Float mean_;
81  Float k_;
82 };
83 
84 IMPCORE_END_NAMESPACE
85 
86 #endif /* IMPCORE_HARMONIC_H */