core/Harmonic.h

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/**
 *  \file IMP/core/Harmonic.h    \brief Harmonic function.
 *
 *  Copyright 2007-2017 IMP Inventors. All rights reserved.
 */

#ifndef IMPCORE_HARMONIC_H
#define IMPCORE_HARMONIC_H

#include <IMP/core/core_config.h>
#include <IMP/UnaryFunction.h>
#include <IMP/utility.h>

IMPCORE_BEGIN_NAMESPACE

//! %Harmonic function (symmetric about the mean)
/** This is a simple score modeling an harmonic oscillator. The score is
    0.5 * k * x * x, where k is the 'force constant' and x is the distance
    from the mean.
    \see TruncatedHarmonic
    \see HarmonicUpperBound
    \see HarmonicLowerBound
 */
class Harmonic : public UnaryFunction {
 public:
  /** Create with the given mean and the spring constant k */
  Harmonic(Float mean, Float k) : mean_(mean), k_(k) {}

  virtual DerivativePair evaluate_with_derivative(double feature) const {
    return DerivativePair(0.5 * k_ * square(feature - mean_),
                          k_ * (feature - mean_));
  }

  virtual double evaluate(double feature) const {
    return 0.5 * k_ * square(feature - mean_);
  }

  IMP_OBJECT_METHODS(Harmonic);

  //! Return the mean of this function
  Float get_mean() const { return mean_; }

  //! Return the spring constant
  Float get_k() const { return k_; }

  //! Set the mean of this function
  void set_mean(Float mean) { mean_ = mean; }

  //! Set the spring constant
  void set_k(Float k) { k_ = k; }

  //! Return the k to use for a given %Gaussian standard deviation.
  /** Given the standard deviation of a %Gaussian distribution, get
      the force constant of the harmonic score function that yields that
      same distribution. For temperature in Kelvin, this assumes the score
      function is energy in kcal/mol, and thus returns a force constant in
      kcal/mol/A/A.
      \param[in] sd  %Gaussian standard deviation, in angstroms
      \param[in] t   System temperature, in Kelvin
      \return        Force constant
   */
  static Float get_k_from_standard_deviation(Float sd, Float t = 297.15) {
    // Gas constant in kcal/mol K
    const static Float R = 8.31441 / 4186.8;
    return R * t / square(sd);
  }

 private:
  Float mean_;
  Float k_;
};

IMPCORE_END_NAMESPACE

#endif /* IMPCORE_HARMONIC_H */