WormLikeChain.h

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/**
 *  \file IMP/misc/WormLikeChain.h
 *  \brief Worm-like-chain score for polymer chains.
 *
 *  Copyright 2007-2016 IMP Inventors. All rights reserved.
 */

#ifndef IMPMISC_WORM_LIKE_CHAIN_H
#define IMPMISC_WORM_LIKE_CHAIN_H

#include <IMP/misc/misc_config.h>
#include <IMP/UnaryFunction.h>
#include <IMP/internal/constants.h>
#include <IMP/internal/units.h>

IMPMISC_BEGIN_NAMESPACE

//! Worm-like-chain energy for polymer chains
/** This function implements one polymer force/extension curve. It
    is a physical energy and all the inputs are in angstroms
    and the outputs in kcal/mol (/angstrom).

    \note The actual worm like chain force blows up as the extension approaches
    the maximum. Since that makes optimization problematic, we
    just linearly extend the force after 99% of maximum.
 */
class WormLikeChain : public UnaryFunction {
 public:
  //! Define the energy term
  /** \param[in] l_max maximum length of the chain in angstroms
      \param[in] lp persistence length in angstroms
   */
  WormLikeChain(Float l_max, Float lp) : lmax_(l_max), lp_(lp) {
    IMP_USAGE_CHECK(l_max > lp, "The persistence length should be less "
                                    << "than the total length for this model");
  }

  virtual DerivativePair evaluate_with_derivative(double feature) const;

  virtual double evaluate(double feature) const;

  IMP_OBJECT_METHODS(WormLikeChain);

  void do_show(std::ostream &out) const;

 private:
  unit::Piconewton cderiv(unit::Angstrom l) const {
    unit::Piconewton pn = IMP::internal::KB *
                          IMP::internal::DEFAULT_TEMPERATURE / lp_ *
                          (.25 / square(1.0 - (l / lmax_)) - .25 + (l / lmax_));
    return pn;
  }

  unit::Picojoule eval(unit::Angstrom m) const {
    unit::Picojoule J =
        IMP::internal::KB * IMP::internal::DEFAULT_TEMPERATURE / lp_ *
        (.25 * square(lmax_) / (lmax_ - m) - m * .25 + .5 * square(m) / lmax_);
    return J;
  }

  unit::Angstrom cutoff() const { return .99 * lmax_; }

  unit::Angstrom lmax_, lp_;
};

#ifndef IMP_DOXYGEN
inline double WormLikeChain::evaluate(double v) const {
  return evaluate_with_derivative(v).first;
}

inline DerivativePair WormLikeChain::evaluate_with_derivative(double v) const {
  static const unit::Picojoule zero = eval(unit::Angstrom(0));
  unit::Angstrom l(v);
  if (l < unit::Angstrom(0)) l = unit::Angstrom(0);
  unit::Picojoule ret;

  unit::Piconewton doubled;
  if (l < cutoff()) {
    ret = (eval(l) - zero);
    doubled = cderiv(l);
  } else {
    unit::Picojoule springterm = (l - cutoff()) * cderiv(cutoff());
    ret = (eval(cutoff()) + springterm - zero);
    doubled = cderiv(cutoff());
    IMP_LOG_VERBOSE("Overstretched " << cderiv(cutoff()) << " " << doubled
                                     << " " << l << " " << lmax_ << " "
                                     << cutoff() << std::endl);
  }
  unit::YoctoKilocalorie zc = convert_J_to_Cal(ret);
  double value = (zc * unit::ATOMS_PER_MOL).get_value();
  // std::cout << "Force is " << doubled << " for length " << l << std::endl;
  // convert from picoNewton
  unit::YoctoKilocaloriePerAngstrom du = unit::convert_J_to_Cal(doubled);

  double deriv = (du * unit::ATOMS_PER_MOL).get_value();
  // std::cout << "Which converts to " << d << std::endl;
  return std::make_pair(value, deriv);
}

inline void WormLikeChain::do_show(std::ostream &out) const {
  out << "params " << lmax_ << " " << lp_ << std::endl;
}
#endif

IMPMISC_END_NAMESPACE

#endif /* IMPMISC_WORM_LIKE_CHAIN_H */