WormLikeChain.h

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/**
 *  \file IMP/misc/WormLikeChain.h
 *  \brief Worm-like-chain score for polymer chains.
 *
 *  Copyright 2007-2013 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 */