SimulatedTempering.hh

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// vi: set ts=2 noet:
//
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/// @file /protocols/canonical_sampling/MetropolisHastingsMover.hh
/// @brief
/// @author  Oliver Lange ( oliver.lange@tum.de )

#ifndef INCLUDED_protocols_canonical_sampling_SimulatedTempering_hh
#define INCLUDED_protocols_canonical_sampling_SimulatedTempering_hh

// Unit Headers
#include <protocols/canonical_sampling/SimulatedTempering.fwd.hh>
#include <protocols/canonical_sampling/TemperingBase.hh>

#include <protocols/moves/Mover.hh>

// Project Headers
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <numeric/random/WeightedSampler.hh>
#include <protocols/jd2/Job.fwd.hh>

// Utility Headers
#include <core/types.hh>
#include <utility/vector1.hh>

namespace protocols {
namespace canonical_sampling {

///@details
class SimulatedTempering : public protocols::canonical_sampling::TemperingBase {
  typedef TemperingBase Parent;
public:

  SimulatedTempering();

  SimulatedTempering( SimulatedTempering const& );

  virtual
  void apply( core::pose::Pose& ) {};

  virtual
  std::string
  get_name() const;

  protocols::moves::MoverOP
  clone() const;

  virtual
  protocols::moves::MoverOP
  fresh_instance() const;

  virtual
  void
  parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & data,
    protocols::filters::Filters_map const & filters,
    protocols::moves::Movers_map const & movers,
    core::pose::Pose const & pose
  );

  /// @brief execute the temperatur move ( called by observer_after_metropolis )
  /// returns the current temperatur in kT.
  core::Real
  temperature_move( core::Real score);

  /// @brief callback executed before any Monte Carlo trials
  virtual void
  initialize_simulation(
    core::pose::Pose & pose,
    protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover,
    core::Size cycle   //non-zero if trajectory is restarted
  );

  /// @brief callback executed after all Monte Carlo trials
  virtual
  void
  finalize_simulation(
    core::pose::Pose & pose,
    protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover
  );

  void
  finalize_simulation( std::string const& output_name );

protected:
  void set_defaults();

  /// @brief Assigns user specified values to primitive members using command line options
  virtual
  void init_from_options();

  /// @brief update weights based on current counts
  void reweight();

  /// @brief reset the raw counts per state (not the weighted ones) to 0
  void reset_raw_counter();

  /// @brief initialize temperatures and weights from file, return false if IO error occurrs
  virtual
  bool initialize_from_file( std::string const& filename );

  virtual
  void write_to_file( std::string const& file_in, std::string const& output_name, utility::vector1< core::Real > const& wcounts );

/// ------------------ register cmdline options ---------------------------

private:
  static bool options_registered_;

public:
  static void register_options();

/// ---------------- member variables --------------------------

private:

  /// --- configurables ----
  // add to score -- can help to get effective weights closer to 1
  core::Real score_offset_;

  // how likely is a self-transition in temperature moves
  core::Real self_transition_; //not in options currently --- probably useless

  // allows jumps to any temperature in single step
  bool temperature_jumps_;

  // reweight after X steps -- 0 for now reweighting
  core::Size reweight_stride_;

  /// ---- state -----
  utility::vector1< core::Real > weights_;
  utility::vector1< core::Size > counts_;
  utility::vector1< core::Real > weighted_counts_;
  core::Size total_count_;


}; //end SimulatedTempering

} //namespace canonical_sampling
} //namespace protocols

#endif //INCLUDED_protocols_canonical_sampling_SimulatedTempering_HH