BiasedFragmentMover.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file protocols/nonlocal/BiasedFragmentMover.hh
/// @author Christopher Miles (cmiles@uw.edu)

#ifndef INCLUDED_PROTOCOLS_NONLOCAL_BIASEDFRAGMENTMOVER_HH
#define INCLUDED_PROTOCOLS_NONLOCAL_BIASEDFRAGMENTMOVER_HH

// Unit header
#include <protocols/nonlocal/BiasedFragmentMover.fwd.hh>

// C/C++ headers
#include <string>

// External headers
#include <boost/unordered/unordered_map.hpp>

// Utility headers
#include <utility/vector1.hh>

// Project headers
#include <core/fragment/FragData.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/moves/Mover.hh>

// Package headers
#include <protocols/nonlocal/Policy.hh>

namespace protocols {
namespace nonlocal {

/// @class A kinematically-aware mover for performing fragment insertion.
/// User-specified, per-residue sampling probabilities allow fine grained
/// control over the simulation.
class BiasedFragmentMover : public protocols::moves::Mover {
  typedef boost::unordered_map<unsigned, core::fragment::Frame> FrameMap;
  typedef core::fragment::FragSetCOP FragSetCOP;
  typedef utility::vector1<double> Probabilities;

 public:
  /// @brief Creates a new BiasedFragmentMover that selects uniformly from the
  /// available fragments at the selected insertion position.
  BiasedFragmentMover(const PolicyOP& policy, const Probabilities& probs);

  ~BiasedFragmentMover() {}

  /// @brief Inserts a single fragment into pose.
  ///
  /// Insertion position is chosen in a biased manner using the per-residue
  /// probabilities provided in the constructor. The decision on which fragment
  /// to insert from the fragment library is delegated to the policy specified
  /// in the constructor.
  ///
  /// Respects the underlying kinematics of the system.
  void apply(core::pose::Pose& pose);

  /// @brief Returns the name of this mover
  std::string get_name() const;

 private:
  /// @brief Creates a position-indexable list of Frames
  void initialize_library();

  /// @brief Generates cdf from pdf
  void initialize_probabilities();

  /// @brief Verifies that the probability of selecting invalid positions is 0
  void verify_probabilities_or_die(const core::kinematics::FoldTree& tree) const;

  /// @brief Returns a randomly chosen position according to the input probabilities
  unsigned random_position() const;


  // -- Members --

  /// @brief Avoid creating a useless MoveMap for each call to Frame::apply().
  core::kinematics::MoveMap movable_;

  /// @brief Fragment library
  FragSetCOP fragments_;

  /// @brief Position-indexable Frame lookup
  FrameMap frames_;

  /// @brief Guidance for selecting the fragment to be inserted at a given position
  PolicyOP policy_;

  /// @brief PDF of residue sampling probabilities. Must remain in sync with cdf_.
  Probabilities pdf_;

  /// @brief CDF of residue sampling probabilities. Must remain in sync with pdf_.
  Probabilities cdf_;
};

}  // namespace nonlocal
}  // namespace protocols

#endif  // PROTOCOLS_NONLOCAL_BIASED_FRAGMENT_MOVER_HH_