GunnCostScore.hh

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/// @file   protocols/frag_picker/scores/GunnCostScore.hh
/// @brief  Object that scores a fragment by Gunn cost function (how it fits to the local structure)
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_GunnCostScore_hh
#define INCLUDED_protocols_frag_picker_scores_GunnCostScore_hh

// package headers
#include <protocols/frag_picker/FragmentCandidate.fwd.hh>
#include <protocols/frag_picker/scores/CachingScoringMethod.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>
#include <protocols/frag_picker/scores/GunnCost.hh>


#include <core/types.hh>

#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <iostream>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

typedef utility::vector1<utility::vector1<Real> > Matrix;

/// @brief  scores a fragment by its crmsd to the given reference structure
class GunnCostScore: public CachingScoringMethod {
public:

  /// @brief  creates a crmsd-based scoring function.
  /// @detailed fragments will be compared to a given pose, which should have the same number of residues a the query sequence
  GunnCostScore(Size, Real, bool, core::pose::PoseOP,utility::vector1<Size>,Size);

  ~GunnCostScore();

  void do_caching(VallChunkOP);
  void clean_up();
  bool score(FragmentCandidateOP, FragmentScoreMapOP);
  bool cached_score(FragmentCandidateOP, FragmentScoreMapOP);

  void computeGunnTuples(core::pose::Pose &,Size,utility::vector1<GunnTuple> &);

private:
  Size n_atoms_;
  pose::PoseOP reference_pose_;
  utility::vector1<Size> frag_sizes_;
  Size max_chunk_size_;
  utility::vector1<utility::vector1<GunnTuple> > ref_gunn_data_;
  utility::vector1<utility::vector1<GunnTuple> > chunk_gunn_data_;
  GunnCost gunn_cost_;
};

/// @brief  Maker class that produces a new GunnCostScore object
class MakeGunnCostScore: public MakeFragmentScoringMethod {
public:

  MakeGunnCostScore() :
    MakeFragmentScoringMethod("GunnCostScore") {
  }

  FragmentScoringMethodOP make(Size, Real, bool, FragmentPickerOP, std::string);
};

} // scores
} // frag_picker
} // protocols

#endif // INCLUDED_protocols_frag_picker_scores_GunnCostScore_HH