SecondarySimilarity.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/frag_picker/scores/SecondarySimilarity.hh
/// @brief  scores a fragment by secondary structure similarity
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_SecondarySimilarity_hh
#define INCLUDED_protocols_frag_picker_scores_SecondarySimilarity_hh

// type headers
#include <core/types.hh>

// package headers
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.hh>
#include <protocols/frag_picker/scores/CachingScoringMethod.hh>

#include <core/fragment/SecondaryStructure.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

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

class SecondarySimilarity;
typedef utility::pointer::owning_ptr< SecondarySimilarity > SecondarySimilarityOP;
typedef utility::pointer::owning_ptr< SecondarySimilarity const > SecondarySimilarityCOP;

/// @brief  scores a fragment by secondary structure similarity
/// @detail The score for each position is P(H), P(L) or P(E) if
/// a vall residue is within Helix, Loop or Extended secondary stucture element, respectively.
/// P(H), P(L) and P(E) denotes the probability that a given residue in a query
/// is within Helix, Loop or Extended secondary stucture element.
/// The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms\n
/// If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function
/// should be the same as SecondaryIdentity, although the later one is faster.
class SecondarySimilarity: public CachingScoringMethod {
public:

  SecondarySimilarity(Size priority, Real lowest_acceptable_value, bool use_lowest,
      core::fragment::SecondaryStructureOP query_prediction, std::string prediction_name,
      Size sequence_length, utility::vector1<Size> & frag_sizes, Size longest_vall_chunk);

  ~SecondarySimilarity() {}

  void do_caching(VallChunkOP);
  void do_caching_simple(VallChunkOP);
  bool cached_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map);
  void clean_up() {}

  /// @brief Computes the score
  virtual bool score(FragmentCandidateOP, FragmentScoreMapOP);

  /// @brief returns the secondary structure porediction object that is used by this score
  inline core::fragment::SecondaryStructureOP get_secondary_prediction() { return query_ss_; }

        inline std::string& get_prediction_name() { return prediction_name_; };
protected:
  Matrix scores_;
  utility::vector1< Matrix > cache_;
private:
  std::string prediction_name_;
  core::fragment::SecondaryStructureOP query_ss_;
  utility::vector1< utility::vector1< Real > > raw_probs_;
  Size query_len_;

  std::string cached_scores_id_;
};

/// @brief  Maker class that produces a new SecondarySimilarity object
class MakeSecondarySimilarity: public MakeFragmentScoringMethod {
public:

  MakeSecondarySimilarity() :
    MakeFragmentScoringMethod("SecondarySimilarity") {
  }

  FragmentScoringMethodOP make(Size priority, Real lowest_acceptable_value, bool use_lowest,
      FragmentPickerOP picker, std::string prediction_id) {

    Size sequence_length = picker->get_query_seq()->length();
    Size vall_max_len = picker->get_vall()->get_largest_chunk_size();

    return (FragmentScoringMethodOP) new SecondarySimilarity(priority,
            lowest_acceptable_value, use_lowest,
            picker->get_query_ss(prediction_id),prediction_id,
            sequence_length,picker->frag_sizes_,vall_max_len);
  }
};

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


#endif /* INCLUDED_protocols_frag_picker_scores_SecondarySimilarity_HH */