ProfileScoreSubMatrix.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// 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/frag_picker/scores/ProfileScoreSubMatrix.hh
/// @brief  scores a fragment by substitution matrix (e.g. Blosum62) profile score
/// @author Dan Kulp (dwkulp@gmail.com), based on code from Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_ProfileScoreSubMatrix_HH
#define INCLUDED_protocols_frag_picker_scores_ProfileScoreSubMatrix_HH

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


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

#include <utility/vector1.hh>



namespace protocols {
namespace frag_picker {
namespace scores {

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

/// @brief  a fragment candidate
class ProfileScoreSubMatrix: public CachingScoringMethod {
public:

  ProfileScoreSubMatrix(Size priority, Real lowest_acceptable_value, bool use_lowest,                          std::string sequence,Size longest_vall_chunk,std::string subMatrixFile);
  ~ProfileScoreSubMatrix();

  void do_caching(VallChunkOP);
  void clean_up() {
  }
  bool score(FragmentCandidateOP, FragmentScoreMapOP);
  bool cached_score(FragmentCandidateOP, FragmentScoreMapOP);
  // Undefinede, commenting out to fix PyRosetta build  bool describe_score(FragmentCandidateOP, FragmentScoreMapOP, std::ostream&);
protected:
  Matrix scores_;

private:
  std::string sequence_;
  std::string subMatrixFile_;

  utility::vector1< utility::vector1< Real > > sub_matrix_;
  std::string cached_scores_id_;
  void clear();
};

class MakeProfileScoreSubMatrix: public MakeFragmentScoringMethod {
public:

  MakeProfileScoreSubMatrix() :
    MakeFragmentScoringMethod("ProfileScoreSubMatrix") {
  }

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

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


#endif /* INCLUDED_protocols_frag_picker_scores_ProfileScoreSubMatrix_HH */