ABEGO_SS_Score.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.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/frag_picker/scores/ABEGO_SS_Score.hh
/// @brief  scores a fragment by secondary structure similarity
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_ABEGO_SS_Score_hh
#define INCLUDED_protocols_frag_picker_scores_ABEGO_SS_Score_hh

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

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

#include <protocols/frag_picker/quota/ABEGO_SS_Config.hh>
#include <protocols/frag_picker/quota/ABEGO_SS_Map.hh>

// AUTO-REMOVED #include <core/fragment/SecondaryStructure.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

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

class ABEGO_SS_Score;
typedef utility::pointer::owning_ptr< ABEGO_SS_Score > ABEGO_SS_ScoreOP;
typedef utility::pointer::owning_ptr< ABEGO_SS_Score const > ABEGO_SS_ScoreCOP;

class ABEGO_SS_Score: public CachingScoringMethod {
public:

  ABEGO_SS_Score(Size priority, Real lowest_acceptable_value, bool use_lowest,
      std::string prediction_file_name,Size longest_vall_chunk) :
    CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "ABEGO_SS_Score") {

    quota::ABEGO_SS_Config prediction_file(prediction_file_name);
    query_len_ = prediction_file.size();
    n_classes_ = prediction_file.n_columns();
    for (Size i = 1; i <= query_len_; ++i) {
      utility::vector1<Real> row(longest_vall_chunk);
      scores_.push_back(row);
    }
    for(Size iseq=1;iseq<=query_len_;iseq++) {
        utility::vector1<Real> row;
        for(Size ibin=1;ibin<=n_classes_;ibin++)
      row.push_back(prediction_file.probability(iseq,ibin));
        ratios_.push_back( row );
    }
    for(Size ibin=1;ibin<=n_classes_;ibin++)
        maps_.push_back( new quota::ABEGO_SS_Map(prediction_file.get_pool_bins(ibin)) );
  }

  ~ABEGO_SS_Score() {}

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

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

private:
  Size query_len_;
  Size n_classes_;
  utility::vector1<quota::ABEGO_SS_MapOP> maps_;
  utility::vector1< utility::vector1<Real> > ratios_;
  std::string cached_scores_id_;
  Matrix scores_;
};

/// @brief  Maker class that produces a new ABEGO_SS_Score object
class MakeABEGO_SS_Score: public MakeFragmentScoringMethod {
public:

  MakeABEGO_SS_Score() :
    MakeFragmentScoringMethod("ABEGO_SS_Score") {
  }

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

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


#endif /* INCLUDED_protocols_frag_picker_scores_ABEGO_SS_Score_HH */