HydrophobicityProfileSimilarity.hh

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/// @file   protocols/frag_picker/scores/HydrophobicityProfileSimilarity.hh
/// @brief  Object that scores a fragment by hydrophobicity
/// @author David E Kim

#ifndef INCLUDED_protocols_frag_picker_scores_HydrophobicityProfileSimilarity_hh
#define INCLUDED_protocols_frag_picker_scores_HydrophobicityProfileSimilarity_hh

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

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

// mini headers
#include <core/sequence/SequenceProfile.hh>

#include <map>

namespace protocols {
namespace frag_picker {
namespace scores {


/// @brief  scores a fragment by its hydrophobicity similarity
class HydrophobicityProfileSimilarity: public CachingScoringMethod {
public:

  /// @brief  creates a hydrophobicity-based scoring function.
  HydrophobicityProfileSimilarity(Size priority, Real lowest_acceptable_value, bool use_lowest,
        std::string & fastaQuerySequence, sequence::SequenceProfileOP query_profile) :
      CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "HydrophobicityProfileSimilarity"),  query_(fastaQuerySequence) {

    query_profile_ = query_profile;

    // initialize hydrophobic aa map
    // V, I, L, F, Y, W, M
    if (is_hydrophobic_.empty()) {
      is_hydrophobic_['A'] = false;
      is_hydrophobic_['C'] = false;
      is_hydrophobic_['D'] = false;
      is_hydrophobic_['E'] = false;
      is_hydrophobic_['F'] = true;
      is_hydrophobic_['G'] = false;
      is_hydrophobic_['H'] = false;
      is_hydrophobic_['I'] = true;
      is_hydrophobic_['K'] = false;
      is_hydrophobic_['L'] = true;
      is_hydrophobic_['M'] = true;
      is_hydrophobic_['N'] = false;
      is_hydrophobic_['P'] = false;
      is_hydrophobic_['Q'] = false;
      is_hydrophobic_['R'] = false;
      is_hydrophobic_['S'] = false;
      is_hydrophobic_['T'] = false;
      is_hydrophobic_['V'] = true;
      is_hydrophobic_['W'] = true;
      is_hydrophobic_['Y'] = true;
      is_hydrophobic_['a'] = false;
      is_hydrophobic_['c'] = false;
      is_hydrophobic_['d'] = false;
      is_hydrophobic_['e'] = false;
      is_hydrophobic_['f'] = true;
      is_hydrophobic_['g'] = false;
      is_hydrophobic_['h'] = false;
      is_hydrophobic_['i'] = true;
      is_hydrophobic_['k'] = false;
      is_hydrophobic_['l'] = true;
      is_hydrophobic_['m'] = true;
      is_hydrophobic_['n'] = false;
      is_hydrophobic_['p'] = false;
      is_hydrophobic_['q'] = false;
      is_hydrophobic_['r'] = false;
      is_hydrophobic_['s'] = false;
      is_hydrophobic_['t'] = false;
      is_hydrophobic_['v'] = true;
      is_hydrophobic_['w'] = true;
      is_hydrophobic_['y'] = true;
    }

  }

  ~HydrophobicityProfileSimilarity() {};

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

private:
  std::string cached_scores_id_;
  std::string & query_;
  sequence::SequenceProfileOP query_profile_;
  static std::map<char,bool> is_hydrophobic_;
};

/// @brief  Maker class that produces a new HydrophobicityProfileSimilarity object
class MakeHydrophobicityProfileSimilarity: public MakeFragmentScoringMethod {
public:

  MakeHydrophobicityProfileSimilarity() :
    MakeFragmentScoringMethod("HydrophobicityProfileSimilarity") {
  }

  FragmentScoringMethodOP make(Size priority, Real lowest_acceptable_value, bool use_lowest,
        FragmentPickerOP picker, std::string) {
    return (FragmentScoringMethodOP) new HydrophobicityProfileSimilarity(priority,
        lowest_acceptable_value, use_lowest, picker->get_query_seq_string(), picker->get_query_seq());
  }

};

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

#endif // INCLUDED_protocols_frag_picker_scores_HydrophobicityProfileSimilarity_hh