SolventAccessibility.hh

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/// @file   protocols/frag_picker/scores/SolventAccessibility.hh
/// @brief  Object that scores a fragment by predicted solvent accessibility
/// @author David E Kim

#ifndef INCLUDED_protocols_frag_picker_scores_SolventAccessibility_hh
#define INCLUDED_protocols_frag_picker_scores_SolventAccessibility_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>
#include <protocols/frag_picker/Faraggi_SA.hh>

// utility headers
#include <utility/exit.hh>

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

#include <utility/vector1.hh>



namespace protocols {
namespace frag_picker {
namespace scores {

using namespace core;

/// @brief  scores a fragment by its predicted solvent accessibility
class SolventAccessibility: public CachingScoringMethod {
public:

  /// @brief  creates a predicted solvent accessibility based scoring function.
  SolventAccessibility(Size priority, Real lowest_acceptable_value, bool use_lowest,
        std::string & fastaQuerySequence, utility::vector1<core::Real> & predicted_sa) :
      CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "SolventAccessibility"),  query_(fastaQuerySequence) {

        if (query_.length() != predicted_sa.size())
          utility_exit_with_message("Query length does not match predicted solvent accessiblity");

        // get normalized ASA values
        //   just divide by the maximum values from Faraggi et al. Proteins 2008 (Table II)
        for (Size i=1;i<=predicted_sa.size();++i)
          predicted_sa_norm_.push_back( predicted_sa[i]/protocols::frag_picker::sa_faraggi_max( query_[i-1] ) );
  }

  ~SolventAccessibility() {};

  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_;
  utility::vector1<Real> predicted_sa_norm_;
};

/// @brief  Maker class that produces a new SolventAccessibility object
class MakeSolventAccessibility: public MakeFragmentScoringMethod {
public:

  MakeSolventAccessibility() :
    MakeFragmentScoringMethod("SolventAccessibility") {
  }

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

};

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

#endif // INCLUDED_protocols_frag_picker_scores_SolventAccessibility_hh