ABEGOEval.hh

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// vi: set ts=2 noet:
//
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/// @file   core/fragment/picking_old/vall/eval/ABEGOEval.hh
/// @brief  scores a fragment based on ABEGO
/// @author Nobuyasu Koga (nobuyasu@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_eval_ABEGOEval_hh
#define INCLUDED_core_fragment_picking_old_vall_eval_ABEGOEval_hh


// unit headers
#include <core/fragment/picking_old/vall/eval/ABEGOEval.fwd.hh>
// AUTO-REMOVED #include <core/fragment/picking_old/vall/eval/IdentityEval.hh>
#include <core/util/ABEGOManager.fwd.hh>

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

// package headers
#include <core/fragment/picking_old/vall/eval/VallFragmentEval.hh>
#include <core/fragment/picking_old/vall/VallLibrary.fwd.hh>

#include <utility/vector1.hh>




namespace core {
namespace fragment {
namespace picking_old {
namespace vall {
namespace eval {


/// @brief scores a fragment based on sum of secondary structure identity and sequence identity
class ABEGOEval : public VallFragmentEval {


private: // typedefs


  typedef VallFragmentEval Super;


public: // typedefs


  typedef Super::VallFragmentScore VallFragmentScore;

  typedef std::string String;
  typedef core::Real Real;

  typedef core::util::ABEGOManager ABEGOManager;
  typedef core::util::ABEGOManagerOP ABEGOManagerOP;

public: // concept typedefs


  /// @brief typedef for ExtentEvaluator concept
  typedef Super::PageConstIterator PageConstIterator;


  /// @brief typedef for ExtentEvaluator concept
  typedef Super::Extent Extent;


public: // concept translation typedefs


  typedef PageConstIterator VallResidueConstIterator;


public: // construct/destruct


  /// @brief default constructor
  ABEGOEval();


  /// @brief full values constructor
  /// @param ss secondary structure string to match against
  /// @param aa amino acid structure string to match against
  ABEGOEval(
    utility::vector1< String > const & input,
    Real const penalty = 1.0,
    bool const randomize = true
  );


  /// @brief default copy constructor
  ABEGOEval( ABEGOEval const & rval );


  /// @brief default destructor
  virtual
  ~ABEGOEval();


public: // copy assignment


  /// @brief copy assignment
  ABEGOEval & operator =( ABEGOEval const & rval );


public: // virtual constructors


  /// @brief clone this object
  virtual
  VallFragmentEvalOP clone() const;


public: // virtual evaluation methods


  /// @brief for a fragment extent, evaluate and store results in a VallFragmentScore
  /// @return true, so score is always stored during VallLibrarian::catalog()
  virtual
  bool eval_impl(
    Extent const & extent,
    VallFragmentScore & fs
  );


public: // accessor/mutators


  /// @brief get secondary structure string
  inline
  utility::vector1< String > const & abego_str() const {
    return abego_;
  }

  /// @brief set abego vector of string
  inline
  void abego_str( utility::vector1< String > const & abego ) {
    abego_ = abego;
  }

  /// @brief get secondary structure penalty
  inline
  Real penalty() const {
    return penalty_;
  }

  /// @brief adding random noise to score?
  inline
  bool randomize() const {
    return randomize_;
  }


public: // additional hooks


  /// @brief operation to be perform before catalog() starts
  virtual
  void pre_catalog_op( VallLibrary const & );


private: // data


  /// @brief abego string to match against
  utility::vector1< String > abego_;

  /// @brief abego penalty if non-matching
  Real penalty_;

  /// @brief flag to add random noise between [0, 0.001) into score
  bool randomize_;

  ABEGOManagerOP am_;


};


} // namespace eval
} // namespace vall
} // namespace picking_old
} // namespace fragment
} // namespace core


#endif /* INCLUDED_core_fragment_picking_old_vall_eval_ABEGOEval_HH */