IdentityEval.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.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file   core/fragment/picking_old/vall/eval/IdentityEval.hh
/// @brief  scores a fragment based on secondary structure identity and sequence identity
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_eval_IdentityEval_hh
#define INCLUDED_core_fragment_picking_old_vall_eval_IdentityEval_hh


// unit headers
#include <core/fragment/picking_old/vall/eval/IdentityEval.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>


// C++ headers


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 IdentityEval : public VallFragmentEval {


private: // typedefs


  typedef VallFragmentEval Super;


public: // typedefs


  typedef Super::VallFragmentScore VallFragmentScore;

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


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
  IdentityEval();


  /// @brief full values constructor
  /// @param ss secondary structure string to match against
  /// @param aa amino acid structure string to match against
  IdentityEval(
    String const & ss,
    String const & aa,
    Real const ss_penalty = 1.0,
    Real const aa_penalty = 1.0,
    bool const randomize = true
  );


  /// @brief secondary structure constructor
  IdentityEval(
    String const & ss,
    Real const ss_penalty = 1.0,
    bool const randomize = true
  );


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


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


public: // copy assignment


  /// @brief copy assignment
  IdentityEval & operator =( IdentityEval 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
  String const & ss_str() const {
    return ss_;
  }


  /// @brief set secondary structure string
  inline
  void ss_str( String const & ss ) {
    ss_ = ss;
  }


  /// @brief get amino acid string
  inline
  String const & aa_str() const {
    return aa_;
  }


  /// @brief set amino acid string
  inline
  void aa_str( String const & aa ) {
    aa_ = aa;
  }


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


  /// @brief set secondary structure penalty
  inline
  void ss_penalty( Real const penalty ) {
    ss_penalty_ = penalty;
  }


  /// @brief get amino acid penalty
  inline
  Real aa_penalty() const {
    return aa_penalty_;
  }


  /// @brief set amino acid penalty
  inline
  void aa_penalty( Real const penalty ) {
    aa_penalty_ = penalty;
  }


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


  /// @brief set flag to add random noise between [0, 0.001) to score
  inline
  void randomize( bool const flag ) {
    randomize_ = flag;
  }


public: // additional hooks


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


private: // data


  /// @brief secondary structure string to match against
  String ss_;


  /// @brief amino acid string to match against
  String aa_;


  /// @brief secondary structure penalty if non-matching
  Real ss_penalty_;


  /// @brief amino acid penalty if non-matching
  Real aa_penalty_;


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


};


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


#endif /* INCLUDED_core_fragment_picking_old_vall_eval_IdentityEval_HH */