SecStructGen.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/gen/SecStructGen.hh
/// @brief  Generator that requires fragments to have a specific secondary
///         structure string.
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_gen_SecStructGen_hh
#define INCLUDED_core_fragment_picking_old_vall_gen_SecStructGen_hh

// unit headers
#include <core/fragment/picking_old/vall/gen/SecStructGen.fwd.hh>
#include <core/fragment/picking_old/vall/gen/VallFragmentGen.hh>

#include <utility/vector1.hh>


// C++ headers


namespace core {
namespace fragment {
namespace picking_old {
namespace vall {
namespace gen {


/// @brief Generator that requires fragments to have a specific secondary
///  structure string.
/// @remarks assumes that Pages in the Book are stored in a container
///  capable of returning a RandomAccessIterator, such as std::vector
class SecStructGen : public VallFragmentGen {


private: // typedefs


  typedef VallFragmentGen Super;


public: // typedefs


  typedef Super::Size Size;
  typedef std::string String;


public: // concept typedefs


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


  /// @brief typedef for ExtentGenerator concept
  typedef Super::PageIterator PageIterator;


public: // concept translation typedefs


  typedef PageIterator VallResidueIterator;


public: // construct/destruct


  /// @brief default constructor
  SecStructGen();


  /// @brief secondary structure string constructor
  /// @param[in] ss the required secondary structure string of the fragment
  SecStructGen( String const & ss );


  /// @brief copy constructor
  SecStructGen( SecStructGen const & rval );


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


public: // copy assignment


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


public: // virtual constructors


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


public: // extent generation


  /// @brief return the desired fragment extent w/ length equal to the
  ///  secondary structure string
  /// @return Valid (true) extent if the extent has exactly the required
  ///  secondary structure string and the end of the extent does not go past
  ///  section_end.  Invalid (false) extent otherwise.
  /// @remarks we assume VallResidueIterator is a type of RandomAccessIterator, such as
  ///  those used in std::vector
  virtual
  Extent operator ()( VallResidueIterator extent_begin, VallResidueIterator section_end ) const;


private: // data


  /// @brief the required secondary structure of desired fragment
  String ss_;

};


} // namespace gen
} // namespace vall
} // namespace picking_old
} // namespace fragment
} // namespace core

#endif /* INCLUDED_core_fragment_picking_old_vall_gen_SecStructGen_HH */