ConstantLengthFragSet.hh

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/// @file   core/fragments/ConstantLengthFragSet.hh
/// @brief  yields a simple implementation of a fragset
/// @author Oliver Lange ( olange@u.washington.edu)
/// @date   Wed Aug 22 12:08:31 2007
///

#ifndef INCLUDED_core_fragment_ConstantLengthFragSet_HH
#define INCLUDED_core_fragment_ConstantLengthFragSet_HH

// Unit Headers
#include <core/fragment/ConstantLengthFragSet.fwd.hh>

// Package Headers
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameList.hh>

// Project Headers
// AUTO-REMOVED #include <utility/io/izstream.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/types.hh>

// ObjexxFCL Headers

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>
#include <utility/io/izstream.fwd.hh>


// Package Headers

// std Headers

/* Just a mad thought: with fragments becoming ever more "Residue" like one might want to use the
   packer to choose a combination of good fragments instead of makeing independent choices.
   I guess, it is only a question of keeping the combinatorics in control...
   maybe it makes sense to pack with only "unconfident" regions of the backbone flexible ..
*/

namespace core {
namespace fragment {

/* classic 9mer Frags would be in one of those */
/// @brief A set of fragments that contains fragments of a constant length read
/// in from a fragment file.
/// @note this object is a simple implementation of the FragSet
/// @note for custom fragments, check out https://robetta.bakerlab.org/fragmentsubmit.jsp
///
/// example:
///     ninemers = ConstantLengthFragSet(9)
///     ninemers.read_fragment_file("test9_fragments")
/// See also:
///     Pose
///     ClassicFragmentMover
class ConstantLengthFragSet : public FragSet {
  typedef FragSet Parent;
// ConstantLengthFragSet is a FragSet with only one frame per position!
public:

  ConstantLengthFragSet( Size frag_length ) {
    set_max_frag_length( frag_length );
  };

  ConstantLengthFragSet( Size frag_length, std::string filename );

  ConstantLengthFragSet() {};

  ~ConstantLengthFragSet();

  ConstantLengthFragSet( FragSet const& fragments );

  virtual FragSetOP clone() const
  {
    return new ConstantLengthFragSet( *this );
  }

  virtual FragSetOP empty_clone() const
  {
    return new ConstantLengthFragSet();
  }

  /// @brief Loads the contents of  <filename>  into the ConstantLengthFragSet
  ///
  /// example:
  ///     ninemers.read_fragment_file("test9_fragments")
  /// See also:
  ///     ConstantLengthFragSet
  ///     Pose
  ///     Pose.omega
  ///     Pose.phi
  ///     Pose.psi
  ///     ClassicFragmentMover
  void read_fragment_file( std::string filename, Size top25 = 0, Size ncopies = 1, bool bAnnotation = false  );

  void read_fragment_stream( utility::io::izstream & data, Size top25 = 0, Size ncopies = 1, bool bAnnotation = false  );

  // void print_fragments();
  ///@brief there is only one Frame per position, end / max_overlap are ignored
  Size region(
    kinematics::MoveMap const& mm,
    core::Size start,
    core::Size end,
    core::Size , //min_overlap not used
    core::Size , //min_length not used
    FrameList &frames
  ) const;

//  /// @brief Accessor for the Frames at the specified insertion position. Returns 0=false if
//  /// there is no frame at the specified position.
//  virtual Size frames(
//    Size pos,
//    FrameList & frame
//  );

  FrameIterator begin() const;

  FrameIterator end() const;

  virtual bool empty() const {
    return frames_.size()==0;
  }
protected:
  virtual void add_( FrameOP aframe );

private:
  FrameList frames_;
};

}
}

#endif