FragmentReader.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.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (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  protocols/jd2/parser/FragmentReader.hh
/// @brief
/// @author Nobuyasu Koga ( nobuyasu@uw.edu )

#ifndef INCLUDED_protocols_jd2_parser_FragmentReader_hh
#define INCLUDED_protocols_jd2_parser_FragmentReader_hh

// Unit Headers
#include <protocols/jd2/parser/FragmentReader.fwd.hh>
#include <protocols/jd2/parser/BluePrint.fwd.hh>
// Project Headers
#include <core/pose/Pose.fwd.hh>
#include <core/fragment/FragSet.fwd.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/tag/Tag.fwd.hh>


// c++ headers
#include <string>

#include <utility/vector1.hh>


namespace protocols {
namespace jd2 {
namespace parser {

class FragmentReader : public utility::pointer::ReferenceCount {
public:


  typedef utility::pointer::ReferenceCount Parent;


public:

  typedef core::Size Size;
  typedef std::string String;
  typedef core::pose::Pose Pose;
  typedef core::fragment::FragSetOP FragSetOP;

  typedef utility::tag::Tag Tag;
  typedef utility::tag::TagPtr TagPtr;


public:


  /// @brief default constructor
  FragmentReader();

  /// @brief value constructor
  FragmentReader( TagPtr const & tag );

  /// @brief destructor
  virtual ~FragmentReader();

public:


  ///@brief main opeartion
  void apply( FragSetOP & fragset );


private:


  ///@brief parse tag
  void parse_tag( TagPtr const & tag );

  ///@brief set fragments just for helper function
  void set_fragments( Pose const & pose, FragSetOP const & fragset );


private:

  /// @brief way of reading fragments from pdbs, silent, fragfiles, or vall
  String read_type_;

  /// @brief input file name, pdbs, silent, fragfiles of vall
  String filename_;

  /// @brief length of fragments
  Size frag_size_;

  /// @brief the begin of sequence positions where fragments are stealed
  Size begin_;

  /// @brief the end of sequence positions where fragments are stealed
  Size end_;

  /// @brief number of stealing fragments if read_type_ is pdbs or silent
  Size steal_times_;

  /// @brief maximum number of fragments when a silent file is used
  Size nfrags_;

  /// @brief secondary structure assignment to pick fragment from vall
  String ss_;

  /// @brief amino acids to pick fragment from vall
  String aa_;

  /// @brief abego assignment to pick fragment from vall
  bool use_abego_;

  /// @brief blueprint
  protocols::jd2::parser::BluePrintOP blueprint_;

};

} //namespace parser
} //namespace jd2
} //namespace protocols

#endif