BluePrint.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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file ./src/protocols/fldsgn/BluePrint.hh
/// @brief the basic idea of BluePrint is on the remodel Possu wrote in rosetta++.
/// @author Nobuyasu Koga (nobuyasu@uw.edu)

#ifndef INCLUDED_protocols_jd2_parser_BluePrint_HH
#define INCLUDED_protocols_jd2_parser_BluePrint_HH

// Unit  header
#include <protocols/jd2/parser/BluePrint.fwd.hh>

// Project headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>

#include <string>
#include <map>

#include <core/kinematics/MoveMap.fwd.hh>
#include <utility/vector1.hh>

////////////////////////////////////////////////////////////////////////////////////////////////////////////////

namespace protocols {
namespace jd2 {
namespace parser {


class BluePrint : public utility::pointer::ReferenceCount {
public:


  typedef std::string String;
  typedef core::Size Size;
  typedef core::Real Real;
  typedef core::pose::Pose Pose;
  typedef core::kinematics::MoveMapOP MoveMapOP;

public: // constructor/destructor


  /// @brief default constructor
  BluePrint();

  /// @brief value constructor
  BluePrint( String const & filename );

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

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


public: // accessor


  /// @brief total residue number defined in blueprint file
  Size total_residue() const;

  /// @brief total residue number without ligand defined in blueprint file
  Size total_residue_wolig() const;
  
  /// @brief sequence defined in blueprint file
  String sequence() const;

  /// @brief a~mino acid type at a position in blueprint file
  char sequence( Size seqpos ) const;

  /// @brief secondary structures defined in blueprint file
  String secstruct() const;

  /// @brief secondary structure at a position in blueprint file
  char secstruct( Size seqpos ) const;

  /// @brief abego defined in bludprint file
  utility::vector1< String > abego() const;

  /// @brief secondary structure at a position in blueprint file
  String abego( Size seqpos ) const;

  /// @brief residue number at each position in blueprint file
  Size resnum( Size seqpos ) const;

  /// @brief translate residue number of pose to that of blueprint file
  Size resnum_map( Size resnum_pose ) const;

  /// @brief return build type at each position
  char buildtype( Size seqpos ) const;

  /// @brief return build type at each position
  String extra( Size seqpos ) const;

  String insertion( Size i ) const;

  /// @brief helix pairings defined at the line of HHPAIR in blueprint
  String helix_pairings() const;

  /// @brief strand pairings defined at the line of SSPAIR in blueprint
  String strand_pairings() const;

  /// @brief strand pairings defined at the line of SSPAIR in blueprint
  String hss_triplets() const;

  /// @brief secondary structure information
  //SS_Info2_OP ssinfo() const;


public: //


  /// @brief reading blueprint files
  bool read_blueprint( String const & );

  /// @brief set secondary structure into pose
  void insert_ss_into_pose( Pose & pose );

  /// @brief set movemap based on blueprint
  void set_movemap( MoveMapOP & movemap );


private: // to be removed


  /// @brief set strand pairings
  /// removed StrandPairings set_strand_pairings( SS_Info2_OP const & ssinfo, StrandPairings const & spairs ) const;


private: // data

  /// @brief total residue number defined in blueprint
  Size total_residue_;
  
  /// @brief total residue without ligand
  Size total_residue_wolig_;

  /// @brief sequence defined in blueprint
  String sequence_;

  /// @brief amino acid sequence defined in blueprint
  String secstruct_;

  /// @brief residue number of each position in blueprint
  utility::vector1< Size > resnum_;

  /// @brief amino acid type at a position in blueprint
  utility::vector1< char > resname_;

  /// @brief secondary structure type defined in blueprint
  utility::vector1< char > sstype_;

  /// @brief abego type defined in blueprint
  utility::vector1< String > abego_;

  /// @brief build type at each position in blueprint
  utility::vector1< char > buildtype_;

  /// @brief extra infomation at each position in blueprint
  utility::vector1< String > extra_;

  /// @brief pdb file name for insertion
  utility::vector1< String > insertion_;

  /// @brief translate pose residue number to blueprint residue number
  std::map< Size, Size > resnum_map_;

  /// @brief secondary structure information
  // SS_Info2_OP ss_info_;

  /// @brief strand pairings defined at the line of SSPAIR in blueprint
  String strand_pairings_;

  /// @brief helix pairings defined at the line of HHPAIR in blueprint
  String helix_pairings_;

  /// @brief helix-strand-strand triple defined at the line of HSSTRIPLE in blueprint
  String hss_triplets_;


}; //BluePrint

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

#endif