RNA_DataReader.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:
//  CVS information:
//  $Revision: 1.1.2.1 $
//  $Date: 2005/11/07 21:05:35 $
//  $Author: rhiju $
// (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.

#ifndef INCLUDED_protocols_rna_RNA_DataReader_hh
#define INCLUDED_protocols_rna_RNA_DataReader_hh

#include <protocols/rna/RNA_DataReader.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/rna/RNA_DataInfo.hh>
#include <core/kinematics/Jump.hh>
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>

// C++ Headers
#include <string>
// AUTO-REMOVED #include <map>
#include <iostream>
// AUTO-REMOVED #include <list>

#include <utility/vector1.hh>




namespace protocols {
namespace rna {


//////////////////////////////////////////////////////////////////////////////////////////////
class RNA_DataReader : public utility::pointer::ReferenceCount {
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~RNA_DataReader();

  //constructor
  RNA_DataReader();

  void
  initialize(
    core::pose::Pose & pose,
    std::string const rna_data_file
  );


private:

  void
  read_burial_info( std::istringstream & line_stream, ObjexxFCL::FArray1D< bool > & array_to_fill );

  void
  read_data_info( std::istringstream & line_stream );

  void
  read_data_from_file( std::string const & rna_data_file );

  void
  setup_rna_data( core::pose::Pose & pose );


  private:

  core::scoring::rna::RNA_DataInfo rna_data_info_;
  ObjexxFCL::FArray1D< bool> backbone_burial_;
  ObjexxFCL::FArray1D< bool> backbone_exposed_;

};


} //rna
} //protocols

#endif