JCouplingIO.cc

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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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file   protocols/frag_picker/CSTalosIO.cc
/// @brief
/// @author Nikolas Sgourakis sgourn@u.w.edu

// unit headers
#include <protocols/frag_picker/JCouplingIO.hh>

// project headers
#include <core/types.hh>

#include <basic/Tracer.hh>

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

#include <string>
#include <map>
#include <utility/exit.hh>

// boost headers
// AUTO-REMOVED #include <boost/tuple/tuple.hpp>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/option.hh>

namespace protocols {
namespace frag_picker {

using namespace basic::options;
using namespace basic::options::OptionKeys;
using namespace core;

static basic::Tracer trJCouplingIO("protocols.frag_picker.TalosReader");


void JCouplingIO::read(std::string const & file_name) {

  utility::io::izstream data(file_name.c_str());
  trJCouplingIO.Info << "read Jcoupling data from " << file_name << std::endl;
  if (!data)
    utility_exit_with_message("[ERROR] Unable to open Jcoupling file: "
        + file_name);

  std::string line;
  Size len;
  Real a, b, c, theta;

  getline(data, line);
  std::istringstream line_stream(line);
  line_stream >> len >> a >> b >> c >> theta;

  utility::vector1< Real > tmpv(len);
  utility::vector1< utility::vector1< Real > > temp_data( 1, tmpv );

  while (!data.eof()) {
    getline(data, line);
    std::istringstream line_stream(line);
    Real val, dev;
    Size res;
    line_stream >> res >> val >> dev;

    if (!(option[frags::filter_JC].user() && (val >4) && (val<6)  )) {
      temp_data[res].push_back(val);
      temp_data[res].push_back(dev);
//   std::cout << "DATA " << res << " " << val << " " << dev << std::endl;
    }
    //std::cout << "DATA " << res << " " << val << " " << dev << std::endl;

  }

  //Space for error checking and asserts

  data_ = temp_data;
  A_ = a;
  B_ = b;
  C_ = c;
  THETA_ = theta;
  sequence_length_ = len;
}

std::pair< Real, Real > JCouplingIO::get_data( Size const res_num, bool & has_data ){

  has_data = false;

  std::pair< Real, Real > temp;

  //std::cout << "GETTING " << res_num << " " << data_[res_num].size() << std::endl;

  if (data_[res_num].size() == 2) {
    temp.first = data_[res_num][1];
    temp.second = data_[res_num][2];
    has_data = true;
  }
  return temp;
}

utility::vector1< Real > JCouplingIO::get_parameters() {

  utility::vector1<Real> params;

  params.push_back(A_);
  params.push_back(B_);
  params.push_back(C_);
  params.push_back(THETA_);

  return params;
}


} // frag_picker
} // protocols