PhiPsiTalosIO.cc

Go to the documentation of this file.

// -*- 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/PhiPsiTalosIO.cc
/// @brief
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

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

// project headers

#include <core/types.hh>
#include <basic/Tracer.hh>

// utility headers
#include <utility/exit.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/io/izstream.hh>
// AUTO-REMOVED #include <utility/io/ozstream.hh>

// C++ headers
#include <string>
#include <map>

// boost headers
#include <boost/tuple/tuple.hpp>
// AUTO-REMOVED #include <boost/algorithm/string.hpp>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {

static basic::Tracer
    tr("protocols.frag_picker.PhiPsiTalosIO");

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

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

  std::string line;
  last_residue_index_ = 0;
  first_residue_index_ = 1;
  bool first_not_found = true;
  utility::vector1< std::string > vars;
  while ( getline(data, line) ) {
    std::istringstream line_stream(line);
    utility::vector1<std::string> strs;
    std::string token;
    while ( line_stream >> token ) {
      strs.push_back(token);
    }
    if ( strs.size()==0 ) continue;
    tr.Trace << "token: " << strs.size() << " in line " << line << std::endl;
    if (strs[1] == "DATA") {
      if (strs[2] == "SEQUENCE") {
        for (Size i = 3; i <= strs.size(); ++i) {
          sequence_ += strs[i];
        }
      } else if (strs[2] == "FIRST_RESID") {
        first_not_found = false;
        line_stream >> first_residue_index_;
        tr.Info << "FIRST_RESID entry in TALOS file. Setting first-residue to " << first_residue_index_ << std::endl;
      } else {
        tr.Warning << "Unrecognized DATA entry:" << line
            << std::endl;
      }
    }
    if (strs[1] == "VARS") {
      for (Size i = 2; i <= strs.size(); ++i) {
        vars.push_back(strs[i]);
      }
      if ( ( vars.size()!=10 && vars.size()!=11 ) || vars[1]!="RESID" || vars[2]!="RESNAME" || vars[9]!="COUNT" || vars.back()!="CLASS" ) {
        tr.Warning << "incompatible format in TALOS+ file "+file_name
          +".\n Expected VARS  RESID RESNAME PHI PSI DPHI DPSI DIST S2 COUNT CS_COUNT CLASS\n "
          +" or      VARS  RESID RESNAME PHI PSI DPHI DPSI DIST S2 COUNT CLASS\n "
          +" found instead: ";
        tr.Warning << vars.size() << " VARS: ";
        for (Size i=1; i<=vars.size(); ++i) {
          tr.Warning << vars[i] << " ";
        }
        tr.Warning << " LAST VAR: ->" << vars.back() << ":";
        tr.Warning << std::endl;
      }
    }
    if (strs[1] == "FORMAT") {
      data_format_ = line.substr(7);
    }

    if ((strs.size() == vars.size()) && (strs[1] != "REMARK")) {
      char aa;
      std::istringstream line_stream(line);
      Real phi, psi, d_phi, d_psi, dist, s2;
      Size res_id, count;
      std::string cls;
      if ( vars.size()==10 ) {
        line_stream >> res_id >> aa >> phi >> psi >> d_phi >> d_psi >> dist
                    >> s2 >> count >> cls;
      } else {
        Size cs_count;
        line_stream >> res_id >> aa >> phi >> psi >> d_phi >> d_psi >> dist
                    >> s2 >> count >> cs_count >> cls;
      }
      data_format_ = " %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %5.3f %2d %s";
      //this adds sequence twice    sequence_ += aa;
      typedef boost::tuple<Size, char, Real,Real, Real, Real, Real, Real, Size, std::string> PhiPsiTalosLineEntry;
      PhiPsiTalosLineEntry  t(res_id, aa, phi, psi, d_phi, d_psi, dist,
          s2, count, cls);
      entries_.insert(std::pair<Size, PhiPsiTalosLineEntry > ( res_id,  t) );
      if (last_residue_index_ < res_id)
        last_residue_index_ = res_id;
    }
  }

  if (first_not_found) {
    tr.Warning
        << "FIRST_RESID keyword didn't show up in a file header\n\tAssuming the first residue id is 1"
        << std::endl;
  }
  if (sequence_.length() == 0) {
    for (Size i = first_residue_index_; i <= last_residue_index_; ++i) {
      if (has_entry(i)) {
        sequence_ += entries_.find(i)->second.get<1> ();
      } else {
        sequence_ += 'X';
      }
    }
    tr.Warning << "Could not find DATA SEQUENCE in file "<<file_name << std::endl
                            << "Sequence based on entires is:"  << std::endl
                            << sequence_ << std::endl;
  }
}


void PhiPsiTalosIO::write(std::ostream& out) {

  out << "DATA FIRST_RESID " << first_residue_index_ << "\n";
  out << "DATA SEQUENCE " << sequence_ << "\n";
  out << "VARS";
  for (Size i = 1; i <= column_names_.size(); i++)
    out << " " << column_names_[i];
  out << "\n" << "FORMAT " << data_format_ << std::endl << "\n";
  char buffer[100];
  char c1[2];
  c1[1] = 0;
  for (Size i = 1; i <= entries_.size(); i++) {
    c1[0] = entries_[i].get<1> ();
    sprintf(buffer, data_format_.c_str(), entries_[i].get<0> (), c1,
        entries_[i].get<2> (), entries_[i].get<3> (),
        entries_[i].get<4> (), entries_[i].get<5> (),
        entries_[i].get<6> (), entries_[i].get<7> (),
        entries_[i].get<8> (), entries_[i].get<9> ().c_str());
    out << buffer << "\n";
  }
  out << std::endl;
}

} // frag_picker
} // protocols