PdbIdChunkFilter.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/VallChunkFilter.cc
/// @brief  defines two basic chunk filters based on pdb id
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

// package headers
#include <protocols/frag_picker/PdbIdChunkFilter.hh>

// mini
#include <utility/exit.hh>
#include <utility/io/izstream.hh>
#include <basic/Tracer.hh>


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

#include <protocols/frag_picker/VallChunk.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {

static basic::Tracer trPdbFilter("protocols.frag_picker.PdbIdChunkFilter");

void PdbIdChunkFilter::load_pdb_id_from_file(std::string file_name) {

  utility::io::izstream data(file_name.c_str());
  trPdbFilter.Info << "read allowed PDB ids  from: " << file_name
      << std::endl;
  if (!data)
    utility_exit_with_message("[ERROR] Unable to open a file fith allowed PDB ids: "
        + file_name);
  std::string line, pdb_id;
  while (getline(data, line)) {
    if (line.size() && line[0] == '#') continue;
    std::istringstream line_stream( line );
    line_stream >> pdb_id;
    add_pdb_id(pdb_id);

    if (pdb_id.size() > 4 && pdb_id[4] == '_') {
      pdb_id[4] = 'A';
      add_pdb_id(pdb_id);
    }
  }
  data.close();
}

void PdbIdChunkFilter::show_pdb_ids(std::ostream& out) {

  Size cnt = 0;
  std::map<std::string, bool>::iterator iter;
  out << '\n';
  for (iter = pdb_hash_.begin(); iter != pdb_hash_.end(); ++iter) {
    out << iter->first << " ";
    cnt++;
    if (cnt % 12 == 0)
      out << '\n';
  }
  out << std::endl;
}

bool DenyPdbIdFilter::test_chunk(VallChunkOP a_chunk) {

  std::string id = a_chunk->get_pdb_id() + a_chunk->get_chain_id();
  trPdbFilter.Debug << "Testing " << id << " ... ";
  if (pdb_hash_.find(id) != pdb_hash_.end()) {
    trPdbFilter.Debug << "FAILED" << std::endl;
    return false;
  }
  if (pdb_hash_.find(a_chunk->get_pdb_id()) != pdb_hash_.end()) {
    trPdbFilter.Debug << "FAILED" << std::endl;
    return false;
  }
  trPdbFilter.Debug << "OK" << std::endl;
  return true;
}

bool AllowPdbIdFilter::test_chunk(VallChunkOP a_chunk) {

  std::string id = a_chunk->get_pdb_id() + a_chunk->get_chain_id();
  trPdbFilter.Debug << "Testing " << id << " ... ";
  if (pdb_hash_.find(id) != pdb_hash_.end()) {
    trPdbFilter.Debug << "OK" << std::endl;
    return true;
  }
  if (pdb_hash_.find(a_chunk->get_pdb_id()) != pdb_hash_.end()) {
    trPdbFilter.Debug << "OK" << std::endl;
    return true;
  }
  trPdbFilter.Debug << "FAILED" << std::endl;
  return false;
}
} // frag_picker
} // protocols