util.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:
//
// (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/core/pose_stream/util.hh
/// @brief
/// @author James Thompson

#ifndef INCLUDED_core_pose_stream_util_HH
#define INCLUDED_core_pose_stream_util_HH


#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/ExtendedPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/LazySilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>

#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>

#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

#include <string>

#include <utility/io/izstream.hh>

#include <utility/vector1.hh>
#include <boost/bind.hpp>


namespace core {
namespace import_pose {
namespace pose_stream {


utility::vector1< utility::file::FileName > filenames_from_list_file(
  utility::vector1< utility::file::FileName > const & list_fns
) {

  using std::string;
  using utility::vector1;
  using utility::file::FileName;

  vector1< FileName > fns_to_return;

  for ( vector1< FileName >::const_iterator it = list_fns.begin(),
        it_end = list_fns.end();
        it != it_end; ++it
  ) {
    std::string filename( it->name() );
    utility::io::izstream data( filename.c_str() );
    if ( !data.good() )
      utility_exit_with_message( "Unable to open file: " + filename + '\n' );

    std::string line;
    while( getline(data, line) ) {
      fns_to_return.push_back( utility::file::FileName(line) );
    }
    data.close();
  }

  return fns_to_return;
}

MetaPoseInputStream streams_from_cmd_line() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  MetaPoseInputStream input;
  if ( option[ in::file::s ].user() ) {
    PDBPoseInputStreamOP pdb_input(
      new PDBPoseInputStream( option[ in::file::s ]() )
    );
    input.add_pose_input_stream( pdb_input );
  }
  if ( option[ in::file::l ].user() ) {
    PDBPoseInputStreamOP pdb_list_input(
      new PDBPoseInputStream( filenames_from_list_file( option[ in::file::l ]() ) )
    );
    input.add_pose_input_stream( pdb_list_input );
  }

  if ( option[ in::file::silent ].user() ) {
    if ( option[ in::file::lazy_silent ]() ) {
      LazySilentFilePoseInputStreamOP silent_input(
        new LazySilentFilePoseInputStream( option[ in::file::silent ]() )
      );
      input.add_pose_input_stream(silent_input);

      if ( option[ in::file::silent_list ].user() ) {
        LazySilentFilePoseInputStreamOP silent_list_input(
          new LazySilentFilePoseInputStream( filenames_from_list_file(
            option[ in::file::silent_list ]()
          ) )
        );
        input.add_pose_input_stream(silent_list_input);
      }
    } else {
      SilentFilePoseInputStreamOP silent_input;
      if ( option[ in::file::tags ].user() ) {
        silent_input =
          new SilentFilePoseInputStream(
            option[ in::file::silent ](),
            option[ in::file::tags ](),
            option[ in::file::silent_energy_cut ]()
          );
      } else {
        silent_input = new SilentFilePoseInputStream(
          option[ in::file::silent ](), option[ in::file::silent_energy_cut ]()
        );
      }
      silent_input->renumber_decoys( option[ in::file::silent_renumber ]() );
      input.add_pose_input_stream( silent_input );
    }
  }

  if ( option[ in::file::extended_pose ].user() ) {
    Size const ntimes = option[ in::file::extended_pose ]();

    using utility::vector1;
    using utility::file::FileName;

    vector1< FileName > fasta_files( option[ in::file::fasta ]() );
    for ( vector1< FileName >::const_iterator it = fasta_files.begin(),
          end = fasta_files.end(); it != end; ++it
    ) {

      std::string sequence
        = core::sequence::read_fasta_file( option[ in::file::fasta ]()[1] )[1]->sequence();

      PoseInputStreamOP extended_protein_input(
        new ExtendedPoseInputStream( sequence, ntimes )
      );
      input.add_pose_input_stream( extended_protein_input );
    }
  }

  return input;
} // streams_from_cmd_line

} // pose_stream
} // import_pose
} // core

#endif