PDBPoseInputStream.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:
//
// (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/import_pose/pose_stream/PDBPoseInputStream.cc
/// @brief
/// @author James Thompson

// libRosetta headers

#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>

#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>

#include <basic/datacache/BasicDataCache.hh>

#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>

#include <basic/datacache/CacheableString.hh>

// C++ headers
#include <string>
#include <utility/exit.hh>

// Boost Headers
#include <boost/foreach.hpp>

#include <utility/vector1.hh>

#define foreach BOOST_FOREACH

namespace core {
namespace import_pose {
namespace pose_stream {


void PDBPoseInputStream::set_filenames(
  utility::vector1< utility::file::FileName > filenames
) {
  filenames_ = filenames;
  current_position_ = filenames_.begin();
}

utility::vector1< utility::file::FileName > PDBPoseInputStream::get_filenames() {
  return filenames_;
}

bool PDBPoseInputStream::has_another_pose() {
  return ( current_position_ != filenames_.end() );
}

void PDBPoseInputStream::reset(){
  current_position_ = filenames_.begin();
}

void PDBPoseInputStream::fill_pose(
  core::pose::Pose & pose,
  core::chemical::ResidueTypeSet const & residue_set
) {
  // check to make sure that we have more poses!
  if ( !has_another_pose() ) {
    utility_exit_with_message(
      "PDBPoseInputStream: called fill_pose, but I have no more Poses!"
    );
  }

  core::import_pose::pose_from_pdb( pose, residue_set, *current_position_ );
  // set up a tag using input filename.
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( *current_position_ )
  );
  ++current_position_;
  preprocess_pose( pose );
}

void PDBPoseInputStream::fill_pose(
  core::pose::Pose & pose
) {
  // check to make sure that we have more poses!
  if ( !has_another_pose() ) {
    utility_exit_with_message(
      "PDBPoseInputStream: called fill_pose, but I have no more Poses!"
    );
  }

  core::import_pose::pose_from_pdb( pose, *current_position_ );
  // set up a tag using input filename.
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( *current_position_ )
  );
  ++current_position_;
  preprocess_pose( pose );
}

utility::vector1< core::pose::Pose > PDBPoseInputStream::get_all_poses(
  core::chemical::ResidueTypeSet const & residue_set
) {
  utility::vector1< core::pose::Pose > pose_list;
  pose_list.resize( filenames_.size() );

  while( has_another_pose() ) {
    core::pose::Pose pose;
    fill_pose( pose, residue_set );
    pose_list.push_back( pose );
  }

  return pose_list;
}

/// @brief adds a list of files each containing lists of PDBs
void PDBPoseInputStream::add_list_filenames(
  utility::vector1< utility::file::FileName > list_fns
) {
  using utility::vector1;
  bool init_current_position( filenames_.size() == 0 );

  foreach(utility::file::FileName filename_obj, list_fns){
    std::string filename( filename_obj.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) ) {
      filenames_.push_back( utility::file::FileName(line) );
    }
    data.close();
  }

  if ( init_current_position ) {
    current_position_ = filenames_.begin();
  }
} // add_list_files

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