LazySilentFilePoseInputStream.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/LazySilentFilePoseInputStream.hh
/// @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/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/LazySilentFilePoseInputStream.hh>
#include <core/pose/util.hh>

#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
// AUTO-REMOVED #include <utility/file/file_sys_util.hh>

#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileData.fwd.hh>

#include <basic/Tracer.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>

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

// C++ headers
#include <string>

//Auto Headers

namespace core {
namespace import_pose {
namespace pose_stream {

static basic::Tracer tr( "core.io.pose_stream" );

typedef std::string string;
typedef utility::file::FileName FileName;

bool LazySilentFilePoseInputStream::has_another_pose() {
  bool has_another(true);
  if ( current_filename_ == filenames_.end() && current_struct_ == sfd_.end() ) {
    has_another = false;
  }
  return has_another;
}

void LazySilentFilePoseInputStream::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(
      "LazySilentFilePoseInputStream: called fill_pose, but I have no more Poses!"
    );
  }

  static basic::Tracer tr( "core.io.pose_stream.lazy_silent_file" );

  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  if ( option[ run::debug ]() ) {
    core::Real debug_rmsd = current_struct_->get_debug_rmsd();
    tr.Debug << "RMSD to original coordinates for tag "
      << current_struct_->decoy_tag() << " = " << debug_rmsd << std::endl;
  }

  current_struct_->fill_pose( pose, residue_set );
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( current_struct_->decoy_tag() )
  );
  tr.Debug << "decoy_tag() == " << current_struct_->decoy_tag() << std::endl;

  core::pose::setPoseExtraScores( pose, "silent_score", current_struct_->get_energy( "score" ) );
  preprocess_pose( pose );

  // increment counters
  ++current_struct_;
  if ( current_struct_ == sfd_.end() && current_filename_ != filenames_.end() ) {
    ++current_filename_;
    if ( current_filename_ != filenames_.end() ) {
      sfd_.clear();
      tr.Debug << "reading silent-file named " << *current_filename_ << std::endl;
      sfd_.read_file( *current_filename_ );
      current_struct_ = sfd_.begin();
    }
  }

  tr.flush_all_channels();
} // fill_pose

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

  static basic::Tracer tr( "core.io.pose_stream.lazy_silent_file" );

  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  if ( option[ run::debug ]() ) {
    core::Real debug_rmsd = current_struct_->get_debug_rmsd();
    tr.Debug << "RMSD to original coordinates for tag "
      << current_struct_->decoy_tag() << " = " << debug_rmsd << std::endl;
  }

  current_struct_->fill_pose( pose );
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( current_struct_->decoy_tag() )
  );
  tr.Debug << "decoy_tag() == " << current_struct_->decoy_tag() << std::endl;

  core::pose::setPoseExtraScores( pose, "silent_score", current_struct_->get_energy( "score" ) );
  preprocess_pose( pose );

  // increment counters
  ++current_struct_;
  if ( current_struct_ == sfd_.end() && current_filename_ != filenames_.end() ) {
    ++current_filename_;
    if ( current_filename_ != filenames_.end() ) {
      sfd_.clear();
      tr.Debug << "reading silent-file named " << *current_filename_ << std::endl;
      sfd_.read_file( *current_filename_ );
      current_struct_ = sfd_.begin();
    }
  }

  tr.flush_all_channels();
} // fill_pose

void LazySilentFilePoseInputStream::reset() {
  filenames_        = utility::vector1< FileName >();
  current_filename_ = filenames_.end();
  current_struct_   = sfd_.end();
}

utility::vector1< FileName > const & LazySilentFilePoseInputStream::filenames() const {
  return filenames_;
}

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