SilentFilePoseInputStream.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/SilentFilePoseInputStream.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/SilentFilePoseInputStream.hh>
#include <core/pose/util.hh>

#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#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>

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;

void SilentFilePoseInputStream::tags( utility::vector1< string > tags ) {
  tags_ = tags;
}

void SilentFilePoseInputStream::filenames(
  utility::vector1< FileName > filenames
) {
  filenames_  = filenames;
  // read in SilentStruct objects from all of the filenames
  read_all_files_();
  current_position_ = sfd_->begin();
}

void SilentFilePoseInputStream::reset()
{
  current_position_ = sfd_->begin();
}

/////////////////////////////////////////////////////
void
SilentFilePoseInputStream::set_silent_file_data(
  core::io::silent::SilentFileDataOP & sfd
) {
  sfd_ = sfd;

  filenames_.clear();

  if ( renumber_decoys() ) {
    tr.Debug << "renumbering decoys." << std::endl;
    sfd_->renumber_all_decoys();
  }

  if ( order_by_energy_ ) {
    tr.Debug << "ordering by energy" << std::endl;
    sfd_->order_by_energy();
  }

  current_position_ = sfd_->begin();
  tags_ = sfd_->tags();
}

void SilentFilePoseInputStream::renumber_decoys( bool const setting ) {
  renumber_decoys_ = setting;
}

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

utility::vector1< std::string > SilentFilePoseInputStream::tags() const {
  return tags_;
}

bool SilentFilePoseInputStream::renumber_decoys() const {
  return renumber_decoys_;
}

core::Real SilentFilePoseInputStream::energy_cut() const {
  return energy_cut_;
}

bool SilentFilePoseInputStream::has_another_pose() {
  if ( current_position_ != sfd_->end() ) {
    return true;
  } else {
    return false;
  }
}

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

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

  current_position_->fill_pose( pose, residue_set );
  // set up a tag using decoy_tag from SilentStruct
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( current_position_->decoy_tag() )
  );
  tr.Debug << "decoy_tag() == " << current_position_->decoy_tag() << std::endl;

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

  preprocess_pose( pose );

  ++current_position_;
} // fill_pose

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

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

  current_position_->fill_pose( pose );
  // set up a tag using decoy_tag from SilentStruct
  pose.data().set(
    core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG,
    new basic::datacache::CacheableString( current_position_->decoy_tag() )
  );
  tr.Debug << "decoy_tag() == " << current_position_->decoy_tag() << std::endl;

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

  preprocess_pose( pose );

  ++current_position_;
} // fill_pose



core::io::silent::SilentStructOP
SilentFilePoseInputStream::next_struct()
{
  // check to make sure that we have more poses!
  if ( !has_another_pose() ) {
    utility_exit_with_message(
      "SilentFilePoseInputStream: called next_struct, but I have no more structs!"
    );
  }

  core::io::silent::SilentStructOP silent_struct( *(current_position_) );
  ++current_position_;
  return silent_struct;
} // fill_pose


void SilentFilePoseInputStream::read_all_files_() {
  static basic::Tracer tr("core.io.pose_stream.silent");
  using utility::vector1;

  if (record_source_) sfd_->set_record_source( true );

  for ( vector1< FileName >::const_iterator current_fn_ = filenames_.begin();
        current_fn_ != filenames_.end(); ++current_fn_
  ) {

    if ( !file_exists( *current_fn_ ) ) {
      tr.Error << "Hey! Could not find " + std::string(*current_fn_)
        << std::endl;
      continue;
    }

    tr.Debug << "reading " << *current_fn_ << std::endl;
    if ( tags_.size() > 0 ) {
      sfd_->read_file( *current_fn_, tags_ );
    } else {
      sfd_->read_file( *current_fn_ );
    }
  }

  if ( renumber_decoys() ) {
    tr.Debug << "renumbering decoys." << std::endl;
    sfd_->renumber_all_decoys();
  }

  if ( energy_cut() != 1.0 ) {
    sfd_->score_filter( energy_cut() );
  }

  if ( order_by_energy_ ) {
    tr.Debug << "ordering by energy" << std::endl;
    sfd_->order_by_energy();
  }
}

void
SilentFilePoseInputStream::set_order_by_energy( bool const & setting ) {
  order_by_energy_ = setting;
}

void
SilentFilePoseInputStream::set_record_source( bool const & setting ) {
  record_source_ = setting;
}

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