PDBJobOutputter.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   protocols/jd2/PDBJobOutputter.cc
/// @brief  August 2008 job distributor as planned at RosettaCon08 - PDBJobOutputter
/// @author Steven Lewis smlewi@gmail.com

///Unit headers
#include <protocols/jd2/PDBJobOutputter.hh>
#include <protocols/jd2/PDBJobOutputterCreator.hh>
#include <protocols/jd2/Job.hh>

///Project headers
// AUTO-REMOVED #include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>
//#include <core/pose/datacache/CacheableDataType.hh>
#include <core/io/pdb/pose_io.hh>
// AUTO-REMOVED #include <core/scoring/Energies.hh>
// AUTO-REMOVED #include <core/scoring/EnergyMap.hh>

//#include <basic/datacache/CacheableStringFloatMap.hh>
//#include <basic/datacache/BasicDataCache.hh>

///Utility headers
#include <basic/Tracer.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
//#include <utility/file/FileName.hh>
#include <core/types.hh>
#include <basic/options/option.hh>

///C++ headers
//#include <string>
//#include <map>
#include <sstream>

// option key includes

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

#include <core/io/pdb/file_data.hh>
#include <utility/vector1.hh>




static basic::Tracer TR("protocols.jd2.PDBJobOutputter");

namespace protocols {
namespace jd2 {

protocols::jd2::PDBJobOutputter::PDBJobOutputter()
  : parent(), extension_(".pdb")
{
  using namespace basic::options::OptionKeys;
  using basic::options::option;

  TR.Debug << "Using PDBJobOutputter (base class) for JobDistributor" << std::endl;

  if ( option[ out::pdb_gz ] ) {
    extension_ = ".pdb.gz";
  }

  if ( option[ out::path::pdb ].user() ) {
    path_ = option[ out::path::pdb ]().path();
  } else if (option[ out::path::all ].user() ) {
    path_ = option[ out::path::all ]().path();
  } else {
    path_ = "";
  }
}

protocols::jd2::PDBJobOutputter::~PDBJobOutputter(){}

//////////////////////////////creating output functions/////////////////////////////////////////

void protocols::jd2::PDBJobOutputter::final_pose(
  JobCOP job,
  core::pose::Pose const & pose
)
{
    using namespace basic::options::OptionKeys;
  using basic::options::option;
  TR.Debug << "PDBJobOutputter::final_pose" << std::endl;

    utility::io::ozstream out( path_ + extended_name(job) );
  if ( !out.good() ) utility_exit_with_message( "Unable to open file: " + path_ + extended_name(job) + "\n" );
  dump_pose(job, pose, out);
  out.close();
  scorefile(job, pose);
}

void protocols::jd2::PDBJobOutputter::other_pose(
  JobCOP job,
  core::pose::Pose const & pose,
  std::string const & tag,
  int /*copy_count*/, /*default -1 */
  bool /* score_only*/ /*default false*/
){
  TR.Debug << "PDBJobOutputter::other_pose" << std::endl;
  runtime_assert( !tag.empty() ); //else you'll overwrite your pdb when the job finishes

  std::string const file(tag + extended_name(job));
  utility::io::ozstream out( file );
  if ( !out.good() ) utility_exit_with_message( "Unable to open file: " + file + "\n" );
  dump_pose(job, pose, out);
  out.close();

  //these are separate options because leaving the default on other_pose_scorefile is totally valid, but you can't both specify it on the command line and leave it blank
  //THIS FUNCTIONALITY IS GOING TO BE DEPRECATED SOON
  if( basic::options::option[ basic::options::OptionKeys::run::other_pose_to_scorefile ].value() ){
    scorefile(job, pose, tag, basic::options::option[ basic::options::OptionKeys::run::other_pose_scorefile ].value());
  }
}

///@details private function (just prevents code duplication) to fill ozstream
void protocols::jd2::PDBJobOutputter::dump_pose(
  JobCOP job,
  core::pose::Pose const & pose,
  utility::io::ozstream & out
)
{
  core::io::pdb::FileData::dump_pdb( pose, out );
  extract_scores(pose, out);
  //extract_extra_scores(pose, out);
  extract_data_from_Job( job, out );
}

/////////////////////////////////state of output functions/////////////////////////////////
bool protocols::jd2::PDBJobOutputter::job_has_completed( JobCOP job ){
  return utility::file::file_exists( path_ + extended_name(job) );
}

std::string protocols::jd2::PDBJobOutputter::output_name( JobCOP job ){
  return affixed_numbered_name( job );
}

std::string protocols::jd2::PDBJobOutputter::extended_name( JobCOP job ){
  return output_name(job) + extension_;
}

////////////////////////////////////////score-related functions///////////////////////////////////

///@brief this function extracts the pose's scores for printing
/// @details In order for this to work as expected, the Pose's cached energies
/// must match up with the (current) conformation.
/// A good time to do this is at the end of your protocol's apply() method:
///   scorefxn( pose );
void protocols::jd2::PDBJobOutputter::extract_scores(
  core::pose::Pose const & pose,
  utility::io::ozstream & out
)
{
  core::io::pdb::extract_scores( pose, out );
}

//THIS FUNCTION WILL MOVE HIGHER IN THE HIERARCHY AT SOME POINT
///@brief this function extracts the pose's scores for printing
void protocols::jd2::PDBJobOutputter::extract_data_from_Job( JobCOP job, utility::io::ozstream & out ){
  //TR << "protocols::jd2::PDBJobOutputter::extract_data_from_Job" << std::endl;

  for( Job::Strings::const_iterator it(job->output_strings_begin()), end(job->output_strings_end());
       it != end;
       ++it) {
    out << *it << std::endl;
    //TR << *it << std::endl;
  }

  for( Job::StringStringPairs::const_iterator it(job->output_string_string_pairs_begin()), end(job->output_string_string_pairs_end());
       it != end;
       ++it) {
    out << it->first << " " << it->second << std::endl;
    //TR << it->first << " " << it->second << std::endl;
  }

  for( Job::StringRealPairs::const_iterator it(job->output_string_real_pairs_begin()), end(job->output_string_real_pairs_end());
       it != end;
       ++it) {
    out << it->first << " " << it->second << std::endl;
    //TR << it->first << " " << it->second << std::endl;
  }

}


//This function is deprecated for now - might return in the future
// ///@brief this function extracts the pose's extra data/scores for printing
// ///@details YOU are responsible for putting things into the pose's ARBITRARY_FLOAT_DATA in the DataCache.  I suggest core::pose::util::setPoseExtraScores.
// void protocols::jd2::PDBJobOutputter::extract_extra_scores(
//                                                         core::pose::Pose const & pose,
//                                                         utility::io::ozstream & out)
// {
//  using namespace core::pose::datacache;
//  //is there extra data?
//  if( !pose.data().has( ( CacheableDataType::ARBITRARY_FLOAT_DATA ) ) ){
//    //TR << "no ARBITRARY_FLOAT_DATA" << std::endl;
//    return;
//  }

//  //get the data
//  //basic::CacheableStringFloatMapCOP data( dynamic_cast< basic::datacache::CacheableStringFloatMap const* > (pose.data().get_const_ptr(CacheableDataType::ARBITRARY_FLOAT_DATA)() ) );
//  //runtime_assert( data != NULL );
//  typedef std::map< std::string, float > StringFloatMap;
//  StringFloatMap data( (dynamic_cast< basic::datacache::CacheableStringFloatMap const* > (pose.data().get_const_ptr(CacheableDataType::ARBITRARY_FLOAT_DATA)() ) )->map() );

//  if (data.empty()) return;

//  //TR << "POSE EXTRA SCORES:" << std::endl;
//  out << "POSE EXTRA SCORES:" << std::endl;

//  //iterate through the map
//  for(StringFloatMap::const_iterator it(data.begin()), end(data.end()); it != end; ++it){
//    //TR << it->first << " " << it->second << std::endl;
//    out << it->first << " " << it->second << std::endl;
//  }

//  return;
// }

//CREATOR SECTION
std::string
PDBJobOutputterCreator::keyname() const
{
        return "PDBJobOutputter";
}

protocols::jd2::JobOutputterOP
PDBJobOutputterCreator::create_JobOutputter() const {
        return new PDBJobOutputter;
}

}//jd2
}//protocols