PDBJobInputter.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:
//
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/// @file   protocols/jd2/PDBJobInputter.cc
/// @brief  August 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter
/// @author Steven Lewis smlewi@gmail.com

///Unit headers
#include <protocols/jd2/PDBJobInputter.hh>
#include <protocols/jd2/PDBJobInputterCreator.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/InnerJob.hh>

///Project headers

// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <core/pose/Pose.hh>

///Utility headers
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <utility/vector1.hh>

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

#include <core/import_pose/import_pose.hh>


// option key includes

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

namespace protocols {
namespace jd2 {

protocols::jd2::PDBJobInputter::PDBJobInputter(){
  TR << "Instantiate PDBJobInputter" << std::endl;
}

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

///@details This function will first see if the pose already exists in the Job.  If not, it will read it into the pose reference, and hand a COP cloned from that pose to the Job. If the pose pre-exists it just copies the COP's pose into it.
void protocols::jd2::PDBJobInputter::pose_from_job( core::pose::Pose & pose, JobOP job){
  TR << "PDBJobInputter::pose_from_job" << std::endl;

  if( !job->inner_job()->get_pose() ){
    TR << "filling pose from PDB " << job->input_tag() << std::endl;
    core::import_pose::pose_from_pdb( pose, job->input_tag() );
    load_pose_into_job(pose, job);
  } else {
    TR << "filling pose from saved copy " << job->input_tag() << std::endl;
    pose = *(job->inner_job()->get_pose());
  }
}

///@details this function determines what jobs exist from -s/-l
void protocols::jd2::PDBJobInputter::fill_jobs( Jobs & jobs ){
  TR << "PDBJobInputter::fill_jobs" << std::endl;

  jobs.clear(); //should already be empty anyway

  utility::vector1< std::string > const inputs( basic::options::start_files() );
  core::Size const nstruct( get_nstruct() );

  for( core::Size i(1); i <= inputs.size(); ++i){
    //protocols::jobdist::BasicJob = protocols::jd2::InnerJob
    //note that we are not really using the second and third fields in this implementation
    InnerJobOP ijob( new InnerJob( inputs[i], nstruct ) );

    for( core::Size index(1); index <= nstruct; ++index){
      jobs.push_back( JobOP( new Job( ijob, index ) ) );
      TR << "pushing " << inputs[i] << " nstruct index " << index << std::endl;
    }//loop over nstruct
  }//loop over inputs
}//fill_jobs

/// @brief Return the type of input source that the PDBJobInputter is currently
///  using.
/// @return Always <em>PDB_FILE</em>.
JobInputterInputSource::Enum PDBJobInputter::input_source() const {
  return JobInputterInputSource::PDB_FILE;
}

//CREATOR SECTION
std::string
PDBJobInputterCreator::keyname() const
{
  return "PDBJobInputter";
}

protocols::jd2::JobInputterOP
PDBJobInputterCreator::create_JobInputter() const {
  return new PDBJobInputter;
}

}//jd2
}//protocols