ThreadingJob.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/comparative_modeling/ThreadingJob.hh
/// @brief  header file for ThreadingJob classes
/// @author

#ifndef INCLUDED_protocols_comparative_modeling_ThreadingJob_hh
#define INCLUDED_protocols_comparative_modeling_ThreadingJob_hh

//unit headers
#include <protocols/comparative_modeling/ThreadingJob.fwd.hh>
#include <protocols/jd2/InnerJob.hh>
#include <core/sequence/SequenceAlignment.hh>

//project headers
// AUTO-REMOVED #include <core/pose/Pose.hh>

#include <protocols/jd2/Parser.fwd.hh> //for friendship

//utility headers
#include <utility/pointer/ReferenceCount.hh>
#include <core/types.hh>

//C++ headers
#include <string>
// AUTO-REMOVED #include <list>

#include <protocols/loops/Loops.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace comparative_modeling {

///@details The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is.  InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct.  The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs).  InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.
class ThreadingJob : public protocols::jd2::InnerJob {
public:
  ///@brief ctor.  Note that it takes only the input tag and max nstruct,
  /// pose instantiation is deferred until the pose is needed
  ThreadingJob(
    core::pose::PoseCOP template_pdb,
    core::sequence::SequenceAlignmentCOP alignment,
    std::string const & input_tag,
    core::Size nstruct_max
  );

  ///@brief the alignment for this Job
  core::sequence::SequenceAlignment const & alignment() const {
    return *alignment_;
  }

  ///@brief convenience : alignment id
  std::string alignment_id() const {
    return alignment().alignment_id();
  }

  ///@brief returns the "standard" loop definition (as conservative as possible)
  protocols::loops::Loops loops( core::Size nres ) const;

  ///@brief returns list of extra residues to steal
  utility::vector1< core::Size > const & extra_residues_to_steal() const;
  void extra_residues_to_steal( utility::vector1< core::Size > const & res );

  //NOTE:
  //get_pose() will give you the parent_pdb and not the starting model, the starting model is created from the ThreadingJobInputter
  // i have done it like this, since we can have multiple parent decoys for a given alignment read in via a silent file.
  // thus, to keep track which job should work on which parent-pdb + alignment I put them here.
  // alternative: have get_pose() refer to the starting_model
  // InnerJob --> contains a sufficiently uniq id ( or pointer ) to fish out the parent_decoy when starting the job.
private:
  core::sequence::SequenceAlignmentCOP alignment_; // alignment from input .ali file
  core::sequence::SequenceAlignmentCOP fasta2template_;
  core::Size nres_template_;
    // alignment from template seq (in .ali) to template pdb
    //    accounts for missing density in the input file
  utility::vector1< core::Size > extra_residues_to_steal_;
};

} // namespace comparative_modeling
} // namespace protocols

#endif //INCLUDED_protocols_comparative_modeling_ThreadingJob_HH