AtomTreeDiffJobInputter.hh

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/// @file   protocols/jd2/AtomTreeDiffJobInputter.hh
/// @brief  header file for AtomTreeDiffJobInputter class
/// @author Gordon Lemmon (gordon.h.lemmon@vanderbilt.edu); Rocco Moretti (rmoretti@u.washington.edu)


#ifndef INCLUDED_protocols_jd2_AtomTreeDiffJobInputter_hh
#define INCLUDED_protocols_jd2_AtomTreeDiffJobInputter_hh

//unit headers
#include <protocols/jd2/JobInputter.hh>
#include <protocols/jd2/AtomTreeDiffJobInputter.fwd.hh>
#include <protocols/jd2/Job.fwd.hh>

//project headers
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/atom_tree_diffs/atom_tree_diff.hh>

#include <utility/vector1.hh>


//utility headers

namespace protocols {
namespace jd2 {

///@details This is the simplest implementation of JobInputter, which reads from -s/-l and AtomTree files.
class AtomTreeDiffJobInputter : public protocols::jd2::JobInputter
{
public:

  AtomTreeDiffJobInputter();

  virtual ~AtomTreeDiffJobInputter();

  /// @brief this function is responsible for filling the pose reference with
  /// the pose indicated by the job.  The Job object (within its InnerJob)
  /// contains a PoseCOP.  This function needs to either fill the pose
  /// reference from the InnerJob or, on first demand of a pose from that
  /// InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill
  /// the reference.  This implementation uses pose_from_pdb
  virtual void pose_from_job( core::pose::Pose & pose, JobOP job );

  /// @brief this function determines what jobs exist from -in::file::silent and
  /// -in::file::tags.
  virtual void fill_jobs( Jobs & jobs );

  /// @brief Return the type of input source that the AtomTreeDiffJobInputter is currently
  ///  using.
  /// @return Always <em>ATOM_TREE_FILE</em>.
  virtual JobInputterInputSource::Enum input_source() const;

  /// @brief Utility function to allow mutatable (!) access to the reference
  /// poses of the undelying AtomTreeDiff object. Use with caution.
  ///
  /// @details This exists to allow setup on stored reference poses for properties that
  /// don't get saved/restored in PDB format, like covalent constraints for enzyme design.
  core::pose::PoseOPs const & all_ref_poses() const;

private:
  core::import_pose::atom_tree_diffs::AtomTreeDiff atom_tree_diff_;

}; // AtomTreeDiffJobInputter

} // namespace jd2
} // namespace protocols

#endif //INCLUDED_protocols_jd2_AtomTreeDiffJobInputter_HH