NonlocalFrags.hh

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/// @file protocols/frag_picker/nonlocal/NonlocalFrags.hh
/// @author David Kim (dekim@u.washington.edu)

#ifndef INCLUDED_PROTOCOLS_FRAG_PICKER_NONLOCAL_NONLOCALFRAGS_HH
#define INCLUDED_PROTOCOLS_FRAG_PICKER_NONLOCAL_NONLOCALFRAGS_HH

// Unit header
#include <protocols/frag_picker/nonlocal/NonlocalFrags.fwd.hh>

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

// Package headers

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <protocols/moves/Mover.hh>

// Utility headers
#include <utility/vector1.hh>

namespace protocols {
namespace frag_picker {
namespace nonlocal {


class NonlocalFrags : public protocols::moves::Mover {

public:
  /// @brief Constructs a new mover
  NonlocalFrags();

  /// @brief Finds interacting non-local fragment pairs
  void apply(core::pose::Pose& pose);

  /// @brief Returns the name of this mover.
  std::string get_name() const;

  /// @brief Creates a copy of this instance
  protocols::moves::MoverOP clone() const;

  /// @brief Creates a new instance by calling the no-argument constructor
  protocols::moves::MoverOP fresh_instance() const;

  /// @brief Registers applicable options
  static void register_options();

private:

  void initialize();


  bool recover_checkpoint( const std::string tag, core::pose::Pose& pose );

  void write_checkpoint( const std::string tag, const std::string data );

  void read_checkpoint_file();

  /* Members */

  bool single_chain_;
  bool relax_input_;
  bool relax_input_with_coordinate_constraints_;
  Size relax_frags_repeats_;

  std::string checkpointfile_;
  std::map< std::string, std::string > checkpoints_map_;

  utility::vector1<Size> frag_sizes_;

  Size min_seq_sep_;
  core::Real ca_dist_squared_;
  Size min_contacts_per_res_;
  core::Real max_rmsd_after_relax_;
  core::Real max_ddg_score_;

  bool output_frags_pdbs_;
  bool output_idealized_;
};

}  // namespace nonlocal
}  // namespace frag_picker
}  // namespace protocols

#endif  // PROTOCOLS_FRAG_PICKER_NONLOCAL_FRAGS_NONLOCALFRAGS_HH_