DockMCMProtocol.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file docking_initialization_protocols
/// @brief initialization protocols for docking
/// @detailed
///   This contains the functions that create initial positions for docking
///   You can either randomize partner 1 or partner 2, spin partner 2, or
///   perform a simple perturbation.
/// @author Monica Berrondo
/// @author Modified by Sergey Lyskov


#ifndef INCLUDED_protocols_docking_DockMCMProtocol_hh
#define INCLUDED_protocols_docking_DockMCMProtocol_hh

// Unit Headers
#include <protocols/docking/DockingHighRes.hh>
#include <protocols/docking/DockMCMProtocol.fwd.hh>
// AUTO-REMOVED #include <protocols/docking/DockMCMCycle.hh>

// Package headers
#include <core/pose/Pose.fwd.hh>

#include <protocols/docking/DockFilters.fwd.hh>

#include <protocols/docking/DockMCMCycle.fwd.hh>
#include <utility/vector1.hh>
#include <core/kinematics/MoveMap.fwd.hh>

namespace protocols {
namespace docking {

class DockMCMProtocol : public DockingHighRes
{
  typedef core::Real Real;
public:

  /// @brief Default constructor
  DockMCMProtocol();

  /// @brief Constructor with one argument - the jump number.
  DockMCMProtocol(
    core::Size const rb_jump
  );

  /// @brief Constructor with three arguments. The first is the jump number, the second is the docking scorefunction
  /// and the third is the packing scorefxn.
  DockMCMProtocol(
    core::Size const rb_jump,
    core::scoring::ScoreFunctionOP scorefxn,
    core::scoring::ScoreFunctionOP scorefxn_pack
  );

  /// @brief Constructor with two arguments. The first is the DockJumps, the second is a scorefunction that will be
  /// used for docking and packing.
  DockMCMProtocol(
    DockJumps const movable_jumps,
    core::scoring::ScoreFunctionOP scorefxn
  );

  /// @brief Constructor with three arguments. The first is the DockJumps, the second is the docking scorefunction
  /// and the third is the packing scorefunction.
  DockMCMProtocol(
    DockJumps const movable_jumps,
    core::scoring::ScoreFunctionOP scorefxn,
    core::scoring::ScoreFunctionOP scorefxn_pack
  );

  // destructor
  ~DockMCMProtocol();

  //clone
  protocols::moves::MoverOP clone() const;

  /// @brief Performs the setup specific to this subclass of DockingHighRes (sets up filters).
  void init();

  void set_filter( DockingHighResFilterOP filter );

  // protocol functions
  virtual void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;
    
  void set_move_map(core::kinematics::MoveMapOP movemap );
  void set_second_cycle(Size const & num);
  void set_first_cycle(Size const & num);

  core::scoring::ScoreFunctionCOP scorefxn_docking() const;
  core::scoring::ScoreFunctionCOP scorefxn_packing() const;
  friend std::ostream & operator<<(std::ostream& out, const DockMCMProtocol & dmp );

private:
  DockingHighResFilterOP filter_;
  DockMCMCycleOP dock_mcm_; //JQX: make it as a memmber
    bool movemap_reset_ ;
    core::kinematics::MoveMapOP movemap_;
    Size num_of_first_cycle_;
    Size num_of_second_cycle_;
};

} // docking
} // protocols

#endif