DockMCMCycle.hh

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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 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_DockMCMCycle_hh
#define INCLUDED_protocols_docking_DockMCMCycle_hh

#include <protocols/docking/types.hh>
#include <protocols/docking/DockMCMCycle.fwd.hh>
// AUTO-REMOVED #include <protocols/docking/DockTaskFactory.hh>

// Package headers
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>

#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/TrialMover.fwd.hh>

#include <core/scoring/ScoreFunction.fwd.hh>

#include <protocols/moves/MoverContainer.fwd.hh>
#include <utility/vector1.hh>
#include <iostream>



// option key includes

namespace protocols {
namespace docking {

class DockMCMCycle : public moves::Mover
{
  typedef core::Real Real;
public:

  /// @brief Default constructor
  DockMCMCycle();

  /// @brief Constructor with two arguments: The first argument is the jump number to dock over.
  ///   The second is a scorefunction that will be used for docking and packing.
  DockMCMCycle(
    core::Size const rb_jump,
    core::scoring::ScoreFunctionOP scorefxn
  );

  /// @brief Constructor with arguments: The first argument is the jump number to dock over.
  ///   The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing.
  DockMCMCycle(
    core::Size const rb_jump,
    core::scoring::ScoreFunctionOP scorefxn,
    core::scoring::ScoreFunctionOP scorefxn_pack
  );

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

  ~DockMCMCycle();

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

  /// @brief Sets the default values for all members
  void set_default();

  void set_move_map( core::kinematics::MoveMapOP movemap );
  void set_min_type( std::string min_type ) { min_type_ = min_type; }
  void set_task_factory( core::pack::task::TaskFactoryCOP tf );

  moves::MonteCarloOP get_mc() { return mc_; }

  // protocol functions
  virtual void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

  void show( std::ostream & out=std::cout ) const;
  friend std::ostream & operator<<(std::ostream& out, const DockMCMCycle & dp );


  //JQX: allow the DockMCMProtocol.cc file to change the index of the CycleMover
  void reset_cycle_index();
  void init_mc(core::pose::Pose & pose);

    void set_scmin(bool setting){scmin_=setting;}
    void set_rtmin(bool setting){rtmin_=setting;}
    void set_rot_magnitude(core::Real value){rot_magnitude_=value;}

  DockJumps const & movable_jumps() const;

private:
  core::scoring::ScoreFunctionOP scorefxn_;
  core::scoring::ScoreFunctionOP scorefxn_pack_;
  core::kinematics::MoveMapOP movemap_;
  // moves::TrialMoverOP dock_mcm_mover_;
  moves::CycleMoverOP dock_mcm_cycle_; //JQX define it
  moves::MonteCarloOP mc_;



  // docking
  DockJumps movable_jumps_;
  core::Real trans_magnitude_, rot_magnitude_;
  bool rtmin_, scmin_; // belongs to the packer task

  void setup_protocol( core::pose::Pose & pose );
  /// @brief tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below
  core::pack::task::TaskFactoryOP tf_;
  /// @brief task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF!
  /// init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory
  core::Size repack_period_;

  bool norepack1_; // belongs to the packer task
  bool norepack2_; // belongs to the packer task

  // minimization
  core::Real min_tolerance_;
  bool nb_list_;
  std::string min_type_;
};

} // docking
} // protocols

#endif