DockingHighRes.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:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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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_DockingHighRes_hh
#define INCLUDED_protocols_docking_DockingHighRes_hh

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

// Package headers
#include <protocols/docking/types.hh>
#include <protocols/docking/DockTaskFactory.fwd.hh>

// Project Headers
#include <core/pose/Pose.fwd.hh>

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

#include <protocols/moves/Mover.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <protocols/toolbox/task_operations/InterfaceTaskOperation.fwd.hh>


#include <utility/vector1.hh>


// option key includes

namespace protocols {
namespace docking {

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

  /// @brief Default constructor
  DockingHighRes();

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

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

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

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

  //Copy constructor
  DockingHighRes( DockingHighRes const & old_instance );

  virtual ~DockingHighRes();

  //clone
  //protocols::moves::MoverOP clone() const = 0;

  void set_task_factory( core::pack::task::TaskFactoryCOP tf );
  //allows one to ignore the DockTaskFactoryOP and allow use of whatever is given in set_task_factory()
  //only works for DockMCMProtocol at the moment
  void set_ignore_default_task( bool ignore_default_task );
  bool ignore_default_task();
  void set_scorefxn( core::scoring::ScoreFunctionOP scorefxn );
  void set_scorefxn_pack( core::scoring::ScoreFunctionOP scorefxn_pack );

  DockJumps & movable_jumps() { return movable_jumps_; }
  DockJumps const & movable_jumps() const { return movable_jumps_; }
  core::pack::task::TaskFactoryCOP task_factory();

  // protocol functions
  virtual void apply( core::pose::Pose & pose ) = 0;
  virtual std::string get_name() const = 0;

  void set_sc_min( bool sc_min ){ sc_min_ = sc_min; }
  void set_rt_min( bool rt_min ){ rt_min_ = rt_min; }
  void set_partners( std::string partners ) { partners_ = partners; }
    void set_interface_definition_task_operation( protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition );
    void set_additional_task_operarations( utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations );
    void add_additional_task_operaration( core::pack::task::operation::TaskOperationOP task_operation );
    utility::vector1< core::pack::task::operation::TaskOperationOP > get_additional_task_operarations();

    
  bool sc_min() { return sc_min_; }
  bool rt_min() { return rt_min_; }
  std::string partners() { return partners_; }

  core::scoring::ScoreFunctionOP scorefxn() const;
  core::scoring::ScoreFunctionOP scorefxn_pack() const;

protected:
  protocols::docking::DockTaskFactoryOP tf2();  //JQX: change COP to OP

private:
  bool sc_min_;
  bool rt_min_;
  std::string partners_;

  core::scoring::ScoreFunctionOP scorefxn_;
  core::scoring::ScoreFunctionOP scorefxn_pack_;

  // docking
  DockJumps movable_jumps_;

  // the task factory that will be used for all parts of docking
  core::pack::task::TaskFactoryOP tf_;
  protocols::docking::DockTaskFactoryOP tf2_; // tf2 = task factory factory - we use this to create our task factories
  bool ignore_default_task_; //will ignore the DockTaskFactoryOP and allow use of whatever is given in set_task_factory()
  void init( DockJumps const movable_jumps );
};

} // docking
} // protocols

#endif