SymDockProtocol.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file   protocols/symmetric_docking/SymDockProtocol.hh
///
/// @brief
/// @author Ingemar Andre


#ifndef INCLUDED_protocols_symmetric_docking_SymDockProtocol_hh
#define INCLUDED_protocols_symmetric_docking_SymDockProtocol_hh

#include <protocols/moves/Mover.hh>
#include <protocols/symmetric_docking/SymDockProtocol.fwd.hh>
// AUTO-REMOVED #include <protocols/symmetric_docking/SymDockBaseProtocol.hh>

#include <core/types.hh>

#include <core/kinematics/MoveMap.fwd.hh>

#include <core/pack/task/TaskFactory.fwd.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.fwd.hh>
#include <protocols/symmetric_docking/SymDockingHiRes.fwd.hh>
#include <core/conformation/symmetry/SymmetricConformation.fwd.hh>
#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>

#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.fwd.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace symmetric_docking {

void SymDock_main();

class SymDockProtocol : public moves::Mover
{
public:

typedef core::conformation::symmetry::SymmetricConformation SymmetricConformation;
typedef core::conformation::symmetry::SymmetryInfo SymmetryInfo;

public:

  SymDockProtocol();

  SymDockProtocol(
    bool const fullatom,
    bool const local_refine,
    bool const view=false
  );

  SymDockProtocol(
    bool const fullatom,
    bool const local_refine,
    bool const view,
    core::scoring::ScoreFunctionOP docking_score_low,
    core::scoring::ScoreFunctionOP docking_score_high
  );

  virtual ~SymDockProtocol();

  /// @brief setup that is called from constructor
  void set_default();

  void register_options();

  /// @brief setter

  void set_dock_rtmin( bool dock_rtmin_in );

  void set_sc_min( bool sc_min_in );
  void set_max_repeats( Size const max_repeats_in );
  void set_dock_ppk( bool dock_ppk_in );

  void set_fullatom( bool const fullatom_in );

  void set_local_refine( bool const local_refine_in );

  void set_view( bool view_in );

  void set_lowres_scorefxn( core::scoring::ScoreFunctionOP docking_score_low_in );

  void set_highres_scorefxn( core::scoring::ScoreFunctionOP docking_score_high_in );

  void set_highres_scorefxn(
    core::scoring::ScoreFunctionOP docking_score_high_in,
    core::scoring::ScoreFunctionOP docking_score_pack_in );

  bool docking_lowres_filter( core::pose::Pose & pose );
  bool docking_highres_filter( core::pose::Pose & pose );

  core::Real
  calc_interaction_energy( core::pose::Pose & pose );

  core::Real
  calc_rms( core::pose::Pose & pose );

  /// @brief recovers the side-chains from the native-pose
  void recover_sidechains( core::pose::Pose & pose, const core::pose::Pose & native_pose );

  void task_factory( core::pack::task::TaskFactoryOP task_factory );

  // turn on design of partner2 during docking. Not thoroughly tested!
  void design( bool const des );
  bool design() const;

  // skip population of the score map
  void hurry( bool const hurry );

  core::pack::task::TaskFactoryOP task_factory() const;
  core::pack::task::TaskFactoryOP & task_factory();

  void score_only( core::pose::Pose & pose );

  virtual void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;
  virtual protocols::moves::MoverOP clone() const;

private:

 void
  classic_mcm_protocol(
    core::pose::Pose & pose,
    core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn,
    protocols::moves::MonteCarloOP monteCarlo,
    core::Size num_cycles,
    core::Size repack_every_Nth
  ) const;

  protocols::moves::MoverOP
  make_dockmcm_mover(
    core::pose::Pose const & pose,
    protocols::moves::MoverOP repack_mover,
    protocols::moves::MoverOP rigbod_mover,
    core::kinematics::MoveMapOP movemap, //< would be COP but MinMover wants OP
    core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn,
    protocols::moves::MonteCarloOP monteCarlo
  ) const;

private:

/// information about the mode
  bool fullatom_;
  bool local_refine_;
  bool rtmin_;
  bool sc_min_;
  Size max_repeats_;
  bool dock_ppk_;

  /// the jump number across which to do rigid_body transformations
  utility::vector1<core::Size> movable_jumps_;
  //core::Size rb_jump_;
  /// should docking change the foldtree?
  bool autofoldtree_;
  /// whether or not to initialize the viewer (for opengl)
  bool view_;
  bool design_;
  bool passed_lowres_filter_;
  bool passed_highres_filter_;
  bool hurry_; // skip populating the score map
  // for outputting scorefiles
  std::map < std::string, core::Real > score_map_;

  // for scoring
  core::scoring::ScoreFunctionOP docking_score_low_;
  core::scoring::ScoreFunctionOP docking_score_high_;
  core::scoring::ScoreFunctionOP docking_score_high_min_;
  core::scoring::ScoreFunctionOP docking_score_pack_;

  moves::MonteCarloOP mc_;

  //protocols
  protocols::symmetric_docking::SymDockingLowResOP docking_low_;
  protocols::symmetric_docking::SymDockingHiResOP docking_high_;
  core::pack::task::TaskFactoryOP init_task_factory_; // use this to restrict the packer task for docking protocol

};

} // symmetric_docking
} // protocols
#endif //INCLUDED_protocols_symmetric_docking_SymDockProtocol_HH