LoopMover_KIC.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.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @brief
/// @author Mike Tyka
/// @author Daniel J. Mandell

#ifndef INCLUDED_protocols_loops_loop_mover_refine_LoopMover_KIC_hh
#define INCLUDED_protocols_loops_loop_mover_refine_LoopMover_KIC_hh

#include <protocols/loops/loop_mover/refine/LoopMover_KIC.fwd.hh>
#include <protocols/loops/loop_mover/IndependentLoopMover.hh>
#include <protocols/moves/Mover.hh>

#include <core/types.hh>
// AUTO-REMOVED #include <basic/Tracer.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
// AUTO-REMOVED #include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.fwd.hh>

#include <utility/vector1.hh>


// C++ Headers


///////////////////////////////////////////////////////////////////////////////
namespace protocols {
namespace loops {
namespace loop_mover {
namespace refine {

class LoopMover_Refine_KIC: public loop_mover::LoopMover {
public:
  //constructors
  LoopMover_Refine_KIC();
    
    LoopMover_Refine_KIC(
    protocols::loops::LoopsOP  loops_in
  );

  LoopMover_Refine_KIC(
    protocols::loops::LoopsOP const loops_in,
    core::scoring::ScoreFunctionCOP  scorefxn
  );

  //destructor
  ~LoopMover_Refine_KIC();
    
    void init( core::scoring::ScoreFunctionCOP  scorefxn );
  void set_default_settings();

  void set_redesign_loop( bool value = true ){ redesign_loop_ = value; }
  bool get_redesign_loop(){ return redesign_loop_; }
  void set_flank_residue_min(bool value) {flank_residue_min_ = value;} // by JQX

  void set_task_factory( core::pack::task::TaskFactoryOP value );
  bool get_task_factory();

  /// @brief Clone this object
  virtual protocols::moves::MoverOP clone() const;

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

  ///@brief update the vector of movemaps, one for each loop in loops_
  void
  update_movemap_vectors(
    core::pose::Pose & pose,
    utility::vector1<core::kinematics::MoveMap> & move_maps );

  ///@brief update the vector of vectors of moveable side-chain positions, one for each loop in loops_
  void
  update_allow_sc_vectors(
    core::pose::Pose & pose,
    utility::vector1< utility::vector1< bool > > & allow_sc_vectors );

  void
  set_rottrials_from_kic_segment(
    core::pose::Pose & pose,
    core::pack::task::PackerTaskOP & rottrials_packer_task,
    Size kic_start,
    Size kic_end );

  void
  set_movemap_from_kic_segment(
    core::pose::Pose & pose,
    core::kinematics::MoveMap & cur_mm,
    Size kic_start,
    Size kic_end );

protected:

  core::pack::task::TaskFactoryOP task_factory;
  bool redesign_loop_;
    virtual basic::Tracer & tr() const;

private:

  core::Real neighbor_dist_; // CB distance to loop to consider scaffold side-chain for rot trials, repack, dfpmin
  core::Size max_seglen_; // maximum KIC segment length
  bool recover_low_; // flag to recover the lowest energy MC conformation rather than the last conformation
  bool min_after_repack_; // should inner cycle repacking steps be followed by minimization
  bool fix_natsc_; // should side-chains neighboring the loop be fixed
  bool optimize_only_kic_region_sidechains_after_move_; // Should we perform rotamer trials and minimization after every
                                // KIC move but only within the neighbor_dist of the KIC segment
  bool flank_residue_min_; //JQX
};

} //namespace refine
} //namespace loop_mover
} //namespace loops
} //namespace protocols

#endif //INCLUDED_protocols_loops_loop_mover_refne_LoopMover_KIC_HH