RefineOneCDRLoopCentroid.hh

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// vi: set ts=2 noet:
//
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/// @file protocols/antibody2/RefineOneCDRLoopCentroid.hh
/// @brief Build a homology model of an antibody2
/// @detailed
///
///
/// @author Jianqing Xu (xubest@gmail.com)



#ifndef INCLUDED_protocols_antibody2_RefineOneCDRLoopCentroid_hh
#define INCLUDED_protocols_antibody2_RefineOneCDRLoopCentroid_hh


#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/simple_moves/MinMover.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.fwd.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <protocols/antibody2/AntibodyInfo.hh>
#include <protocols/antibody2/RefineOneCDRLoopCentroid.fwd.hh>



using namespace core;
namespace protocols {
namespace antibody2 {

class RefineOneCDRLoopCentroid: public moves::Mover {


public:

    /// @brief constructor with arguments
    RefineOneCDRLoopCentroid(AntibodyInfoCOP antibody_info,
               AntibodyCDRNameEnum const & loop_name);
  
  RefineOneCDRLoopCentroid(AntibodyInfoCOP antibody_info,
               AntibodyCDRNameEnum const & loop_name,
              core::scoring::ScoreFunctionCOP scorefxn );
  
    /// @brief constructor with arguments
    RefineOneCDRLoopCentroid( loops::Loop const & a_cdr_loop);
  
  RefineOneCDRLoopCentroid( loops::Loop const & a_cdr_loop,
               core::scoring::ScoreFunctionCOP scorefxn );

    /// @brief default destructor
  ~RefineOneCDRLoopCentroid();
    

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

  void set_benchmark(bool const & setting){
        benchmark_ = setting;
    }
  void set_snugfit(bool const & setting){
        snug_fit_ = setting;
    }
  void set_refine_input_loop(bool const & setting){
        refine_input_loop_ = setting;
    }
  
  void set_score_function(core::scoring::ScoreFunctionCOP scorefxn);

  
private:
  void set_default();
    void finalize_setup( core::pose::Pose const & pose );
  void loop_centroid_relax(
                             pose::Pose & pose,
                             Size const loop_begin,
                             Size const loop_end );
  
private:
    loops::Loop the_cdr_loop_;
    
    bool benchmark_;
  bool snug_fit_;
  bool refine_input_loop_;
  scoring::ScoreFunctionOP lowres_scorefxn_;

};





} // namespace antibody2
} // namespace protocols

#endif