RefineOneCDRLoop.hh

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



#ifndef INCLUDED_protocols_antibody2_RefineOneCDRLoop_hh
#define INCLUDED_protocols_antibody2_RefineOneCDRLoop_hh


#include <core/pose/Pose.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/antibody2/AntibodyInfo.hh>
#include <protocols/antibody2/RefineOneCDRLoop.fwd.hh>



using namespace core;
namespace protocols {
namespace antibody2 {

class RefineOneCDRLoop: public moves::Mover {


public:

  /// @brief default constructor
  RefineOneCDRLoop();

  /// @brief constructor with arguments
  RefineOneCDRLoop( AntibodyInfoOP antibody_info);

  /// @brief constructor with arguments
  RefineOneCDRLoop(AntibodyInfoOP antibody_info, std::string refine_mode);

  /// @brief constructor with arguments
  RefineOneCDRLoop(AntibodyInfoOP antibody_info, std::string refine_mode,
    core::scoring::ScoreFunctionCOP scorefxn );

    /// @brief constructor with arguments
    RefineOneCDRLoop(AntibodyInfoOP antibody_info, 
                     AntibodyCDRNameEnum const & cdr_loop_name,
                     std::string refine_mode,
                     core::scoring::ScoreFunctionCOP scorefxn );

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


  void turn_on_benchmark(){
    benchmark_=true;
  }
  void set_h3_filter(bool setting){
    H3_filter_=setting;
  }
  void set_num_filter_tries(core::Size setting){
    num_filter_tries_=setting;
  }
  void set_flank_relax(bool setting){
    flank_relax_=setting;
  }
  void set_flank_size(core::Size setting){
    flank_size_=setting;
  }
  void set_refine_mode(std::string refine_mode){
    refine_mode_ = refine_mode;
  }
  virtual void apply( core::pose::Pose & pose );


  void set_score_function(core::scoring::ScoreFunctionCOP scorefxn);

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

    
private:

  AntibodyInfoOP ab_info_;
  bool user_defined_;
  bool benchmark_;
  core::scoring::ScoreFunctionOP scorefxn_;
  core::Size flank_size_;
  bool flank_relax_;
  core::pose::Pose start_pose_;
  core::pack::task::TaskFactoryOP tf_;
    bool H3_filter_;
    core::Size num_filter_tries_;
    std::string refine_mode_;
    AntibodyCDRNameEnum cdr_loop_name_;
    core::Real high_cst_;
    
    void set_default();
    void init();
    void finalize_setup( core::pose::Pose & pose );
    
};







} // namespace antibody2
} // namespace protocols

#endif