GraftCDRLoopsProtocol.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
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// (c) members of the Rosetta Commons. For more information, see
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/// @file protocols/antibody2/GraftCDRLoopsProtocol.hh
/// @brief Build a homology model of an antibody2
/// @detailed
///
///
/// @author Jianqing Xu ( xubest@gmail.com )


#ifndef INCLUDED_protocols_antibody2_GraftCDRLoopsProtocol_hh
#define INCLUDED_protocols_antibody2_GraftCDRLoopsProtocol_hh


#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/antibody2/AntibodyInfo.fwd.hh>
#include <protocols/antibody2/Ab_TemplateInfo.fwd.hh>
#include <protocols/antibody2/GraftCDRLoopsProtocol.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.fwd.hh>


using namespace core;

namespace protocols {
namespace antibody2 {

class GraftCDRLoopsProtocol: public moves::Mover {
public:
    typedef std::map < std::string, bool > GraftMap;

  // default constructor
  GraftCDRLoopsProtocol();

  // default destructor
  ~GraftCDRLoopsProtocol();

  virtual protocols::moves::MoverOP clone() const;

  /// @brief Assigns default values to primitive members
  void set_default();


  virtual void apply( core::pose::Pose & pose );

  // simple inline setters
  void set_graft_l1( bool graft_l1 ) {
    graft_l1_ = graft_l1;
  }
  void set_graft_l2( bool graft_l2 ) {
    graft_l2_ = graft_l2;
  }
  void set_graft_l3( bool graft_l3 ) {
    graft_l3_ = graft_l3;
  }
  void set_graft_h1( bool graft_h1 ) {
    graft_h1_ = graft_h1;
  }
  void set_graft_h2( bool graft_h2 ) {
    graft_h2_ = graft_h2;
  }
  void set_graft_h3( bool graft_h3 ) {
    graft_h3_ = graft_h3;
  }
  void set_h3_stem_graft(bool h3_stem_graft){
    h3_no_stem_graft_=h3_stem_graft;
  }
  void set_packonly_after_graft (bool setting){
    packonly_after_graft_ = setting;
  }
  void set_camelid( bool camelid ) {
    camelid_ = camelid;
  }
  void set_camelid_constraints( bool camelid_constraints ) {
    camelid_constraints_ = camelid_constraints;
  }
  void set_benchmark( bool benchmark ) {
    benchmark_ = benchmark;
  }
    void set_cst_weight(core::Real cst_weight){
    cst_weight_ = cst_weight;
  }
    void set_sc_min (bool scmin) {
    sc_min_ = scmin ;
  }
    void set_rt_min (bool rtmin) {
    rt_min_ = rtmin ;
  }
  virtual std::string get_name() const;

    
    /// @brief Associates relevant options with the AntibodyModeler class
    static void register_options();
    
  void display_constraint_residues( core::pose::Pose & pose );
    
    void show( std::ostream & out=std::cout );
    friend std::ostream & operator<<(std::ostream& out, const GraftCDRLoopsProtocol & ab_m_2 );

    
    
private:
  void finalize_setup( core::pose::Pose & pose );
  void init();
  void setup_objects();
  void init_from_options();
  
private:
  bool graft_l1_, graft_l2_, graft_l3_;
  bool graft_h1_, graft_h2_, graft_h3_;
  bool h3_no_stem_graft_;
  bool packonly_after_graft_;
  bool camelid_;
  bool camelid_constraints_;
    bool sc_min_;
  bool rt_min_;
  bool benchmark_;
    
  core::Real cst_weight_;
  core::scoring::ScoreFunctionOP scorefxn_pack_;

  AntibodyInfoOP ab_info_;
    Ab_TemplateInfoOP ab_t_info_ ;

  pack::task::TaskFactoryOP tf_;

    protocols::moves::SequenceMoverOP graft_sequence_ ;



}; // class GraftCDRLoopsProtocol

    
    
    
    
} // namespace antibody2
} // namespace protocols

#endif