ModelCDRH3.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
// (c) under license. The Rosetta software is developed by the contributing
// (c) members of the Rosetta Commons. For more information, see
// (c) http://www.rosettacommons.org. Questions about this can be addressed to
// (c) University of Washington UW TechTransfer,email:license@u.washington.edu.

/// @file protocols/antibody2/ModelCDRH3.hh
/// @brief
///// @author Jianqing Xu ( xubest@gmail.com )
//


#ifndef INCLUDED_protocols_antibody2_ModelCDRH3_hh
#define INCLUDED_protocols_antibody2_ModelCDRH3_hh

#include <protocols/antibody2/ModelCDRH3.fwd.hh>

#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/FragData.fwd.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/loop_mover/LoopMover.hh>
#include <protocols/moves/Mover.hh>
#include <utility/vector1.fwd.hh>
#include <protocols/antibody2/AntibodyInfo.fwd.hh>
#include <protocols/antibody2/H3PerturbCCD.fwd.hh>
#include <protocols/antibody2/H3CterInsert.fwd.hh>
#include <basic/Tracer.hh>
#include <protocols/loops/loop_mover/IndependentLoopMover.fwd.hh>




using namespace core;

namespace protocols {
namespace antibody2 {

//////////////////////////////////////////////////////////////////////////
/// @brief Ab initio modeling of CDR H3 loop
/// @details
class ModelCDRH3 : public protocols::moves::Mover {
public:
  /// @brief default constructor
  ModelCDRH3();

    /// @brief constructor with arguments
  ModelCDRH3(  AntibodyInfoOP antibody_info );
    
  /// @brief constructor with arguments
  ModelCDRH3(  AntibodyInfoOP antibody_info ,                         
                core::scoring::ScoreFunctionCOP lowres_scorefxn);

  /// @brief default destructor
  ~ModelCDRH3();
    
  void set_default();
  virtual void apply( pose::Pose & pose_in );
  virtual std::string get_name() const;

  /// @brief enable benchmark mode
  inline void enable_benchmark_mode( bool setting ) {
    benchmark_ = setting;
  }

  /// @brief enable camelid modeling mode
  inline void set_camelid( bool setting ) {
    is_camelid_ = setting;
  }


  /// @brief set scorefunction for low resolution of CDR H3 modeling
  void set_lowres_score_func(core::scoring::ScoreFunctionCOP lowres_scorefxn );

  /// @brief set task factory 
    void set_task_factory(pack::task::TaskFactoryCOP tf);
    
    void turn_off_H3_filter();
    
    void turn_off_cter_insert(){
        do_cter_insert_ = false;
    }
        

    void set_perturb_type(std::string setting){
        remodel_ = setting;
    }
    
    void set_bad_nter(bool setting){
        bad_nter_ = setting;
    }
    
private:
  bool user_defined_;
    
    bool do_cter_insert_;

  // constraints
  Real cen_cst_;
    pose::Pose hfr_pose_;
    
    
    /// @brief Number of ADDITIONAL residues modeled from H3_CTERM
  ///        These residues range from H:n-2,n-1,n,n+1 of H3
  Size c_ter_stem_;
    
    Size max_cycle_;
    

  // score functions
    core::scoring::ScoreFunctionOP lowres_scorefxn_;

  /// @brief benchmark flag
  bool benchmark_;
    
  /// @brief loop_building in docking
  bool loops_flag_;
    
  /// @brief insert fragment in docking
  bool dle_flag_;
    
    bool bad_nter_;


  /// @brief is camelid antibody without light chain
  bool is_camelid_;

  antibody2::AntibodyInfoOP ab_info_;

  //packer task
  pack::task::TaskFactoryOP tf_;

  void init();

    H3CterInsertOP h3_cter_insert_mover_;
    H3PerturbCCDOP h3_perturb_ccd_build_;
    loops::loop_mover::IndependentLoopMoverOP remodel_mover_;

    
    std::string remodel_;
    
}; // class ModelCDRH3


    


// JQX: make a class, which inherits from abstract class "loop_mover"
//class my_LoopMover: public protocols::loops::loop_mover::LoopMover {
//protected:
//    virtual basic::Tracer & tr() const;
//};
    



} // antibody2
} // protocols


#endif