H3PerturbCCD.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.
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/// @file protocols/antibody2/H3PerturbCCD.hh
/// @brief Build a homology model of an antibody2
/// @detailed
///
///
/// @author Jianqing Xu (xubest@gmail.com)



#ifndef INCLUDED_protocols_antibody2_H3PerturbCCD_hh
#define INCLUDED_protocols_antibody2_H3PerturbCCD_hh


#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/pose/Pose.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/fragment/FragSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/antibody2/AntibodyInfo.fwd.hh>
#include <protocols/antibody2/H3PerturbCCD.fwd.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>


using namespace core;
namespace protocols {
namespace antibody2 {



class H3PerturbCCD: public moves::Mover {


public:

    /// @brief default constructor
  H3PerturbCCD();
    
  /// @brief constructor with arguments
    H3PerturbCCD(AntibodyInfoOP antibody_in);

    /// @brief constructor with arguments
    H3PerturbCCD(AntibodyInfoOP antibody_in, 
                 core::scoring::ScoreFunctionCOP highres_scorefxn);

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

  /// @brief default destructor
  ~H3PerturbCCD();



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

    virtual std::string get_name() const {
        return "H3PerturbCCD";
    }

    void read_and_store_fragments();


    void pass_the_loop(loops::Loop & input_loop){
        input_loop_ = input_loop;
    }

    void turn_off_H3_filter(){
        H3_filter_ = false;
    }
    
    /// @brief set scorefunction for low resolution of CDR H3 modeling
  void set_lowres_score_func(scoring::ScoreFunctionCOP lowres_scorefxn ){
        lowres_scorefxn_ = new core::scoring::ScoreFunction(*lowres_scorefxn);
    }

private:

    AntibodyInfoOP ab_info_;

    loops::Loop input_loop_;

    bool user_defined_;
    bool is_camelid_;



    void set_default();
    void init();

    void finalize_setup( core::pose::Pose & pose );


    /// @brief Build centroid mode CDR H3 loop
  void build_centroid_loop( core::pose::Pose & pose );

    void scored_frag_close(
                           core::pose::Pose & pose_in,
                           loops::Loop const trimmed_cdr_h3 );



    /// @brief size of loop above which 9mer frags are used
  core::Size cutoff_9_; // default 16

  /// @brief size of loop above which 3mer frags are used
  core::Size cutoff_3_; // default 6

    core::scoring::ScoreFunctionOP lowres_scorefxn_;

    core::Real cen_cst_;

    /// @brief flag indicating that current loop being modeled is CDR H3
  bool current_loop_is_H3_;

    /// @brief actually enables H3 filter for H3 operations
  bool H3_filter_;

    core::Size num_cycles1_;
    core::Size max_ccd_cycles_;

    utility::vector1< core::fragment::FragSetOP > cdr_h3_frags_;

    core::Real h3_fraction_;
    core::Real ccd_threshold_;
    core::Real Temperature_;

    protocols::moves::MonteCarloOP mc_, outer_mc_;

};



} // namespace antibody2
} // namespace protocols

#endif