H3RefineCCD.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:
//
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// (c) members of the Rosetta Commons. For more information, see
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/// @file protocols/antibody2/H3RefineCCD.hh
/// @brief Build a homology model of an antibody2
/// @detailed
///
///
/// @author Jianqing Xu (xubest@gmail.com)



#ifndef INCLUDED_protocols_antibody2_H3RefineCCD_hh
#define INCLUDED_protocols_antibody2_H3RefineCCD_hh


#include <core/pose/Pose.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/kinematics/MoveMap.fwd.hh>

#include <protocols/loops/Loops.hh>

#include <protocols/simple_moves/MinMover.fwd.hh>
#include <protocols/simple_moves/PackRotamersMover.fwd.hh>

#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.fwd.hh>
#include <protocols/moves/ChangeFoldTreeMover.fwd.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>

#include <protocols/antibody2/AntibodyInfo.hh>
#include <protocols/antibody2/H3RefineCCD.fwd.hh>


using namespace core;
namespace protocols {
namespace antibody2 {

class H3RefineCCD: public moves::Mover {


public:

    /// @brief default constructor
  H3RefineCCD();

    /// @brief constructor with arguments
    H3RefineCCD(AntibodyInfoOP antibody_info, AntibodyCDRNameEnum loop_name);
    
    /// @brief constructor with arguments
    H3RefineCCD(AntibodyInfoOP antibody_info, AntibodyCDRNameEnum loop_name, 
                       core::scoring::ScoreFunctionCOP highres_scorefxn );

    /// @brief constructor with arguments
    H3RefineCCD( AntibodyInfoOP antibody_info);


    void set_task_factory(pack::task::TaskFactoryCOP tf);

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

  /// @brief default destructor
  ~H3RefineCCD();


    void pass_start_pose(core::pose::Pose & start_pose);
    void turn_on_benchmark(){benchmark_=true;}
    void turn_off_flank_relax(){flank_relax_ = false;}
    void turn_off_h3_filter(){H3_filter_=false;}

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

    virtual std::string get_name() const;
    
  void set_highres_score_func(core::scoring::ScoreFunctionCOP highres_scorefxn){
        highres_scorefxn_ = new core::scoring::ScoreFunction(*highres_scorefxn);
    }

private:

    AntibodyInfoOP ab_info_;
    AntibodyCDRNameEnum loop_name_;
    loops::Loop the_loop_;
    core::Real high_cst_;
    core::Size loop_begin_,loop_end_,loop_size_;
    core::Size cutpoint_;
    core::Size n_small_moves_;
    core::Size inner_cycles_, outer_cycles_;
    bool include_neighbors_;

    core::kinematics::MoveMapOP cdrh3_map_, flank_cdrh3_map_;
    std::string minimization_type_;

    bool user_defined_;
    bool benchmark_;
    bool is_camelid_;


    // the objects
    moves::ChangeFoldTreeMoverOP change_FT_to_simpleloop_;
    moves::ChangeFoldTreeMoverOP change_FT_to_flankloop_;
    simple_moves::MinMoverOP loop_min_mover_;
    moves::SequenceMoverOP wiggle_cdr_h3_;
    simple_moves::PackRotamersMoverOP loop_repack_;
    moves::MonteCarloOP mc_;

    utility::vector1< bool> allow_repack_;

    core::Real init_temp_, last_temp_, gamma_;

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


    core::Real min_tolerance_;
    core::Real high_move_temp_;
    core::Real neighbor_dist_;

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


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


  /// @brief number of flanking residues:default 5
  core::Size flank_size_;

  /// @brief relax flanking regions of h3
  bool flank_relax_;

    core::pose::Pose start_pose_;

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

    /// @brief just refine input loop
  bool refine_input_loop_;

  core::Size max_cycle_close_trial_;

};







} // namespace antibody2
} // namespace protocols

#endif