SegmentHybridizer.hh

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// vi: set ts=2 noet:
//
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/// @file protocols/seeded_abinitio/SegmentHybridizer.hh
/// @brief repurposing logic and some functions from CartesianHybridze protocols for segment insertions and chain closure
/// @author Eva-Maria Strauch

#ifndef INCLUDED_protocols_seeded_abinitio_SegmentHybridizer_HH
#define INCLUDED_protocols_seeded_abinitio_SegmentHybridizer_HH

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>
#include <boost/unordered/unordered_map.hpp>
#include <core/kinematics/MoveMap.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/Frame.hh>

namespace protocols {
namespace seeded_abinitio {

class SegmentHybridizer : public protocols::moves::Mover
{
public:
  typedef core::pose::Pose Pose;

public:
  SegmentHybridizer();
  virtual ~SegmentHybridizer();
  
  void apply( core::pose::Pose & pose );
  virtual protocols::moves::MoverOP clone() const;
  virtual protocols::moves::MoverOP fresh_instance() const;
  virtual std::string get_name() const;
  void parse_my_tag(  utility::tag::TagPtr const tag,
                                  protocols::moves::DataMap &,
                                  protocols::filters::Filters_map const &,
                                  protocols::moves::Movers_map const &,
                                  core::pose::Pose const & );
  void init();
  void set_scorefunction(core::scoring::ScoreFunctionOP scorefxn_in);
  void hybridize( core::pose::Pose & pose , core::Size insert_pos_start, core::Size insert_pos_stop);
  void apply_frame( core::pose::Pose & pose, core::fragment::Frame &frame );
  void check_and_create_fragments( core::pose::Pose & pose, core::Size insert_start, core::Size insert_stop );
  
private:
  // to output and score full atom again  
  core::scoring::ScoreFunctionOP highres_scorefxn_;
  core::scoring::ScoreFunctionOP lowres_scorefxn_;
  core::scoring::ScoreFunctionOP min_scorefxn_;
  core::scoring::ScoreFunctionOP bonds_scorefxn_;
  core::scoring::ScoreFunctionOP nocst_scorefxn_; 

  // for span/segment declarations
  utility::vector1< std::pair < std::string,std::string > > seg_vector_;

  // movemap for minimization
  core::kinematics::MoveMapOP mm_;
  core::kinematics::MoveMapOP extended_mm_;
  
  // for cartesian alignment
  core::Size cartfrag_overlap_;
  
  // how much outside of the replaced segment should be remodeled
  core::Size extend_outside_;
  core::Size extend_inside_;
  bool auto_mm_;

  /// fragments parts
  core::Real rms_;
  core::Size nfrags_ ;
  core::Size big_; 
  core::Size small_;
  core::fragment::FragSetOP fragments_big_;
  core::fragment::FragSetOP fragments_small_;
  boost::unordered_map<core::Size, core::fragment::Frame> library_;
  bool use_seq_;
  int tries_;
  core::Size mc_cycles_;
  core::Real temp_; 
  bool use_frags_;
  core::Size min_cycles_;
  bool all_movable_;
  bool extra_min_;
};


} // seeded_abinitio
} // protocols

#endif /*INCLUDED_protocols_seeded_abinitio_movers_SegmentHybridizer_HH*/