MatchResidues.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/fldsgn/MatchResidues.hh
/// @brief  header file for MatchResidues class
//  @brief  returns the RMSD between a subset of residues of the movered pose against a list of residues in the reference pose. 
/// @author Javier Castellanos ( javiercv@uw.edu )


#ifndef INCLUDED_protocols_fldsgn_MatchResidues_hh
#define INCLUDED_protocols_fldsgn_MatchResidues_hh

// Unit Headers

// Package Headers
#include <protocols/moves/Mover.fwd.hh>

// Project Headers
#include <core/pose/Pose.hh>
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>

// Parser headers
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <utility/tag/Tag.fwd.hh>

// Boost headers
#include <boost/tuple/tuple.hpp>


namespace protocols {
namespace fldsgn {

class MatchResidues {
public:

  typedef protocols::moves::Mover Mover;
  typedef protocols::moves::MoverOP MoverOP;
  typedef core::Real Real;
  typedef core::Size Size;
  typedef core::pose::Pose Pose;

  typedef utility::tag::TagPtr TagPtr;
  typedef protocols::moves::DataMap DataMap;
  typedef protocols::moves::Movers_map Movers_map;
  typedef protocols::filters::Filters_map Filters_map;
  typedef utility::vector1< Size > VecSize;
  typedef utility::vector1< VecSize > VecVecSize;


public:// constructor/destructor

  // @brief default constructor
  MatchResidues();

  virtual ~MatchResidues();



public:// parser

  void parse_my_tag( TagPtr const tag,
    DataMap &,
    Filters_map const &,
    Movers_map const &,
    Pose const & );


public:
  core::Real compute( core::pose::Pose const & pose, VecSize & best_fit ) const;
  core::Real compute_comb( core::pose::Pose const & pose, VecSize const & comb ) const;
  core::Real superimpose_comb( core::pose::Pose & pose, VecSize const & comb ) const;
  core::Real threshold() const { return threshold_; }
  void threshold(core::Real value) {  threshold_ = value; }

private:
  
  std::map< std::string, boost::tuple<Size, Size> >  map_ss_segments( std::string const & ss) const;

  void cart_product( VecVecSize& rvvi, VecSize&  rvi, VecVecSize::const_iterator me, VecVecSize::const_iterator end ) const;
  VecVecSize cart_product( VecVecSize const & input) const;

private:
  core::pose::Pose reference_pose_;
  VecSize reference_residues_indexes_;
  VecVecSize mod_segment_prod_;

  core::Real threshold_;

};

} // fldsgn
} // protocols

#endif