ResidualDipolarCouplingRigidSegments.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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/// @file   core/scoring/ResidualDipolarCouplingRigidSegments.hh
/// @brief  Creates, stores and manages a list of individual RDC objects for Rigid Segment-based RDC scoring
/// @author Nikolas Sgourakis

#ifndef INCLUDED_protocols_scoring_ResidualDipolarCouplingRigidSegments_hh
#define INCLUDED_protocols_scoring_ResidualDipolarCouplingRigidSegments_hh

#include <protocols/scoring/ResidualDipolarCouplingRigidSegments.fwd.hh>
// AUTO-REMOVED #include <core/scoring/methods/ResidualDipolarCouplingRigidSegmentsEnergy.fwd.hh>
#include <core/types.hh>
#include <numeric/xyzVector.hh>

#include <basic/datacache/CacheableData.hh>
#include <numeric/numeric.functions.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/pose/Pose.fwd.hh>

#include <core/scoring/ResidualDipolarCoupling.hh>
#include <protocols/loops/Loops.hh>
#include <utility/vector1.hh>

namespace protocols {
namespace scoring {

void store_RDC_segments_in_pose(ResidualDipolarCouplingRigidSegmentsOP, core::pose::Pose&);
ResidualDipolarCouplingRigidSegmentsOP retrieve_RDC_segments_from_pose(core::pose::Pose&);
ResidualDipolarCouplingRigidSegmentsCOP retrieve_RDC_segments_from_pose(core::pose::Pose const&);

///@brief ResidualDipolarCouplingRigidSegmentss are mainly handled by this class
///@detail related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling
///                         ResidualDipolarCouplingRigidSegmentsEnergy -- an energy method which triggers computations handled by this class.
///
///
  class ResidualDipolarCouplingRigidSegments: public basic::datacache::CacheableData {
  //  friend class ResidualDipolarCouplingRigidSegmentsEnergy;
public:
  // typedefs
  typedef core::Real Real;
  typedef core::Size Size;
  typedef core::scoring::ResidualDipolarCoupling::RDC_lines RDC_lines;
  typedef utility::vector1< core::scoring::ResidualDipolarCouplingOP > RDC_Segments;

public:
  /// @brief standard c'stor -- will access option -in:file:rdc to read RDC data
  //  ResidualDipolarCouplingRigidSegments() :
  //    nex_(0), nrows_(0) {
  //    reserve_buffers();
  //    read_RDC_file();
  //  }

  ResidualDipolarCouplingRigidSegments() {
    //    std::cout << "Calling Constructor" << std::endl;
    read_RDC_segment_file_from_cmdline();
    sort_into_segments( read_RDCs_from_cmdline() );
  }

  /// @brief alternative c'stor if you have a list of RDC lines
  /*  ResidualDipolarCouplingRigidSegments( RDC_lines data_in, Loops segments ) :
    All_RDC_lines_(data_in) {
  //  preprocess_data();
  //  reserve_buffers();
    }*/

  //explicit copy c'stor to initialize buffers
  //  ResidualDipolarCouplingRigidSegments(ResidualDipolarCouplingRigidSegments const& other);

  //explicit assignment operator to initialize buffers
  // ResidualDipolarCouplingRigidSegments& operator=(ResidualDipolarCouplingRigidSegments const & other);

  //explicit destructor because we use raw pointers for buffers
  // virtual ~ResidualDipolarCouplingRigidSegments();

  //this class lives in the PoseCache.... need to provide clone()
    basic::datacache::CacheableDataOP clone() const {
    return new ResidualDipolarCouplingRigidSegments(*this);
  }

  ///@brief compute dipolar score for given segment definition
  /// alignment tensor optimization will be performed for each segment individually
    core::Real compute_total_score(core::pose::Pose const& pose)const;
    core::Real compute_pairwise_score() const; ///total score must have been evaluated before calls to this method are made.
  ///@brief read RDC data from file
 //  void read_RDC_file();

  // do you need accessor for individual Tensors... do it like this
  //Tensor tensor_of_segment( Size i );

  void show(std::ostream&) const;

private:
  ///@brief read RDC data from file
  void sort_into_segments(RDC_lines all_rdcs);
  RDC_lines read_RDCs_from_cmdline() const;
  void read_RDC_segment_file_from_cmdline();
  void read_RDC_segment_file(std::string const& );
  Size find_segid_from_RDC_line(core::scoring::RDC const& line) const;
  Size find_effective_plane(core::scoring::RDC const& line) const;

private:
  RDC_Segments rdc_segments_;
  protocols::loops::Loops segment_definitions_;
};

  extern std::ostream& operator<<(std::ostream&, ResidualDipolarCouplingRigidSegments const&);

} //scoring
} //core

#endif