DistanceScoreMover.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file CrossPeakList.hh
/// @author Oliver Lange

#ifndef INCLUDED_protocols_noesy_assign_DistanceScoreMover_HH
#define INCLUDED_protocols_noesy_assign_DistanceScoreMover_HH


// Unit Headers
#include <protocols/noesy_assign/DistanceScoreMover.fwd.hh>

// Package Headers
// AUTO-REMOVED #include <protocols/noesy_assign/CrossPeakList.hh>
#include <protocols/noesy_assign/ResonanceList.fwd.hh>
#include <protocols/noesy_assign/PeakAssignment.hh>

// Project Headers
#include <protocols/moves/Mover.hh>
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

// Utility headers
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <protocols/noesy_assign/CrossPeakList.fwd.hh>

#ifdef WIN32
#include <core/scoring/constraints/AmbiguousNMRDistanceConstraint.hh>
#endif

namespace protocols {
namespace noesy_assign {

///@brief maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each
/// cross peak with multiple assignments creates one AmbiguousNMRConstraint ).
/// the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility)


class DistanceScoreMover : public protocols::moves::Mover {
public:
  typedef utility::vector1< core::pose::PoseOP > PoseVector;

  DistanceScoreMover( CrossPeakList&, core::pose::Pose const& pose, core::Real dcut );

  ///@brief set decoy_compatibility in PeakAssignments to zero
  ///
  void prepare_scoring( bool use_for_calibration = false );

  ///@brief sum up decoy_compatibility score in PeakAssignments
  void apply( core::pose::Pose& pose );

  //  void find_violators_with_individual_dist_cutoff( PoseVector poses );
  ///@brief normalize decoy_compatibility of PeakAssignments by count_decoys_
  void finalize_scoring() const;

  //core::Real compute_violation_percentage() const;
  //void eliminate_violated_constraints() const;

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

  void set_dcut( core::Real setting ) {
    dcut_ = setting;
  }

private:
  CrossPeakList& cross_peaks_;
  core::Size count_decoys_; //how many decoys for scoring
  core::Size nr_assignments_;
  typedef utility::vector1< PeakAssignment::NmrConstraintOP > SingleConstraints;
  SingleConstraints constraints_;


  //use this if we have a distance cutoff for each individual peak, based on the structural variation at that point.
  bool individual_distance_cutoff_;
  typedef utility::vector1< core::Real > DistanceBoundVector;
  typedef utility::vector1< DistanceBoundVector > AllStructureDistanceBoundVector;
  AllStructureDistanceBoundVector all_dist_buf_;
  //  typedef utility::vector1< core::scoring::constraints::AmbiguousNMRConstraintOP > PeakConstraints;
  //  PeakConstraints peak_constraints_;


  ///@brief count for each peak how many decoys have violated
  typedef utility::vector1< core::Size > PeakViolationCounts;
  PeakViolationCounts peak_violation_counts_;

  ///@brief cumulative sum of peak_violation_counts_;
  core::Size total_violation_count_;

  //  typedef utility::vector1< core::Real > VectorReal;
  core::Real total_assigned_distances_;


  core::Size active_peaks_; //count nr peaks that have assignment with sufficient Vk

  core::Real final_dist_power_; //eta in Cyana-paper

  bool used_for_calibration_; //if used_for_calibration --> filter peaks and do not update decoy_compatibility score
  core::Real dcut_;
};

}
}

#endif