CrossPeakList.hh

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// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file CrossPeakList.hh
/// @author Oliver Lange

#ifndef INCLUDED_protocols_noesy_assign_CrossPeakList_HH
#define INCLUDED_protocols_noesy_assign_CrossPeakList_HH


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

// Package Headers
// AUTO-REMOVED #include <protocols/noesy_assign/CrossPeak.hh>
#include <protocols/noesy_assign/PeakFileFormat.fwd.hh>
#include <protocols/noesy_assign/PeakAssignmentResidueMap.fwd.hh>
#include <protocols/noesy_assign/PeakCalibrator.fwd.hh>
//#include <devel/noesy_assign/PeakAssignment.hh>
//#include <devel/noesy_assign/ResonanceList.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/id/NamedAtomID.fwd.hh>
// AUTO-REMOVED #include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/io/silent/SilentFileData.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>

// Utility headers
// AUTO-REMOVED #include <utility/exit.hh>
// #include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>
// #include <numeric/numeric.functions.hh>
// #include <core/util/prof.hh>
//#include <core/util/Tracer.hh>
// #include <core/options/option.hh>
// #include <core/options/keys/abinitio.OptionKeys.gen.hh>
// #include <core/options/keys/run.OptionKeys.gen.hh>
//#include <core/options/keys/templates.OptionKeys.gen.hh>

//// C++ headers
// AUTO-REMOVED #include <cstdlib>
// AUTO-REMOVED #include <string>
#include <list>
// AUTO-REMOVED #include <map>

#include <protocols/noesy_assign/CrossPeak.fwd.hh>
#include <protocols/noesy_assign/ResonanceList.fwd.hh>


namespace protocols {
namespace noesy_assign {

class CrossPeakList : public utility::pointer::ReferenceCount {
public:
  typedef std::list< CrossPeakOP > CrossPeaks;
  typedef CrossPeaks::const_iterator const_iterator;
  typedef CrossPeaks::iterator iterator;
  CrossPeakList();
  virtual ~CrossPeakList();

  void read_from_stream( std::istream&, PeakFileFormat& input_adaptor, ResonanceListOP resonances );
  void write_to_stream( std::ostream&, PeakFileFormat& output_adaptor ) const;
  void write_peak_files( std::string const& prefix, PeakFileFormat& output_adaptor ) const;
  void find_assignments();
  void update_chemshiftscore();
  void update_symmetry_score();
  void update_upperdistance_score();

  template < class DecoyIterator >
  void update_decoy_compatibility_score( DecoyIterator const& begin, DecoyIterator const& end ); //core::io::silent::SilentFileData const& sfd

  void eliminate_spurious_peaks();

  template < class DecoyIterator >
  void calibrate( DecoyIterator const& begin, DecoyIterator const& end );
   //  void calibrate( core::io::silent::SilentFileData const& decoys );

#if 0
  core::scoring::constraints::ConstraintSetOP generate_constraints( core::pose::Pose const& pose, bool centroid = false, core::Size min_seq_separation = 2 ) const;
#endif

  void generate_fa_and_cen_constraints(
  core::scoring::constraints::ConstraintSetOP fa_set,
  core::scoring::constraints::ConstraintSetOP cen_set,
  core::pose::Pose const& pose,
  core::pose::Pose const& centroid_pose,
  core::Size min_seq_separation,
  core::Size min_quali,
  core::Size max_quali,
  core::Real padding = 0.0,
  bool ignore_elimination_candidates = true,
  bool elimination_candidates = false
  ) const;

  PeakAssignmentResidueMap const& assignments() const {
    return *assignments_;
  }

  PeakAssignmentResidueMap& assignments() {
    return *assignments_;
  }

//   ResonanceList const& resonances() const {
//     return *resonances_;
//   }

  core::Size count_assignments() const;
  void delete_diagonal_peaks();
  void update_peak_volumina();
  void network_analysis( ResonanceList const& );
  void set_trivial_decoy_compatibility_score();
  CrossPeaks const& peaks() const { return peaks_; }
  const_iterator begin() const { return peaks_.begin(); }
  const_iterator end() const { return peaks_.end(); }
  iterator begin() { return peaks_.begin(); }
  core::Size size() const { return peaks_.size(); }
private:
  void update_assignment_list(); //after find_assignments or delete_diagonal_peaks()

  ///@brief return average upper distance bound
  core::Real calibrate( PeakCalibrator const& calibrator );
  CrossPeaks peaks_;
  //probably good to have all things in this class?
  //  ResonanceListOP resonances_;
  PeakAssignmentResidueMapOP assignments_;
};

}
}

#endif