Resonance.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:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (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_Resonance_hh
#define INCLUDED_protocols_noesy_assign_Resonance_hh


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

// Package Headers
#include <protocols/noesy_assign/FoldResonance.fwd.hh>
#include <protocols/noesy_assign/PeakCalibrator.fwd.hh>

// Project Headers
#include <utility/pointer/ReferenceCount.hh>
#include <core/chemical/AA.hh>
#include <core/types.hh>
#include <core/id/NamedAtomID.hh>

// Utility headers
#include <utility/vector1.hh>

//// C++ headers
#include <deque>

namespace protocols {
namespace noesy_assign {
/*! @detail
Resonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid)
(provided accessor methods of "Resonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )
*/

class Resonance : public utility::pointer::ReferenceCount {
public:
  Resonance();
  Resonance( core::Size label, core::Real freq, core::Real error, core::id::NamedAtomID const& id, core::chemical::AA, core::Real intensity = 1.0 );
  ~Resonance();

  virtual ResonanceOP clone() {
    return new Resonance( *this );
  }

  ///@brief output
  virtual void write_to_stream( std::ostream& ) const;

  virtual void write_to_stream( std::ostream&, core::chemical::AA aa ) const;

  ///@brief ResonanceID
  core::Size label() const { return label_; }

  ///@brief Atom
  core::id::NamedAtomID const& atom() const { return atom_; }
  core::Size resid() const { return atom_.rsd(); }
  std::string const& name() const { return atom_.atom(); }
  bool is_proton() const { return is_proton_; }
  ///@brief resonance frequency (chemical shift)
  core::Real freq() const { return freq_; }
  core::Real error() const { return error_; }
  core::Real tolerance() const { return error_; }

  ///@brief Resonance matches the given cross-peaks frequency
  bool match( core::Real freq, core::Real error, FoldResonance const& folder ) const {
    return pmatch( freq, error, folder ) <= 1.0;
  }

  virtual core::Real pmatch(  core::Real freq, core::Real error, FoldResonance const& folder ) const;

  void combine( std::deque< ResonanceOP >& last_resonances, bool drain );

  core::chemical::AA aa() const { return aa_; }
  ///@brief in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,
  /// whereas I delta methyls are labelled 100%
  core::Real intensity() const { return intensity_; }
  void set_intensity( core::Real setting ) {
    intensity_ = setting;
  }

  ///@brief classification for calibration... e.g., Backbone, sidechain, etc..
  CALIBRATION_ATOM_TYPE calibration_atom_type() const { return calibration_atom_type_; }

  core::Real _pmatch(  core::Real freq, core::Real error, FoldResonance const& folder ) const;

private:
  void _write_to_stream( std::ostream& ) const;
  core::Size label_;
  core::Real freq_;
  core::Real error_;
  bool is_proton_;
  core::id::NamedAtomID atom_;
  core::chemical::AA aa_;
  core::Real intensity_;
  CALIBRATION_ATOM_TYPE calibration_atom_type_;
};

}
}
#endif