TheoreticalGlycanSpectrumGenerator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/GlycanStructure.h>
#include <map>
 
namespace OpenMS
{
class AASequence;
class MSSpectrum;
 
class OPENMS_DLLAPI TheoreticalGlycanSpectrumGenerator
{
public:
  using Composition = ProForma::GlycanComposition;
 
  enum class IonType
  {
    DIAGNOSTIC,
    B,
    C,
    Y,
    Z,
    PEPTIDE
  };
  enum class FragmentationMethod
  {
    HCD,
    ETD,
    ETHCD
  };
 
  struct OPENMS_DLLAPI PeptideRetention
  {
    bool intact = false;            
    bool stripped = true;           
    std::vector<Composition> stubs; 
  };
 
  struct OPENMS_DLLAPI Options
  {
    bool add_diagnostic_ions = true;
    bool add_b_ions = true;
    bool add_y_ions = true;
    bool add_c_ions = false;
    bool add_z_ions = false;
    bool add_internal_fragments = true;
    bool allow_structural = true;  
    Size min_composition_size = 1; 
    Size max_composition_size = 3; 
    Size max_cleavages = 2;        
    Size max_fragments = 10000;    
    Size max_states = 100000;      
    Int min_charge = 1;
    Int max_charge = 2;
    Int min_oxonium_charge = 1;
    Int max_oxonium_charge = 1;
    std::vector<EmpiricalFormula> neutral_losses;                                 
    std::map<std::string, std::vector<EmpiricalFormula>> specific_neutral_losses; 
    std::map<char, PeptideRetention> peptide_retention;                           
  };
 
  struct OPENMS_DLLAPI Fragment
  {
    IonType ion_type = IonType::DIAGNOSTIC;
    Composition composition;
    double neutral_mass = 0.0; 
    Int charge = 1;
    std::optional<Size> attachment_position; 
    std::string attachment_residue;
    std::optional<Size> root_cleavage;
    std::vector<Size> branch_cleavages;
    std::string name; 
    double getMZ() const;
    std::string getAnnotation() const;
  };
 
  TheoreticalGlycanSpectrumGenerator();
  explicit TheoreticalGlycanSpectrumGenerator(const Options& options);
  void setOptions(const Options& options);
  const Options& getOptions() const;
 
  std::vector<Fragment> getFragments(const Composition& composition) const;
 
  std::vector<Fragment> getFragments(const GlycanStructure& structure) const;
 
  std::vector<Fragment>
  getGlycopeptideFragments(const AASequence& peptide, const Composition& composition, Size attachment_position, FragmentationMethod method) const;
  std::vector<Fragment>
  getGlycopeptideFragments(const AASequence& peptide, const GlycanStructure& structure, Size attachment_position, FragmentationMethod method) const;
 
  static MSSpectrum toSpectrum(const std::vector<Fragment>& fragments);
 
private:
  Options options_;
  std::vector<Fragment>
  generate_(const Composition& composition, const GlycanStructure* structure, const AASequence* peptide, Size site, FragmentationMethod method) const;
};
} // namespace OpenMS