ModifiedPeptideGenerator.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/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
 
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <vector>
#include <map>
#include <unordered_map>
#include <set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ModifiedPeptideGenerator
  {
  public:
    struct MapToResidueType { std::unordered_map<const ResidueModification*, const Residue*> val; };
 
    static MapToResidueType getModifications(const StringList& modNames);
 
    static void applyFixedModifications(
      const MapToResidueType& fixed_mods,
      AASequence& peptide);
 
    static void applyVariableModifications(
     const MapToResidueType& var_mods,
     const AASequence& peptide,
     Size max_variable_mods_per_peptide,
     std::vector<AASequence>& all_modified_peptides,
     bool keep_original=true);
 
  protected:
    static const int N_TERM_MODIFICATION_INDEX;
    static const int C_TERM_MODIFICATION_INDEX;
 
    static MapToResidueType createResidueModificationToResidueMap_(const std::vector<const ResidueModification*>& mods);
 
    static void applyAtMostOneVariableModification_(
      const MapToResidueType& var_mods,
      const AASequence& peptide,
      std::vector<AASequence>& all_modified_peptides,
      bool keep_original=true);
 
  private:
    static void applyAllModsAtIdxAndExtend_(std::vector<AASequence>& original_sequences, int idx_to_modify, const std::vector<const ResidueModification*>& mods, const MapToResidueType& var_mods);
    static void applyModToPep_(AASequence& current_peptide, int current_index, const ResidueModification* m, const MapToResidueType& var_mods);
  };
}