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
  {
   /*
    * @brief Modifications can be generated and applied to AASequences. 
    */
 
  public:
    // struct needed to wrap the template for pyOpenMS
    struct MapToResidueType { std::unordered_map<const ResidueModification*, const Residue*> val; };
 
    static MapToResidueType getModifications(const StringList& modNames);
 
    // Applies fixed modifications to a single peptide
    static void applyFixedModifications(
      const MapToResidueType& fixed_mods, 
      AASequence& peptide);
 
    // Applies variable modifications to a single peptide. If keep_original is set the original (e.g. unmodified version) is also returned
    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; // magic constant to distinguish N_TERM only modifications from ANYWHERE modifications placed at N-term residue
    static const int C_TERM_MODIFICATION_INDEX; // magic constant to distinguish C_TERM only modifications from ANYWHERE modifications placed at C-term residue
 
    // Lookup datastructure to allow lock-free generation of modified peptides. Modifications without origin (e.g., "Protein N-term") set the residue to nullptr.
    static MapToResidueType createResidueModificationToResidueMap_(const std::vector<const ResidueModification*>& mods);
 
    // Fast implementation of modification placement. No combinatoric placement is needed in this case - just every site is modified once by each compatible modification. Already modified residues are skipped
    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);
  };
}