ModifiedPeptideGenerator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
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#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 <set>

#include <boost/container/flat_map.hpp>

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 { boost::container::flat_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:
    // Lookup datastructure to allow lock-free generation of modified peptides
    static MapToResidueType createResidueModificationToResidueMap_(const std::vector<const ResidueModification*>& mods);


    // Recursively generate all combinatoric placements at compatible sites
    static void recurseAndGenerateVariableModifiedPeptides_(
      const std::vector<int>& subset_indices, 
      const std::map<int, std::vector<const ResidueModification*> >& map_compatibility, 
      const MapToResidueType& var_mods,
      int depth, 
      const AASequence& current_peptide, 
      std::vector<AASequence>& modified_peptides);

    // 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);

  };
}