OpenMS  3.0.0
ModifiedPeptideGenerator.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
39 
42 #include <vector>
43 #include <map>
44 #include <set>
45 
46 #include <boost/container/flat_map.hpp>
47 
48 namespace OpenMS
49 {
50  class OPENMS_DLLAPI ModifiedPeptideGenerator
51  {
52  /*
53  * @brief Modifications can be generated and applied to AASequences.
54  */
55 
56  public:
57  // struct needed to wrap the template for pyOpenMS
58  struct MapToResidueType { boost::container::flat_map<const ResidueModification*, const Residue*> val; };
59 
70  static MapToResidueType getModifications(const StringList& modNames);
71 
72  // Applies fixed modifications to a single peptide
73  static void applyFixedModifications(
74  const MapToResidueType& fixed_mods,
75  AASequence& peptide);
76 
77  // Applies variable modifications to a single peptide. If keep_original is set the original (e.g. unmodified version) is also returned
78  static void applyVariableModifications(
79  const MapToResidueType& var_mods,
80  const AASequence& peptide,
81  Size max_variable_mods_per_peptide,
82  std::vector<AASequence>& all_modified_peptides,
83  bool keep_original=true);
84 
85  protected:
86  // Lookup datastructure to allow lock-free generation of modified peptides
87  static MapToResidueType createResidueModificationToResidueMap_(const std::vector<const ResidueModification*>& mods);
88 
89 
90  // Recursively generate all combinatoric placements at compatible sites
91  static void recurseAndGenerateVariableModifiedPeptides_(
92  const std::vector<int>& subset_indices,
93  const std::map<int, std::vector<const ResidueModification*> >& map_compatibility,
94  const MapToResidueType& var_mods,
95  int depth,
96  const AASequence& current_peptide,
97  std::vector<AASequence>& modified_peptides);
98 
99  // 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
100  static void applyAtMostOneVariableModification_(
101  const MapToResidueType& var_mods,
102  const AASequence& peptide,
103  std::vector<AASequence>& all_modified_peptides,
104  bool keep_original=true);
105 
106  };
107 }
108 
109 
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
AASequence.h
OpenMS::ModifiedPeptideGenerator::MapToResidueType::val
boost::container::flat_map< const ResidueModification *, const Residue * > val
Definition: ModifiedPeptideGenerator.h:58
OpenMS::ModifiedPeptideGenerator::MapToResidueType
Definition: ModifiedPeptideGenerator.h:58
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
ResidueModification.h
OpenMS::ModifiedPeptideGenerator
Definition: ModifiedPeptideGenerator.h:50
StandardTypes.h
StringListUtils.h