| OpenMS 2.5.0

ModifiedPeptideGenerator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
39
40 #include <OpenMS/CHEMISTRY/ResidueModification.h>
41 #include <OpenMS/CHEMISTRY/AASequence.h>
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::ModifiedPeptideGenerator::MapToResidueType::val
boost::container::flat_map< const ResidueModification *, const Residue * > val
Definition: ModifiedPeptideGenerator.h:58
OpenMS::ModifiedPeptideGenerator::MapToResidueType
Definition: ModifiedPeptideGenerator.h:58
AASequence.h
StandardTypes.h
OpenMS::ModifiedPeptideGenerator
Definition: ModifiedPeptideGenerator.h:50
StringListUtils.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ResidueModification.h