| OpenMS 2.5.0

ProteaseDigestion.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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31 // $Maintainer: Chris Bielow, Xiao Liang $
32 // $Authors: Marc Sturm, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/CHEMISTRY/AASequence.h>
39 #include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
40
41 #include <string>
42 #include <vector>
43
44 namespace OpenMS
45 {
60 class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
61 {
62 public:
63 using EnzymaticDigestion::setEnzyme;
64
66 void setEnzyme(const String& name);
67
78 Size digest(const AASequence& protein, std::vector<AASequence>& output, Size min_length = 1, Size max_length = 0) const;
79
81 Size peptideCount(const AASequence& protein);
82
97 bool isValidProduct(const String& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true, bool allow_nterm_protein_cleavage = false, bool allow_random_asp_pro_cleavage = false) const;
98
100 bool isValidProduct(const AASequence& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true, bool allow_nterm_protein_cleavage = false, bool allow_random_asp_pro_cleavage = false) const;
101
102 };
103
104 } // namespace OpenMS
105
OpenMS::String
A more convenient string class.
Definition: String.h:58
AASequence.h
Types.h
OpenMS::ProteaseDigestion
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EnzymaticDigestion::setEnzyme
virtual void setEnzyme(const DigestionEnzyme *enzyme)
Sets the enzyme for the digestion.
EnzymaticDigestion.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127