OpenMS  3.0.0
ProteaseDigestion.h
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31 // $Maintainer: Chris Bielow, Xiao Liang $
32 // $Authors: Marc Sturm, Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
59  class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
60  {
61  public:
63 
65  void setEnzyme(const String& name);
66 
77  Size digest(const AASequence& protein, std::vector<AASequence>& output, Size min_length = 1, Size max_length = 0) const;
78 
80  Size peptideCount(const AASequence& protein);
81 
96  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;
97 
99  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;
100 
101  };
102 
103 } // namespace OpenMS
104 
Types.h
EnzymaticDigestion.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:66
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
AASequence.h
OpenMS::ProteaseDigestion
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:59
OpenMS::EnzymaticDigestion::setEnzyme
virtual void setEnzyme(const DigestionEnzyme *enzyme)
Sets the enzyme for the digestion.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111