OpenMS
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 
89  Size digest(const AASequence& protein, std::vector<std::pair<size_t,size_t>>& output, Size min_length = 1, Size max_length = 0) const;
90 
92  Size peptideCount(const AASequence& protein);
93 
108  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;
109 
111  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;
112 
113  };
114 
115 } // namespace OpenMS
116 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:64
virtual void setEnzyme(const DigestionEnzyme *enzyme)
Sets the enzyme for the digestion.
Class for the enzymatic digestion of proteins represented as AASequence or String.
Definition: ProteaseDigestion.h:60
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
forwards to isValidProduct using protein.toUnmodifiedString()
Size digest(const AASequence &protein, std::vector< std::pair< size_t, size_t >> &output, Size min_length=1, Size max_length=0) const
Performs the enzymatic digestion of a protein represented as AASequence.
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
Variant of EnzymaticDigestion::isValidProduct() with support for n-term protein cleavage and random D...
Size peptideCount(const AASequence &protein)
Returns the number of peptides a digestion of protein would yield under the current enzyme and missed...
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
Size digest(const AASequence &protein, std::vector< AASequence > &output, Size min_length=1, Size max_length=0) const
Performs the enzymatic digestion of a protein represented as AASequence.
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48