OpenMS  2.8.0
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 <string>
42 #include <vector>
43 
44 namespace OpenMS
45 {
60  class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
61  {
62  public:
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 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:65
virtual void setEnzyme(const DigestionEnzyme *enzyme)
Sets the enzyme for the digestion.
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:61
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()
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.
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:47