OpenMS
ProteaseDigestion.h
Go to the documentation of this file.
1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow, Xiao Liang $
6 // $Authors: Marc Sturm, Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/CONCEPT/Types.h>
14 
15 #include <vector>
16 
17 namespace OpenMS
18 {
31  class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
32  {
33  public:
35 
37  void setEnzyme(const String& name);
38 
49  Size digest(const AASequence& protein, std::vector<AASequence>& output, Size min_length = 1, Size max_length = 0) const;
50 
61  Size digest(const AASequence& protein, std::vector<std::pair<size_t,size_t>>& output, Size min_length = 1, Size max_length = 0) const;
62 
64  Size peptideCount(const AASequence& protein);
65 
80  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;
81 
83  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;
84 
85  };
86 
87 } // namespace OpenMS
88 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:38
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:32
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:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22