Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ModifiedPeptideGenerator.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2017.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_ANALYSIS_RNPXL_MODIFIEDPEPTIDEGENERATOR_H
36 #define OPENMS_ANALYSIS_RNPXL_MODIFIEDPEPTIDEGENERATOR_H
37 
41 #include <vector>
42 #include <map>
43 #include <set>
44 
45 namespace OpenMS
46 {
47  class OPENMS_DLLAPI ModifiedPeptideGenerator
48  {
49  /*
50  * @brief Modifications can be generated and applied to AASequences.
51  */
52 
53  public
54 :
55  // Applies fixed modifications to a single peptide
56  static void applyFixedModifications(const std::vector<ResidueModification>::const_iterator& fixed_mods_begin, const std::vector<ResidueModification>::const_iterator& fixed_mods_end, AASequence& peptide);
57 
58  // Applies variable modifications to a single peptide. If keep_original is set the original (e.g. unmodified version) is also returned
59  static void applyVariableModifications(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, Size max_variable_mods_per_peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);
60 
61  protected:
62  // Recursively generate all combinatoric placements at compatible sites
63  static void recurseAndGenerateVariableModifiedPeptides_(const std::vector<int>& subset_indices, const std::map<int, std::vector<ResidueModification> >& map_compatibility, int depth, const AASequence& current_peptide, std::vector<AASequence>& modified_peptides);
64 
65  // Fast implementation of modification placement. No combinatoric placement is needed in this case - just every site is modified once by each compatible modification. Already modified residues are skipped
66  static void applyAtMostOneVariableModification_(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);
67 
68  };
69 }
70 
71 #endif
72 
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: ModifiedPeptideGenerator.h:47
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13