| OpenMS 2.5.0

Classes | Static Public Member Functions | Static Protected Member Functions | List of all members
ModifiedPeptideGenerator Class Reference

`#include <OpenMS/ANALYSIS/RNPXL/ModifiedPeptideGenerator.h>`

## Classes

struct | MapToResidueType

## Static Public Member Functions

static MapToResidueType | getModifications (const StringList &modNames)
| Retrieve modifications from strings. More...
static void | applyFixedModifications (const MapToResidueType &fixed_mods, AASequence &peptide)
static void | applyVariableModifications (const MapToResidueType &var_mods, const AASequence &peptide, Size max_variable_mods_per_peptide, std::vector< AASequence > &all_modified_peptides, bool keep_original=true)

## Static Protected Member Functions

static MapToResidueType | createResidueModificationToResidueMap_ (const std::vector< const ResidueModification *> &mods)
static void | recurseAndGenerateVariableModifiedPeptides_ (const std::vector< int > &subset_indices, const std::map< int, std::vector< const ResidueModification *> > &map_compatibility, const MapToResidueType &var_mods, int depth, const AASequence &current_peptide, std::vector< AASequence > &modified_peptides)
static void | applyAtMostOneVariableModification_ (const MapToResidueType &var_mods, const AASequence &peptide, std::vector< AASequence > &all_modified_peptides, bool keep_original=true)

## Class Documentation

## ◆ OpenMS::ModifiedPeptideGenerator::MapToResidueType

struct OpenMS::ModifiedPeptideGenerator::MapToResidueType

Class Members
flat_map< const ResidueModification *, const Residue * > | val |

## Member Function Documentation

## ◆ applyAtMostOneVariableModification_()

static void applyAtMostOneVariableModification_ | ( | const MapToResidueType & | var_mods,
|  | const AASequence & | peptide,
|  | std::vector< AASequence > & | all_modified_peptides,
|  | bool | keep_original = `true`
| ) |  |

static protected

## ◆ applyFixedModifications()

static void applyFixedModifications | ( | const MapToResidueType & | fixed_mods,
|  | AASequence & | peptide
| ) |  |

static

## ◆ applyVariableModifications()

static void applyVariableModifications | ( | const MapToResidueType & | var_mods,
|  | const AASequence & | peptide,
|  | Size | max_variable_mods_per_peptide,
|  | std::vector< AASequence > & | all_modified_peptides,
|  | bool | keep_original = `true`
| ) |  |

static

## ◆ createResidueModificationToResidueMap_()

static MapToResidueType createResidueModificationToResidueMap_ | ( | const std::vector< const ResidueModification *> & | mods | ) |

static protected

## ◆ getModifications()

static MapToResidueType getModifications | ( | const StringList & | modNames | ) |

static

Retrieve modifications from strings.

Parameters

  modNames | The list of modification names

Returns
  A map of modifications and associated residue ResidueModifications are referenced by Residues in AASequence objects. Every time an AASequence object with modifications is constructed, it needs to query if the (modified) Residue is already registered in ResidueDB. This implies a lock of the whole db. To make modified peptide generation lock-free, we query and cache all modified residues once so we can directly apply them without further queries.

## ◆ recurseAndGenerateVariableModifiedPeptides_()

static void recurseAndGenerateVariableModifiedPeptides_ | ( | const std::vector< int > & | subset_indices,
|  | const std::map< int, std::vector< const ResidueModification *> > & | map_compatibility,
|  | const MapToResidueType & | var_mods,
|  | int | depth,
|  | const AASequence & | current_peptide,
|  | std::vector< AASequence > & | modified_peptides
| ) |  |

static protected