OpenMS  2.8.0
Classes | Static Public Member Functions | Static Protected Member Functions | List of all members
ModifiedPeptideGenerator Class Reference

#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>


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
Collaboration diagram for 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 

◆ applyFixedModifications()

static void applyFixedModifications ( const MapToResidueType fixed_mods,
AASequence peptide 

◆ 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 

◆ createResidueModificationToResidueMap_()

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

◆ getModifications()

static MapToResidueType getModifications ( const StringList modNames)

Retrieve modifications from strings.

modNamesThe list of modification names
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