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)

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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  )

staticprotected

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 )

staticprotected

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  )

staticprotected