ModifiedPeptideGenerator Class Reference

#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>

Collaboration diagram for ModifiedPeptideGenerator:

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

Static Protected Attributes
static const int	N_TERM_MODIFICATION_INDEX
static const int	C_TERM_MODIFICATION_INDEX

Static Private Member Functions
static void	applyAllModsAtIdxAndExtend_ (std::vector< AASequence > &original_sequences, int idx_to_modify, const std::vector< const ResidueModification * > &mods, const MapToResidueType &var_mods)
	take a vector of AASequences original_sequences, and for each mod in mods, add a version with mod at index idx_to_modify. In-place, with the original sequences recieving the first mod in mods. More...
static void	applyModToPep_ (AASequence &current_peptide, int current_index, const ResidueModification *m, const MapToResidueType &var_mods)
	applies a modification m to the current_peptide at current_index. Overwrites mod if it exists. Looks up in var_mods for existing modified Residue pointers. More...

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Class Documentation

OpenMS::ModifiedPeptideGenerator::MapToResidueType

struct OpenMS::ModifiedPeptideGenerator::MapToResidueType

Collaboration diagram for ModifiedPeptideGenerator::MapToResidueType:

Class Members
unordered_map< const ResidueModification *, const Residue * >	val

Member Function Documentation

applyAllModsAtIdxAndExtend_()

static void applyAllModsAtIdxAndExtend_ ( std::vector< AASequence > &  original_sequences, int  idx_to_modify, const std::vector< const ResidueModification * > &  mods, const MapToResidueType &  var_mods  )

staticprivate

take a vector of AASequences original_sequences, and for each mod in mods, add a version with mod at index idx_to_modify. In-place, with the original sequences recieving the first mod in mods.

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

applyModToPep_()

static void applyModToPep_ ( AASequence &  current_peptide, int  current_index, const ResidueModification *  m, const MapToResidueType &  var_mods  )

staticprivate

applies a modification m to the current_peptide at current_index. Overwrites mod if it exists. Looks up in var_mods for existing modified Residue pointers.

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.

Member Data Documentation

C_TERM_MODIFICATION_INDEX

const int C_TERM_MODIFICATION_INDEX

staticprotected

N_TERM_MODIFICATION_INDEX

const int N_TERM_MODIFICATION_INDEX

staticprotected