Representation of a modification. More...

#include <OpenMS/CHEMISTRY/ResidueModification.h>

Public Types

enum	TermSpecificity { ANYWHERE = 0, C_TERM = 1, N_TERM = 2, PROTEIN_C_TERM = 3, PROTEIN_N_TERM = 4, NUMBER_OF_TERM_SPECIFICITY }
	Position where the modification is allowed to occur. More...

enum	SourceClassification { ARTIFACT = 0, HYPOTHETICAL, NATURAL, POSTTRANSLATIONAL, MULTIPLE, CHEMICAL_DERIVATIVE, ISOTOPIC_LABEL, PRETRANSLATIONAL, OTHER_GLYCOSYLATION, NLINKED_GLYCOSYLATION, AA_SUBSTITUTION, OTHER, NONSTANDARD_RESIDUE, COTRANSLATIONAL, OLINKED_GLYCOSYLATION, UNKNOWN, NUMBER_OF_SOURCE_CLASSIFICATIONS }
	Classification of the modification. More...

Public Member Functions
Constructors and Destructors
	ResidueModification ()
	default constructor More...

	ResidueModification (const ResidueModification &modification)
	copy constructor More...

virtual	~ResidueModification ()
	destructor More...

Assignment operator
ResidueModification &	operator= (const ResidueModification &modification)
	assignment operator More...

Accessors
void	setId (const String &id)
	set the identifier of the modification More...

const String &	getId () const
	returns the identifier of the modification More...

void	setFullId (const String &full_id="")
	Sets the full identifier (Unimod Accession + origin, if available) More...

const String &	getFullId () const
	returns the full identifier of the mod (Unimod accession + origin, if available) More...

void	setUniModRecordId (const Int &id)
	sets the unimod record id More...

const Int &	getUniModRecordId () const
	sets the unimod record id More...

const String	getUniModAccession () const
	returns the unimod accession if available More...

void	setPSIMODAccession (const String &id)
	set the MOD:XXXXX accession of PSI-MOD More...

const String &	getPSIMODAccession () const
	returns the PSI-MOD accession if available More...

void	setFullName (const String &full_name)
	sets the full name of the modification More...

const String &	getFullName () const
	returns the full name of the modification More...

void	setName (const String &name)
	sets the name of modification More...

const String &	getName () const
	returns the PSI-MS-label if available; e.g. Mascot uses this name More...

void	setTermSpecificity (TermSpecificity term_spec)
	Sets the term specificity. More...

void	setTermSpecificity (const String &name)
	Sets the terminal specificity using a name. More...

TermSpecificity	getTermSpecificity () const
	returns terminal specificity More...

String	getTermSpecificityName (TermSpecificity term_spec=NUMBER_OF_TERM_SPECIFICITY) const
	Returns the name of the terminal specificity. More...

void	setOrigin (char origin)
	Sets the origin (i.e. modified amino acid) More...

char	getOrigin () const
	Returns the origin (i.e. modified amino acid) More...

void	setSourceClassification (const String &classification)
	classification as defined by the PSI-MOD More...

void	setSourceClassification (SourceClassification classification)
	sets the source classification More...

SourceClassification	getSourceClassification () const
	returns the source classification, if none was set, it is unspecific More...

String	getSourceClassificationName (SourceClassification classification=NUMBER_OF_SOURCE_CLASSIFICATIONS) const
	returns the classification More...

void	setAverageMass (double mass)
	sets the average mass More...

double	getAverageMass () const
	returns the average mass if set More...

void	setMonoMass (double mass)
	sets the monoisotopic mass More...

double	getMonoMass () const
	return the monoisotopic mass, if set More...

void	setDiffAverageMass (double mass)
	set the difference average mass More...

double	getDiffAverageMass () const
	returns the difference average mass if set More...

void	setDiffMonoMass (double mass)
	sets the difference monoisotopic mass More...

double	getDiffMonoMass () const
	returns the diff monoisotopic mass if set More...

void	setFormula (const String &composition)
	set the formula More...

const String &	getFormula () const
	returns the chemical formula if set More...

void	setDiffFormula (const EmpiricalFormula &diff_formula)
	sets diff formula More...

const EmpiricalFormula &	getDiffFormula () const
	returns the diff formula if one was set More...

void	setSynonyms (const std::set< String > &synonyms)
	sets the synonyms of that modification More...

void	addSynonym (const String &synonym)
	adds a synonym to the unique list More...

const std::set< String > &	getSynonyms () const
	returns the set of synonyms More...

void	setNeutralLossDiffFormula (const EmpiricalFormula &loss)
	sets the neutral loss formula More...

const EmpiricalFormula &	getNeutralLossDiffFormula () const
	returns the neutral loss diff formula (if available) More...

void	setNeutralLossMonoMass (double mono_mass)
	set the neutral loss mono weight More...

double	getNeutralLossMonoMass () const
	returns the neutral loss mono weight More...

void	setNeutralLossAverageMass (double average_mass)
	set the neutral loss average weight More...

double	getNeutralLossAverageMass () const
	returns the neutral loss average weight More...

Predicates
bool	hasNeutralLoss () const
	returns true if a neutral loss formula is set More...

bool	isUserDefined () const
	returns true if it is a user-defined modification (empty id) More...

bool	operator== (const ResidueModification &modification) const
	equality operator More...

bool	operator!= (const ResidueModification &modification) const
	inequality operator More...

Detailed Description

Representation of a modification.

This class represents a modification of a residue. A residue modification has several attributes like the diff formula, a terminal specificity a mass and maybe an origin which means a specific residue which it can be applied to. A residue modification can be represented by its Unimod name identifier, e.g. "Oxidation (M)" or "Oxidation". This is a unique key which only occurs once in an OpenMS instance stored in the ModificationsDB.

Example: methionine sulfoxide formation by oxidation of methionine

Note that some modifications are not explicitly defined from an input file but get added on the fly when reading amino acid sequences with bracket notation, e.g. "PEPTX[999]IDE". If there is no known modification corresponding to the indicated mass, then a new ResidueModification will be created which will return the initial string through "getFullId()" – which will either be "[999]" for internal modifications or ".[999]" for N/C-terminal modifications. Please use "isUserDefined" to check for user-defined modifications.

Member Enumeration Documentation

◆ SourceClassification

enum SourceClassification

Classification of the modification.

Enumerator
ARTIFACT
HYPOTHETICAL
NATURAL
POSTTRANSLATIONAL
MULTIPLE
CHEMICAL_DERIVATIVE
ISOTOPIC_LABEL
PRETRANSLATIONAL
OTHER_GLYCOSYLATION
NLINKED_GLYCOSYLATION
AA_SUBSTITUTION
OTHER
NONSTANDARD_RESIDUE
COTRANSLATIONAL
OLINKED_GLYCOSYLATION
UNKNOWN
NUMBER_OF_SOURCE_CLASSIFICATIONS

◆ TermSpecificity

enum TermSpecificity

Position where the modification is allowed to occur.

Enums The allowed sites are Anywhere Any C-term Any N-term Protein C-term Protein N-term

This does not describe the amino acids which are valid for a specific amino acid!

Enumerator
ANYWHERE
C_TERM
N_TERM
PROTEIN_C_TERM
PROTEIN_N_TERM
NUMBER_OF_TERM_SPECIFICITY

Constructor & Destructor Documentation

◆ ResidueModification() [1/2]

ResidueModification ( )

default constructor

◆ ResidueModification() [2/2]

ResidueModification ( const ResidueModification & modification )

copy constructor

◆ ~ResidueModification()

virtual ~ResidueModification ( )

virtual

destructor

Member Function Documentation

◆ addSynonym()

void addSynonym ( const String & synonym )

adds a synonym to the unique list

◆ getAverageMass()

double getAverageMass ( ) const

returns the average mass if set

◆ getDiffAverageMass()

double getDiffAverageMass ( ) const

returns the difference average mass if set

◆ getDiffFormula()

const EmpiricalFormula& getDiffFormula ( ) const

returns the diff formula if one was set

◆ getDiffMonoMass()

double getDiffMonoMass ( ) const

returns the diff monoisotopic mass if set

Referenced by RNPxlSearch::postScoreHits_().

◆ getFormula()

const String& getFormula ( ) const

returns the chemical formula if set

◆ getFullId()

const String& getFullId ( ) const

returns the full identifier of the mod (Unimod accession + origin, if available)

Returns the full identifier (Unimod Accession + origin, if available)

Note: This field is used for user-defined modifications as well and will be set to a string such as "[999]" for internal modifications or ".[999]" for N/C-terminal modifications. Please use "isUserDefined" to check for user-defined modifications.

◆ getFullName()

const String& getFullName ( ) const

returns the full name of the modification

◆ getId()

const String& getId ( ) const

returns the identifier of the modification

◆ getMonoMass()

double getMonoMass ( ) const

return the monoisotopic mass, if set

◆ getName()

const String& getName ( ) const

returns the PSI-MS-label if available; e.g. Mascot uses this name

◆ getNeutralLossAverageMass()

double getNeutralLossAverageMass ( ) const

returns the neutral loss average weight

◆ getNeutralLossDiffFormula()

const EmpiricalFormula& getNeutralLossDiffFormula ( ) const

returns the neutral loss diff formula (if available)

◆ getNeutralLossMonoMass()

double getNeutralLossMonoMass ( ) const

returns the neutral loss mono weight

◆ getOrigin()

char getOrigin ( ) const

Returns the origin (i.e. modified amino acid)

◆ getPSIMODAccession()

const String& getPSIMODAccession ( ) const

returns the PSI-MOD accession if available

◆ getSourceClassification()

SourceClassification getSourceClassification ( ) const

returns the source classification, if none was set, it is unspecific

◆ getSourceClassificationName()

String getSourceClassificationName ( SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS ) const

returns the classification

◆ getSynonyms()

const std::set<String>& getSynonyms ( ) const

returns the set of synonyms

◆ getTermSpecificity()

TermSpecificity getTermSpecificity ( ) const

returns terminal specificity

◆ getTermSpecificityName()

String getTermSpecificityName ( TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY ) const

Returns the name of the terminal specificity.

By default, returns the name of the specificity set in member term_spec_. Alternatively, returns the name corresponding to argument term_spec.

◆ getUniModAccession()

const String getUniModAccession ( ) const

returns the unimod accession if available

◆ getUniModRecordId()

const Int& getUniModRecordId ( ) const

sets the unimod record id

◆ hasNeutralLoss()

bool hasNeutralLoss ( ) const

returns true if a neutral loss formula is set

◆ isUserDefined()

bool isUserDefined ( ) const

returns true if it is a user-defined modification (empty id)

◆ operator!=()

bool operator!= ( const ResidueModification & modification ) const

inequality operator

◆ operator=()

ResidueModification& operator= ( const ResidueModification & modification )

assignment operator

◆ operator==()

bool operator== ( const ResidueModification & modification ) const

equality operator

◆ setAverageMass()

void setAverageMass ( double mass )

sets the average mass

◆ setDiffAverageMass()

void setDiffAverageMass ( double mass )

set the difference average mass

◆ setDiffFormula()

void setDiffFormula ( const EmpiricalFormula & diff_formula )

sets diff formula

◆ setDiffMonoMass()

void setDiffMonoMass ( double mass )

sets the difference monoisotopic mass

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ setFormula()

void setFormula ( const String & composition )

set the formula

◆ setFullId()

void setFullId ( const String & full_id = "" )

Sets the full identifier (Unimod Accession + origin, if available)

With empty argument, create a full ID based on (short) ID, terminal specificity and residue of origin.

Exceptions

Exception::MissingInformation if both argument full_id and member id_ are empty.

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ setFullName()

void setFullName ( const String & full_name )

sets the full name of the modification

◆ setId()

void setId ( const String & id )

set the identifier of the modification

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ setMonoMass()

void setMonoMass ( double mass )

sets the monoisotopic mass

◆ setName()

void setName ( const String & name )

sets the name of modification

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ setNeutralLossAverageMass()

void setNeutralLossAverageMass ( double average_mass )

set the neutral loss average weight

◆ setNeutralLossDiffFormula()

void setNeutralLossDiffFormula ( const EmpiricalFormula & loss )

sets the neutral loss formula

◆ setNeutralLossMonoMass()

void setNeutralLossMonoMass ( double mono_mass )

set the neutral loss mono weight

◆ setOrigin()

void setOrigin ( char origin )

Sets the origin (i.e. modified amino acid)

origin must be a valid amino acid one-letter code or X, i.e. a letter from A to Y, excluding B and J. X represents any amino acid (for modifications with terminal specificity).

Exceptions

Exception::InvalidValue if origin is not in the valid range

◆ setPSIMODAccession()

void setPSIMODAccession ( const String & id )

set the MOD:XXXXX accession of PSI-MOD

◆ setSourceClassification() [1/2]

void setSourceClassification ( const String & classification )

classification as defined by the PSI-MOD

◆ setSourceClassification() [2/2]

void setSourceClassification ( SourceClassification classification )

sets the source classification

◆ setSynonyms()

void setSynonyms ( const std::set< String > & synonyms )

sets the synonyms of that modification

◆ setTermSpecificity() [1/2]

void setTermSpecificity ( TermSpecificity term_spec )

Sets the term specificity.

Exceptions

Exception::InvalidValue if no valid specificity was given

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ setTermSpecificity() [2/2]

void setTermSpecificity ( const String & name )

Sets the terminal specificity using a name.

Valid names: "C-term", "N-term", "none"

Exceptions

Exception::InvalidValue if no valid specificity was given

◆ setUniModRecordId()

void setUniModRecordId ( const Int & id )

sets the unimod record id

Member Data Documentation

◆ average_mass_

double average_mass_

protected

◆ classification_

SourceClassification classification_

protected

◆ diff_average_mass_

double diff_average_mass_

protected

◆ diff_formula_

EmpiricalFormula diff_formula_

protected

◆ diff_mono_mass_

double diff_mono_mass_

protected

◆ formula_

String formula_

protected

◆ full_id_

String full_id_

protected

◆ full_name_

String full_name_

protected

◆ id_

String id_

protected

◆ mono_mass_

double mono_mass_

protected

◆ name_

String name_

protected

◆ neutral_loss_average_mass_

double neutral_loss_average_mass_

protected

◆ neutral_loss_diff_formula_

EmpiricalFormula neutral_loss_diff_formula_

protected

◆ neutral_loss_mono_mass_

double neutral_loss_mono_mass_

protected

◆ origin_

char origin_

protected

◆ psi_mod_accession_

String psi_mod_accession_

protected

◆ synonyms_

std::set<String> synonyms_

protected

◆ term_spec_

TermSpecificity term_spec_

protected

◆ unimod_record_id_

Int unimod_record_id_

protected

Protected Attributes
String	id_

String	full_id_

String	psi_mod_accession_

Int	unimod_record_id_

String	full_name_

String	name_

TermSpecificity	term_spec_

char	origin_

SourceClassification	classification_

double	average_mass_

double	mono_mass_

double	diff_average_mass_

double	diff_mono_mass_

String	formula_

EmpiricalFormula	diff_formula_

std::set< String >	synonyms_

EmpiricalFormula	neutral_loss_diff_formula_

double	neutral_loss_mono_mass_

double	neutral_loss_average_mass_

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ SourceClassification

◆ TermSpecificity

Constructor & Destructor Documentation

◆ ResidueModification() [1/2]

◆ ResidueModification() [2/2]

◆ ~ResidueModification()

Member Function Documentation

◆ addSynonym()

◆ getAverageMass()

◆ getDiffAverageMass()

◆ getDiffFormula()

◆ getDiffMonoMass()

◆ getFormula()

◆ getFullId()

◆ getFullName()

◆ getId()

◆ getMonoMass()

◆ getName()

◆ getNeutralLossAverageMass()

◆ getNeutralLossDiffFormula()

◆ getNeutralLossMonoMass()

◆ getOrigin()

◆ getPSIMODAccession()

◆ getSourceClassification()

◆ getSourceClassificationName()

◆ getSynonyms()

◆ getTermSpecificity()

◆ getTermSpecificityName()

◆ getUniModAccession()

◆ getUniModRecordId()

◆ hasNeutralLoss()

◆ isUserDefined()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ setAverageMass()

◆ setDiffAverageMass()

◆ setDiffFormula()

◆ setDiffMonoMass()

◆ setFormula()

◆ setFullId()

◆ setFullName()

◆ setId()

◆ setMonoMass()

◆ setName()

◆ setNeutralLossAverageMass()

◆ setNeutralLossDiffFormula()

◆ setNeutralLossMonoMass()

◆ setOrigin()

◆ setPSIMODAccession()

◆ setSourceClassification() [1/2]

◆ setSourceClassification() [2/2]

◆ setSynonyms()

◆ setTermSpecificity() [1/2]

◆ setTermSpecificity() [2/2]

◆ setUniModRecordId()

Member Data Documentation

◆ average_mass_

◆ classification_

◆ diff_average_mass_

◆ diff_formula_

◆ diff_mono_mass_

◆ formula_

◆ full_id_

◆ full_name_

◆ id_

◆ mono_mass_

◆ name_

◆ neutral_loss_average_mass_

◆ neutral_loss_diff_formula_

◆ neutral_loss_mono_mass_

◆ origin_

◆ psi_mod_accession_

◆ synonyms_

◆ term_spec_