Representation of a modification on an amino acid residue. More...

#include <OpenMS/CHEMISTRY/ResidueModification.h>

Collaboration diagram for ResidueModification:

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.

	ResidueModification (const ResidueModification &)=default
	Copy constructor.

	ResidueModification (ResidueModification &&)=default
	Move constructor.

virtual	~ResidueModification ()
	Destructor.

Assignment operator
ResidueModification &	operator= (const ResidueModification &)=default
	Assignment operator.

ResidueModification &	operator= (ResidueModification &&) &=default
	Move assignment operator.

Accessors
void	setId (const std::string &id)
	set the identifier of the modification

const std::string &	getId () const
	returns the identifier of the modification

void	setFullId (const std::string &full_id="")
	Sets the full identifier (Unimod Accession + origin, if available)

const std::string &	getFullId () const
	returns the full identifier of the mod (Unimod accession + origin, if available)

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

const Int &	getUniModRecordId () const
	gets the unimod record id

const std::string	getUniModAccession () const
	returns the unimod accession if available

void	setPSIMODAccession (const std::string &id)
	set the MOD:XXXXX accession of PSI-MOD

const std::string &	getPSIMODAccession () const
	returns the PSI-MOD accession if available

void	setFullName (const std::string &full_name)
	sets the full name of the modification; must NOT contain the origin (or . for terminals!)

const std::string &	getFullName () const
	returns the full name of the modification

void	setName (const std::string &name)
	sets the name of modification

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

void	setTermSpecificity (TermSpecificity term_spec)
	Sets the term specificity.

void	setTermSpecificity (const std::string &name)
	Sets the terminal specificity using a name.

TermSpecificity	getTermSpecificity () const
	returns terminal specificity

std::string	getTermSpecificityName (TermSpecificity term_spec=NUMBER_OF_TERM_SPECIFICITY) const
	Returns the name of the terminal specificity.

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

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

void	setSourceClassification (const std::string &classification)
	classification as defined by the PSI-MOD

void	setSourceClassification (SourceClassification classification)
	sets the source classification

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

std::string	getSourceClassificationName (SourceClassification classification=NUMBER_OF_SOURCE_CLASSIFICATIONS) const
	returns the classification

void	setAverageMass (double mass)
	sets the average mass

double	getAverageMass () const
	returns the average mass if set

void	setMonoMass (double mass)
	sets the monoisotopic mass (this must include the weight of the residue itself!)

double	getMonoMass () const
	return the monoisotopic mass, or 0.0 if not set

void	setDiffAverageMass (double mass)
	set the difference average mass

double	getDiffAverageMass () const
	returns the difference average mass, or 0.0 if not set

void	setDiffMonoMass (double mass)
	sets the difference monoisotopic mass

double	getDiffMonoMass () const
	returns the diff monoisotopic mass, or 0.0 if not set

void	setFormula (const std::string &composition)
	set the formula (no masses will be changed)

const std::string &	getFormula () const
	returns the chemical formula if set

void	setDiffFormula (const EmpiricalFormula &diff_formula)
	sets diff formula (no masses will be changed)

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

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

void	addSynonym (const std::string &synonym)
	adds a synonym to the unique list

const std::set< std::string > &	getSynonyms () const
	returns the set of synonyms

void	setNeutralLossDiffFormulas (const std::vector< EmpiricalFormula > &diff_formulas)
	sets the neutral loss formula

const std::vector< EmpiricalFormula > &	getNeutralLossDiffFormulas () const
	returns the neutral loss diff formula (if available)

void	setNeutralLossMonoMasses (std::vector< double > mono_masses)
	set the neutral loss mono weight

std::vector< double >	getNeutralLossMonoMasses () const
	returns the neutral loss mono weight

void	setNeutralLossAverageMasses (std::vector< double > average_masses)
	set the neutral loss average weight

std::vector< double >	getNeutralLossAverageMasses () const
	returns the neutral loss average weight

Predicates
std::string	id_

std::string	full_id_

std::string	psi_mod_accession_

Int	unimod_record_id_

std::string	full_name_

std::string	name_

TermSpecificity	term_spec_

char	origin_

SourceClassification	classification_

double	average_mass_

double	mono_mass_

double	diff_average_mass_

double	diff_mono_mass_

std::string	formula_

EmpiricalFormula	diff_formula_

std::set< std::string >	synonyms_

std::vector< EmpiricalFormula >	neutral_loss_diff_formulas_

std::vector< double >	neutral_loss_mono_masses_

std::vector< double >	neutral_loss_average_masses_

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

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

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

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

bool	operator< (const ResidueModification &modification) const
	less operator

std::string	toString () const

static const ResidueModification *	createUnknownFromMassString (const std::string &mod, const double mass, const bool delta_mass, const TermSpecificity specificity, const Residue *residue=nullptr)

static const ResidueModification *	combineMods (const ResidueModification base, const std::set< const ResidueModification > &addons, bool allow_unknown_masses=false, const Residue *residue=nullptr)
	Merge a set of mods to a given modification (usually the one which is already present, but can be null)

static std::string	getDiffMonoMassString (const double diff_mono_mass)

static std::string	getDiffMonoMassWithBracket (const double diff_mono_mass)
	return a string of the form '[+>mass<] (the '+' might be a '-', if mass is negative).

static std::string	getMonoMassWithBracket (const double mono_mass)
	return a string of the form '[>mass<]

Detailed Description

Representation of a modification on an amino acid residue.

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 (Id), 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

Function              | Result
----------------------------------------------------
getFullId()           | "Oxidation (M)"
getId()               | "Oxidation"
getFullName()         | "Oxidation or Hydroxylation"
getUniModAccession()  | "UniMod:312"

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 (those without 'Id' but with a 'FullId').

Member Enumeration Documentation

◆ SourceClassification

enum SourceClassification

Classification of the modification.

Enumerator
ARTIFACT	A technical or chemical artefact.
HYPOTHETICAL	A hypothetical modification.
NATURAL	A natural modification.
POSTTRANSLATIONAL	A post-translational modification.
MULTIPLE	A combination of multiple modifications.
CHEMICAL_DERIVATIVE	A chemical derivative.
ISOTOPIC_LABEL	A chemical label (artificial)
PRETRANSLATIONAL	A pre-translational modification.
OTHER_GLYCOSYLATION	Other glycosylation (i.e. neither N nor O-linked)
NLINKED_GLYCOSYLATION	N-linked glycosylation.
AA_SUBSTITUTION	An amino acid substitution that presents like a modification.
OTHER	Other modification.
NONSTANDARD_RESIDUE	A non-standard amino acid.
COTRANSLATIONAL	A co-translational modification.
OLINKED_GLYCOSYLATION	A O-linked glycosylation.
UNKNOWN	An unknown modification.
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 which modifications are valid for a
specific amino acid!

Enumerator
ANYWHERE	The modification can go anywhere.
C_TERM	The modification can only be C-terminal on the peptide.
N_TERM	The modification can only be N-terminal on the peptide.
PROTEIN_C_TERM	The modification can only be protein C-terminal (on a C-terminal peptide)
PROTEIN_N_TERM	The modification can only be protein N-terminal (on a N-terminal peptide)
NUMBER_OF_TERM_SPECIFICITY

Constructor & Destructor Documentation

◆ ResidueModification() [1/3]

ResidueModification ( )

Default constructor.

◆ ResidueModification() [2/3]

ResidueModification ( const ResidueModification & )

default

Copy constructor.

◆ ResidueModification() [3/3]

ResidueModification ( ResidueModification && )

default

Move constructor.

◆ ~ResidueModification()

virtual ~ResidueModification ( )

virtual

Destructor.

Member Function Documentation

◆ addSynonym()

void addSynonym ( const std::string & synonym )

adds a synonym to the unique list

◆ combineMods()

static const ResidueModification * combineMods	(	const ResidueModification *	base,
		const std::set< const ResidueModification * > &	addons,
		bool	allow_unknown_masses = `false`,
		const Residue *	residue = `nullptr`
	)

static

Merge a set of mods to a given modification (usually the one which is already present, but can be null)

If only one mod is combined in total, it is not changed to an unknown mod but remains a 'known' mod. If base is already contained in addons, it is not added again.

All mods given here must have the same term specificity and origin (which might be 'X', i.e. no restriction), otherwise a Precondition exception is thrown.

If base and addons is empty, a null_ptr is returned.

Parameters

[in]	base	An already present mod, can be a nullptr
[in]	addons	A set of mods to add on top of the mod.
[in]	allow_unknown_masses	If any input (incl. base) is already an unknown mass, nothing is done
[in]	residue	[only required for ANYWHERE term spec] Residue with further information (e.g. residue weights) for the new mod

Returns: A (new custom) mod, which is registered in ModificationsDB if needed.

Exceptions

Exception::Precondition if term spec or origins to not match between all given mods

◆ createUnknownFromMassString()

static const ResidueModification * createUnknownFromMassString	(	const std::string &	mod,
		const double	mass,
		const bool	delta_mass,
		const TermSpecificity	specificity,
		const Residue *	residue = `nullptr`
	)

static

Creates a new modification from a mass and adds it to ModificationsDB. If not terminal, needs a Residue to be put on.

Parameters

[in]	mod	The mass to put between the brackets (might contain +/- at the front)
[in]	mass	Basically, the same as mod, just as double (since usually both representations are present when calling this function and to avoid overhead??)
[in]	delta_mass	Is the given mass a delta mass (i.e. does `mod` contain a = or -)?
[in]	specificity	To which site can this mod be applied?
[in]	residue	[only required for ANYWHERE term spec] Residue with further information (e.g. residue weights) for the new mod

Returns: a new or existing mod; registered to ModDB in both cases, so the pointer is non-owning (FullId is e.g. M[+1234.1] and FullName [+1234.1]. Id and Name are empty as defined for a "user-defined" mod.

◆ getAverageMass()

double getAverageMass ( ) const

returns the average mass if set

◆ getDiffAverageMass()

double getDiffAverageMass ( ) const

returns the difference average mass, or 0.0 if not set

◆ getDiffFormula()

const EmpiricalFormula & getDiffFormula ( ) const

returns the diff formula if one was set

◆ getDiffMonoMass()

double getDiffMonoMass ( ) const

returns the diff monoisotopic mass, or 0.0 if not set

◆ getDiffMonoMassString()

static std::string getDiffMonoMassString ( const double diff_mono_mass )

static

converts the mass to a string with preceding '+' or '-' sign e.g. '-19.34' or '+1.003'

◆ getDiffMonoMassWithBracket()

static std::string getDiffMonoMassWithBracket ( const double diff_mono_mass )

static

return a string of the form '[+>mass<] (the '+' might be a '-', if mass is negative).

◆ getFormula()

const std::string & getFormula ( ) const

returns the chemical formula if set

◆ getFullId()

const std::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.

Referenced by hash< OpenMS::AASequence >::operator()().

◆ getFullName()

const std::string & getFullName ( ) const

returns the full name of the modification

◆ getId()

const std::string & getId ( ) const

returns the identifier of the modification

◆ getMonoMass()

double getMonoMass ( ) const

return the monoisotopic mass, or 0.0 if not set

◆ getMonoMassWithBracket()

static std::string getMonoMassWithBracket ( const double mono_mass )

static

return a string of the form '[>mass<]

◆ getName()

const std::string & getName ( ) const

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

◆ getNeutralLossAverageMasses()

std::vector< double > getNeutralLossAverageMasses ( ) const

returns the neutral loss average weight

◆ getNeutralLossDiffFormulas()

const std::vector< EmpiricalFormula > & getNeutralLossDiffFormulas ( ) const

returns the neutral loss diff formula (if available)

◆ getNeutralLossMonoMasses()

std::vector< double > getNeutralLossMonoMasses ( ) const

returns the neutral loss mono weight

◆ getOrigin()

char getOrigin ( ) const

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

◆ getPSIMODAccession()

const std::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()

std::string getSourceClassificationName ( SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS ) const

returns the classification

◆ getSynonyms()

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

returns the set of synonyms

◆ getTermSpecificity()

TermSpecificity getTermSpecificity ( ) const

returns terminal specificity

◆ getTermSpecificityName()

std::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 std::string getUniModAccession ( ) const

returns the unimod accession if available

◆ getUniModRecordId()

const Int & getUniModRecordId ( ) const

gets 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<()

bool operator< ( const ResidueModification & modification ) const

less operator

◆ operator=() [1/2]

ResidueModification & operator= ( const ResidueModification & )

default

Assignment operator.

◆ operator=() [2/2]

ResidueModification & operator= ( ResidueModification && ) &

default

Move 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 (no masses will be changed)

◆ setDiffMonoMass()

void setDiffMonoMass ( double mass )

sets the difference monoisotopic mass

◆ setFormula()

void setFormula ( const std::string & composition )

set the formula (no masses will be changed)

◆ setFullId()

void setFullId ( const std::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.

◆ setFullName()

void setFullName ( const std::string & full_name )

sets the full name of the modification; must NOT contain the origin (or . for terminals!)

◆ setId()

void setId ( const std::string & id )

set the identifier of the modification

◆ setMonoMass()

void setMonoMass ( double mass )

sets the monoisotopic mass (this must include the weight of the residue itself!)

◆ setName()

void setName ( const std::string & name )

sets the name of modification

◆ setNeutralLossAverageMasses()

void setNeutralLossAverageMasses ( std::vector< double > average_masses )

set the neutral loss average weight

◆ setNeutralLossDiffFormulas()

void setNeutralLossDiffFormulas ( const std::vector< EmpiricalFormula > & diff_formulas )

sets the neutral loss formula

◆ setNeutralLossMonoMasses()

void setNeutralLossMonoMasses ( std::vector< double > mono_masses )

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 std::string & id )

set the MOD:XXXXX accession of PSI-MOD

◆ setSourceClassification() [1/2]

void setSourceClassification ( const std::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< std::string > & synonyms )

sets the synonyms of that modification

◆ setTermSpecificity() [1/2]

void setTermSpecificity ( const std::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

◆ setTermSpecificity() [2/2]

void setTermSpecificity ( TermSpecificity term_spec )

Sets the term specificity.

Exceptions

Exception::InvalidValue if no valid specificity was given

◆ setUniModRecordId()

void setUniModRecordId ( const Int & id )

sets the unimod record id

◆ toString()

std::string toString ( ) const

Convert to string (incl. origin/terminal), in order of preference:

using the ID, as X(ID), e.g. 'M(Oxidation)' or '.(Acetyl)'
using the FullName
using the delta_mono_mass, e.g. 'M[+15.65]'
using the mono_mass, e.g. 'M[56.23]'

The mono_mass must not be negative (undistinguishable to delta_mono_mass when parsing)

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_

std::string formula_

protected

◆ full_id_

std::string full_id_

protected

◆ full_name_

std::string full_name_

protected

◆ id_

std::string id_

protected

◆ mono_mass_

double mono_mass_

protected

◆ name_

std::string name_

protected

◆ neutral_loss_average_masses_

std::vector<double> neutral_loss_average_masses_

protected

◆ neutral_loss_diff_formulas_

std::vector<EmpiricalFormula> neutral_loss_diff_formulas_

protected

◆ neutral_loss_mono_masses_

std::vector<double> neutral_loss_mono_masses_

protected

◆ origin_

char origin_

protected

◆ psi_mod_accession_

std::string psi_mod_accession_

protected

◆ synonyms_

std::set<std::string> synonyms_

protected

◆ term_spec_

TermSpecificity term_spec_

protected

◆ unimod_record_id_

Int unimod_record_id_

protected

Public Types

Public Member Functions

Predicates

Detailed Description

Member Enumeration Documentation

◆ SourceClassification

◆ TermSpecificity

Constructor & Destructor Documentation

◆ ResidueModification() [1/3]

◆ ResidueModification() [2/3]

◆ ResidueModification() [3/3]

◆ ~ResidueModification()

Member Function Documentation

◆ addSynonym()

◆ combineMods()

◆ createUnknownFromMassString()

◆ getAverageMass()

◆ getDiffAverageMass()

◆ getDiffFormula()

◆ getDiffMonoMass()

◆ getDiffMonoMassString()

◆ getDiffMonoMassWithBracket()

◆ getFormula()

◆ getFullId()

◆ getFullName()

◆ getId()

◆ getMonoMass()

◆ getMonoMassWithBracket()

◆ getName()

◆ getNeutralLossAverageMasses()

◆ getNeutralLossDiffFormulas()

◆ getNeutralLossMonoMasses()

◆ getOrigin()

◆ getPSIMODAccession()

◆ getSourceClassification()

◆ getSourceClassificationName()

◆ getSynonyms()

◆ getTermSpecificity()

◆ getTermSpecificityName()

◆ getUniModAccession()

◆ getUniModRecordId()

◆ hasNeutralLoss()

◆ isUserDefined()

◆ operator!=()

◆ operator<()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setAverageMass()

◆ setDiffAverageMass()

◆ setDiffFormula()

◆ setDiffMonoMass()

◆ setFormula()

◆ setFullId()

◆ setFullName()

◆ setId()

◆ setMonoMass()

◆ setName()

◆ setNeutralLossAverageMasses()

◆ setNeutralLossDiffFormulas()

◆ setNeutralLossMonoMasses()

◆ setOrigin()

◆ setPSIMODAccession()

◆ setSourceClassification() [1/2]

◆ setSourceClassification() [2/2]

◆ setSynonyms()

◆ setTermSpecificity() [1/2]

◆ setTermSpecificity() [2/2]

◆ setUniModRecordId()

◆ toString()

Member Data Documentation

◆ average_mass_

◆ classification_

◆ diff_average_mass_

◆ diff_formula_

◆ diff_mono_mass_

◆ formula_

◆ full_id_

◆ full_name_

◆ id_