ResidueModification Class Reference

Representation of a modification. More...

#include <OpenMS/CHEMISTRY/ResidueModification.h>

List of all members.

Public Types
enum	Term_Specificity { ANYWHERE = 0, C_TERM = 1, N_TERM = 2, NUMBER_OF_TERM_SPECIFICITY }
	Position where the modification is allowed to occur. More...
enum	Source_Classification {   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 &modification)
	copy constructor
virtual	~ResidueModification ()
	destructor
Assignment operator
ResidueModification &	operator= (const ResidueModification &modification)
	assignment operator
Accessors
void	setId (const String &id)
	set the identifier of the modification
const String &	getId () const
	returns the identifier of the modification
void	setFullId (const String &full_id)
	set full identifier (UniMod Accession + origin, if available)
const String &	getFullId () const
	returns the full id of the mod (UniMod accession + origin, if available)
void	setUniModAccession (const String &id)
	sets the unimod accession
const String &	getUniModAccession () const
	returns the unimod accession if available
void	setPSIMODAccession (const String &id)
	set the MOD:XXXXX accession of PSI-MOD
const String &	getPSIMODAccession () const
	returns the PSI-MOD accession if available
void	setFullName (const String &full_name)
	sets the full name of the modification
const String &	getFullName () const
	returns the full name of the modification
void	setName (const String &name)
	sets the name of modification
const String &	getName () const
	returns the PSI-MS-label if available; e.g. Mascot uses this name
void	setTermSpecificity (Term_Specificity term_spec)
	sets the term specificity
void	setTermSpecificity (const String &name)
	sets the terminal specificity using a name (valid: "C-term","N-term","none")
Term_Specificity	getTermSpecificity () const
	returns terminal specificity
String	getTermSpecificityName (Term_Specificity=NUMBER_OF_TERM_SPECIFICITY) const
	returns the terminal specificity name which is set or given as parameter
void	setOrigin (const String &origin)
	sets the origin (ie amino acid)
const String &	getOrigin () const
	returns the origin (ie amino acid) if set
void	setSourceClassification (const String &classification)
	classification as defined by the PSI-MOD
void	setSourceClassification (Source_Classification classification)
	sets the source classification
Source_Classification	getSourceClassification () const
	returns the source classification, if none was set, it is unspecific
String	getSourceClassificationName (Source_Classification classification=NUMBER_OF_SOURCE_CLASSIFICATIONS) const
	returns the classification
void	setAverageMass (DoubleReal mass)
	sets the average mass
DoubleReal	getAverageMass () const
	returns the average mass if set
void	setMonoMass (DoubleReal mass)
	sets the monoisotopic mass
DoubleReal	getMonoMass () const
	return the monoisotopic mass, if set
void	setDiffAverageMass (DoubleReal mass)
	set the difference average mass
DoubleReal	getDiffAverageMass () const
	returns the difference average mass if set
void	setDiffMonoMass (DoubleReal mass)
	sets the difference monoisotopic mass
DoubleReal	getDiffMonoMass () const
	returns the diff monoisotopic mass if set
void	setFormula (const String &composition)
	set the formula
const String &	getFormula () const
	returns the chemical formula if set
void	setDiffFormula (const EmpiricalFormula &diff_formula)
	sets diff formula
const EmpiricalFormula &	getDiffFormula () const
	returns the diff formula if one was set
void	setSynonyms (const std::set< String > &synonyms)
	sets the synonyms of that modification
void	addSynonym (const String &synonym)
	adds a synonym to the unique list
const std::set< String > &	getSynonyms () const
	returns the set of synonyms
void	setNeutralLossDiffFormula (const EmpiricalFormula &loss)
	sets the neutral loss formula
const EmpiricalFormula &	getNeutralLossDiffFormula () const
	returns the neutral loss diff formula (if available)
void	setNeutralLossMonoMass (DoubleReal mono_mass)
	set the neutral loss mono weight
DoubleReal	getNeutralLossMonoMass () const
	returns the neutral loss mono weight
void	setNeutralLossAverageMass (DoubleReal average_mass)
	set the neutral loss average weight
DoubleReal	getNeutralLossAverageMass () const
	returns the neutral loss average weight
Predicates
bool	hasNeutralLoss () const
	returns true if a neutral loss formula is set
bool	operator== (const ResidueModification &modification) const
	equality operator
bool	operator!= (const ResidueModification &modification) const
	inequality operator
Protected Attributes
String	id_
String	full_id_
String	psi_mod_accession_
String	unimod_accession_
String	full_name_
String	name_
Term_Specificity	term_spec_
String	origin_
Source_Classification	classification_
DoubleReal	average_mass_
DoubleReal	mono_mass_
DoubleReal	diff_average_mass_
DoubleReal	diff_mono_mass_
String	formula_
EmpiricalFormula	diff_formula_
std::set< String >	synonyms_
EmpiricalFormula	neutral_loss_diff_formula_
DoubleReal	neutral_loss_mono_mass_
DoubleReal	neutral_loss_average_mass_

---

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.

---

Member Enumeration Documentation

enum Source_Classification

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

enum Term_Specificity

Position where the modification is allowed to occur.

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

---

Constructor & Destructor Documentation

ResidueModification

(

)

default constructor

ResidueModification

(

const ResidueModification &

modification

)

copy constructor

virtual ~ResidueModification

(

)

[virtual]

destructor

---

Member Function Documentation

void addSynonym

(

const String &

synonym

)

adds a synonym to the unique list

DoubleReal getAverageMass

(

)

const

returns the average mass if set

DoubleReal getDiffAverageMass

(

)

const

returns the difference average mass if set

const EmpiricalFormula& getDiffFormula

(

)

const

returns the diff formula if one was set

DoubleReal getDiffMonoMass

(

)

const

returns the diff monoisotopic mass if set

const String& getFormula

(

)

const

returns the chemical formula if set

const String& getFullId

(

)

const

returns the full id of the mod (UniMod accession + origin, if available)

const String& getFullName

(

)

const

returns the full name of the modification

const String& getId

(

)

const

returns the identifier of the modification

DoubleReal getMonoMass

(

)

const

return the monoisotopic mass, if set

const String& getName

(

)

const

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

DoubleReal getNeutralLossAverageMass

(

)

const

returns the neutral loss average weight

const EmpiricalFormula& getNeutralLossDiffFormula

(

)

const

returns the neutral loss diff formula (if available)

DoubleReal getNeutralLossMonoMass

(

)

const

returns the neutral loss mono weight

const String& getOrigin

(

)

const

returns the origin (ie amino acid) if set

const String& getPSIMODAccession

(

)

const

returns the PSI-MOD accession if available

Source_Classification getSourceClassification

(

)

const

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

String getSourceClassificationName

(

Source_Classification

classification = NUMBER_OF_SOURCE_CLASSIFICATIONS

)

const

returns the classification

const std::set<String>& getSynonyms

(

)

const

returns the set of synonyms

Term_Specificity getTermSpecificity

(

)

const

returns terminal specificity

String getTermSpecificityName

(

Term_Specificity

= NUMBER_OF_TERM_SPECIFICITY

)

const

returns the terminal specificity name which is set or given as parameter

const String& getUniModAccession

(

)

const

returns the unimod accession if available

bool hasNeutralLoss

(

)

const

returns true if a neutral loss formula is set

bool operator!=

(

const ResidueModification &

modification

)

const

inequality operator

ResidueModification& operator=

(

const ResidueModification &

modification

)

assignment operator

bool operator==

(

const ResidueModification &

modification

)

const

equality operator

void setAverageMass

(

DoubleReal

mass

)

sets the average mass

void setDiffAverageMass

(

DoubleReal

mass

)

set the difference average mass

void setDiffFormula

(

const EmpiricalFormula &

diff_formula

)

sets diff formula

void setDiffMonoMass

(

DoubleReal

mass

)

sets the difference monoisotopic mass

void setFormula

(

const String &

composition

)

set the formula

void setFullId

(

const String &

full_id

)

set full identifier (UniMod Accession + origin, if available)

void setFullName

(

const String &

full_name

)

sets the full name of the modification

void setId

(

const String &

id

)

set the identifier of the modification

void setMonoMass

(

DoubleReal

mass

)

sets the monoisotopic mass

void setName

(

const String &

name

)

sets the name of modification

void setNeutralLossAverageMass

(

DoubleReal

average_mass

)

set the neutral loss average weight

void setNeutralLossDiffFormula

(

const EmpiricalFormula &

loss

)

sets the neutral loss formula

void setNeutralLossMonoMass

(

DoubleReal

mono_mass

)

set the neutral loss mono weight

void setOrigin

(

const String &

origin

)

sets the origin (ie amino acid)

void setPSIMODAccession

(

const String &

id

)

set the MOD:XXXXX accession of PSI-MOD

void setSourceClassification

(

const String &

classification

)

classification as defined by the PSI-MOD

void setSourceClassification

(

Source_Classification

classification

)

sets the source classification

void setSynonyms

(

const std::set< String > &

synonyms

)

sets the synonyms of that modification

void setTermSpecificity

(

Term_Specificity

term_spec

)

sets the term specificity

void setTermSpecificity

(

const String &

name

)

sets the terminal specificity using a name (valid: "C-term","N-term","none")

void setUniModAccession

(

const String &

id

)

sets the unimod accession

---

Member Data Documentation

DoubleReal average_mass_ [protected]

Source_Classification classification_ [protected]

DoubleReal diff_average_mass_ [protected]

EmpiricalFormula diff_formula_ [protected]

DoubleReal diff_mono_mass_ [protected]

String formula_ [protected]

String full_id_ [protected]

String full_name_ [protected]

String id_ [protected]

DoubleReal mono_mass_ [protected]

String name_ [protected]

DoubleReal neutral_loss_average_mass_ [protected]

EmpiricalFormula neutral_loss_diff_formula_ [protected]

DoubleReal neutral_loss_mono_mass_ [protected]

String origin_ [protected]

String psi_mod_accession_ [protected]

std::set<String> synonyms_ [protected]

Term_Specificity term_spec_ [protected]

String unimod_accession_ [protected]