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ResidueModification Class Reference

Representation of a modification. More...

#include <OpenMS/CHEMISTRY/ResidueModification.h>

Public Types

enum  Term_Specificity {
  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  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 More...
 
 ResidueModification (const ResidueModification &modification)
 copy constructor More...
 
virtual ~ResidueModification ()
 destructor More...
 
Assignment operator
ResidueModificationoperator= (const ResidueModification &modification)
 assignment operator More...
 
Accessors
void setId (const String &id)
 set the identifier of the modification More...
 
const StringgetId () const
 returns the identifier of the modification More...
 
void setFullId (const String &full_id)
 set full identifier (UniMod Accession + origin, if available) More...
 
const StringgetFullId () const
 returns the full id of the mod (UniMod accession + origin, if available) More...
 
void setUniModAccession (const String &id)
 sets the unimod accession More...
 
const StringgetUniModAccession () const
 returns the unimod accession if available More...
 
void setPSIMODAccession (const String &id)
 set the MOD:XXXXX accession of PSI-MOD More...
 
const StringgetPSIMODAccession () const
 returns the PSI-MOD accession if available More...
 
void setFullName (const String &full_name)
 sets the full name of the modification More...
 
const StringgetFullName () const
 returns the full name of the modification More...
 
void setName (const String &name)
 sets the name of modification More...
 
const StringgetName () const
 returns the PSI-MS-label if available; e.g. Mascot uses this name More...
 
void setTermSpecificity (Term_Specificity term_spec)
 sets the term specificity More...
 
void setTermSpecificity (const String &name)
 sets the terminal specificity using a name (valid: "C-term","N-term","none") More...
 
Term_Specificity getTermSpecificity () const
 returns terminal specificity More...
 
String getTermSpecificityName (Term_Specificity=NUMBER_OF_TERM_SPECIFICITY) const
 returns the terminal specificity name which is set or given as parameter More...
 
void setOrigin (const String &origin)
 sets the origin (i.e. amino acid) More...
 
const StringgetOrigin () const
 returns the origin (i.e. amino acid) if set More...
 
void setSourceClassification (const String &classification)
 classification as defined by the PSI-MOD More...
 
void setSourceClassification (Source_Classification classification)
 sets the source classification More...
 
Source_Classification getSourceClassification () const
 returns the source classification, if none was set, it is unspecific More...
 
String getSourceClassificationName (Source_Classification 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 StringgetFormula () const
 returns the chemical formula if set More...
 
void setDiffFormula (const EmpiricalFormula &diff_formula)
 sets diff formula More...
 
const EmpiricalFormulagetDiffFormula () 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 EmpiricalFormulagetNeutralLossDiffFormula () 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 operator== (const ResidueModification &modification) const
 equality operator More...
 
bool operator!= (const ResidueModification &modification) const
 inequality operator More...
 

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_
 
double average_mass_
 
double mono_mass_
 
double diff_average_mass_
 
double diff_mono_mass_
 
String formula_
 
EmpiricalFormula diff_formula_
 
std::set< Stringsynonyms_
 
EmpiricalFormula neutral_loss_diff_formula_
 
double neutral_loss_mono_mass_
 
double 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.

Example: methionine sulfoxide formation by oxidation of methionine

getFullId() = "Oxidation (M)" getId() = "Oxidation" getFullName() = "Oxidation or Hydroxylation" getUniModAccession() = "UniMod:312"

Member Enumeration Documentation

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 

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 
PROTEIN_C_TERM 
PROTEIN_N_TERM 
NUMBER_OF_TERM_SPECIFICITY 

Constructor & Destructor Documentation

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

double getAverageMass ( ) const

returns the average mass if set

double getDiffAverageMass ( ) const

returns the difference average mass if set

const EmpiricalFormula& getDiffFormula ( ) const

returns the diff formula if one was set

double 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

double 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

double getNeutralLossAverageMass ( ) const

returns the neutral loss average weight

const EmpiricalFormula& getNeutralLossDiffFormula ( ) const

returns the neutral loss diff formula (if available)

double getNeutralLossMonoMass ( ) const

returns the neutral loss mono weight

const String& getOrigin ( ) const

returns the origin (i.e. 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 ( double  mass)

sets the average mass

void setDiffAverageMass ( double  mass)

set the difference average mass

void setDiffFormula ( const EmpiricalFormula diff_formula)

sets diff formula

void setDiffMonoMass ( double  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 ( double  mass)

sets the monoisotopic mass

void setName ( const String name)

sets the name of modification

void setNeutralLossAverageMass ( double  average_mass)

set the neutral loss average weight

void setNeutralLossDiffFormula ( const EmpiricalFormula loss)

sets the neutral loss formula

void setNeutralLossMonoMass ( double  mono_mass)

set the neutral loss mono weight

void setOrigin ( const String origin)

sets the origin (i.e. 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

double average_mass_
protected
Source_Classification classification_
protected
double diff_average_mass_
protected
EmpiricalFormula diff_formula_
protected
double diff_mono_mass_
protected
String formula_
protected
String full_id_
protected
String full_name_
protected
String id_
protected
double mono_mass_
protected
String name_
protected
double neutral_loss_average_mass_
protected
EmpiricalFormula neutral_loss_diff_formula_
protected
double 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

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11