| OpenMS 2.5.0

Protected Attributes | List of all members
ResidueModification Class Reference

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 &)=default
| Copy constructor. More...
| ResidueModification (ResidueModification &&)=default
| Move constructor. More...
virtual | ~ResidueModification ()
| Destructor. More...
Assignment operator
ResidueModification & | operator= (const ResidueModification &)=default
| Assignment operator. More...
ResidueModification & | operator= (ResidueModification &&) &=default
| Move 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
| gets 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...
bool | operator< (const ResidueModification &modification) const
| less operator More...

## 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_

## 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

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.

## 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() [1/3]

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 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

## ◆ 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

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

## ◆ setDiffMonoMass()

void setDiffMonoMass | ( | double | mass | ) |

sets the difference monoisotopic mass

## ◆ 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.

## ◆ 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

## ◆ setMonoMass()

void setMonoMass | ( | double | mass | ) |

sets the monoisotopic mass

## ◆ setName()

void setName | ( | const String & | name | ) |

sets the name of modification

## ◆ 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

## ◆ 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