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 | |
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) |
set full identifier (UniMod Accession + origin, if available) More... | |
const String & | getFullId () 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 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 (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 String & | getOrigin () 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 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 | operator== (const ResidueModification &modification) const |
equality operator More... | |
bool | operator!= (const ResidueModification &modification) const |
inequality operator More... | |
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"
Classification of the modification.
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 | |
PROTEIN_C_TERM | |
PROTEIN_N_TERM | |
NUMBER_OF_TERM_SPECIFICITY |
default constructor
ResidueModification | ( | const ResidueModification & | modification | ) |
copy constructor
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virtual |
destructor
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
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OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:54:06 using doxygen 1.8.9.1 |