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pwiz::data::unimod Namespace Reference

Functions

 BOOST_BITFIELD_EX (Site, PWIZ_API_DECL,(Any)(1<< 0)(NTerminus)(1<< 1)(CTerminus)(1<< 2)(Alanine)(1<< 3)(Cysteine)(1<< 4)(AsparticAcid)(1<< 5)(GlutamicAcid)(1<< 6)(Phenylalanine)(1<< 7)(Glycine)(1<< 8)(Histidine)(1<< 9)(Isoleucine)(1<< 10)(Lysine)(1<< 11)(Leucine)(1<< 12)(Methionine)(1<< 13)(Asparagine)(1<< 14)(Proline)(1<< 15)(Glutamine)(1<< 16)(Arginine)(1<< 17)(Serine)(1<< 18)(Threonine)(1<< 19)(Selenocysteine)(1<< 20)(Valine)(1<< 21)(Tryptophan)(1<< 22)(Tyrosine)(1<< 23)) BOOST_ENUM_EX(Position
() Anywhere() AnyNTerminus()
AnyCTerminus() 
ProteinNTerminus (ProteinCTerminus)) BOOST_BITFIELD_EX(Classification
() Anywhere() AnyNTerminus()
AnyCTerminus()() 
Any (1<< 0)(Artifact)(1<< 1)(ChemicalDerivative)(1<< 2)(CoTranslational)(1<< 3)(IsotopicLabel)(1<< 4)(Multiple)(1<< 5)(NLinkedGlycosylation)(1<< 6)(NonStandardResidue)(1<< 7)(OLinkedGlycosylation)(1<< 8)(OtherGlycosylation)(1<< 9)(Other)(1<< 10)(PostTranslational)(1<< 11)(PreTranslational)(1<< 12)(Substitution)(1<< 13)) struct PWIZ_API_DECL Modification
 a modification from Unimod
PWIZ_API_DECL Site site (char symbol)
 returns the Site given a one-letter residue code, or: 'x' for Site::Any, 'n' for Site::NTerminus, 'c' for Site::CTerminus
PWIZ_API_DECL Position position (CVID cvid=CVID_Unknown)
 returns a Position corresponding to one of the following CVIDs: CVID_Unknown: Position::Anywhere MS_modification_specificity_N_term: Position::AnyNTerminus MS_modification_specificity_C_term: Position::AnyCTerminus Else: invalid_argument exception
PWIZ_API_DECL const
std::vector< Modification > & 
modifications ()
 the entire list of Unimod modifications
PWIZ_API_DECL std::vector
< Modification
modifications (double mass, double tolerance, tribool monoisotopic=true, tribool approved=true, Site site=Site::Any, Position position=Position::Anywhere, Classification classification=Classification::Any, tribool hidden=indeterminate)
 get a list of modifications by mass and tolerance;
PWIZ_API_DECL const Modificationmodification (CVID cvid)
 find a modification by CVID
PWIZ_API_DECL const Modificationmodification (const std::string &title)
 find a modification by title, e.g. "Phospho" not "Phosphorylation"

Variables

 PWIZ_API_DECL

Function Documentation

pwiz::data::unimod::BOOST_BITFIELD_EX ( Site  ,
PWIZ_API_DECL  ,
(Any)(1<< 0)(NTerminus)(1<< 1)(CTerminus)(1<< 2)(Alanine)(1<< 3)(Cysteine)(1<< 4)(AsparticAcid)(1<< 5)(GlutamicAcid)(1<< 6)(Phenylalanine)(1<< 7)(Glycine)(1<< 8)(Histidine)(1<< 9)(Isoleucine)(1<< 10)(Lysine)(1<< 11)(Leucine)(1<< 12)(Methionine)(1<< 13)(Asparagine)(1<< 14)(Proline)(1<< 15)(Glutamine)(1<< 16)(Arginine)(1<< 17)(Serine)(1<< 18)(Threonine)(1<< 19)(Selenocysteine)(1<< 20)(Valine)(1<< 21)(Tryptophan)(1<< 22)(Tyrosine)(1<< 23)   
)
() Anywhere() AnyNTerminus() AnyCTerminus() pwiz::data::unimod::ProteinNTerminus ( ProteinCTerminus  )

Referenced by test().

() Anywhere() AnyNTerminus() AnyCTerminus()() pwiz::data::unimod::Any ( 1<<  0)

a modification from Unimod

Definition at line 81 of file Unimod.hpp.

References position(), and site().

Referenced by test().

{
struct PWIZ_API_DECL Specificity
{
Site site;
Position position;
bool hidden;
Classification classification;
};
CVID cvid;
std::string name;
Formula deltaComposition;
double deltaMonoisotopicMass() const;
double deltaAverageMass() const;
bool approved;
std::vector<Specificity> specificities;
};
PWIZ_API_DECL Site pwiz::data::unimod::site ( char  symbol)

returns the Site given a one-letter residue code, or: 'x' for Site::Any, 'n' for Site::NTerminus, 'c' for Site::CTerminus

Referenced by Any(), and test().

PWIZ_API_DECL Position pwiz::data::unimod::position ( CVID  cvid = CVID_Unknown)

returns a Position corresponding to one of the following CVIDs: CVID_Unknown: Position::Anywhere MS_modification_specificity_N_term: Position::AnyNTerminus MS_modification_specificity_C_term: Position::AnyCTerminus Else: invalid_argument exception

Referenced by Any(), and test().

PWIZ_API_DECL const std::vector<Modification>& pwiz::data::unimod::modifications ( )

the entire list of Unimod modifications

Referenced by test().

PWIZ_API_DECL std::vector<Modification> pwiz::data::unimod::modifications ( double  mass,
double  tolerance,
tribool  monoisotopic = true,
tribool  approved = true,
Site  site = Site::Any,
Position  position = Position::Anywhere,
Classification  classification = Classification::Any,
tribool  hidden = indeterminate 
)

get a list of modifications by mass and tolerance;

  • mass is treated as monoisotopic if monoisotopic=true; if indeterminate, both average and monoisotopic lookups are done
  • if approved is not indeterminate, only approved/unapproved modifications are considered
  • the site, position, and classification parameters filter the resulting modifications such that every modification must have at least one specificity matching all three criteria;
  • if hidden is not indeterminate, matching site/position/classification specificities must be hidden (or not)
PWIZ_API_DECL const Modification& pwiz::data::unimod::modification ( CVID  cvid)

find a modification by CVID

Referenced by pwiz::tradata::TextWriter::operator()(), test(), and testConversion().

PWIZ_API_DECL const Modification& pwiz::data::unimod::modification ( const std::string &  title)

find a modification by title, e.g. "Phospho" not "Phosphorylation"


Variable Documentation

() Anywhere() AnyNTerminus() AnyCTerminus() pwiz::data::unimod::PWIZ_API_DECL

Definition at line 71 of file Unimod.hpp.