ResidueModification#

class pyopenms.ResidueModification#

Bases: object

Cython implementation of _ResidueModification

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: ResidueModification) None

Methods

__init__

Overload:

addSynonym(self, synonym)

Adds a synonym to the unique list

getAverageMass(self)

Returns the average mass if set

getDiffAverageMass(self)

Returns the difference average mass, or 0.0 if not set

getDiffFormula(self)

Returns the diff formula if one was set

getDiffMonoMass(self)

Returns the diff monoisotopic mass, or 0.0 if not set

getFormula(self)

Returns the chemical formula if set

getFullId(self)

getFullName(self)

Returns the full name of the modification

getId(self)

Returns the identifier of the modification

getMonoMass(self)

Return the monoisotopic mass, or 0.0 if not set

getName(self)

Returns the PSI-MS-label if available; e.g.

getNeutralLossAverageMasses(self)

Returns the neutral loss average weight

getNeutralLossDiffFormulas(self)

Returns the neutral loss diff formula (if available)

getNeutralLossMonoMasses(self)

Returns the neutral loss mono weight

getOrigin(self)

Returns the origin (i.e.

getPSIMODAccession(self)

Returns the PSI-MOD accession if available

getSourceClassification(self)

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

getSourceClassificationName(self, classification)

Returns the classification

getSynonyms(self)

Returns the set of synonyms

getTermSpecificity(self)

Returns terminal specificity

getTermSpecificityName(self, in_0)

Returns the name of the terminal specificity

getUniModAccession(self)

Returns the unimod accession if available

getUniModRecordId(self)

Gets the unimod record id

hasNeutralLoss(self)

Returns true if a neutral loss formula is set

isUserDefined(self)

Returns true if it is a user-defined modification (empty id)

setAverageMass(self, mass)

Sets the average mass

setDiffAverageMass(self, mass)

Sets the difference average mass

setDiffFormula(self, diff_formula)

Sets diff formula (no masses will be changed)

setDiffMonoMass(self, mass)

Sets the difference monoisotopic mass

setFormula(self, composition)

Sets the formula (no masses will be changed)

setFullId(self, full_id)

Sets the full identifier (Unimod Accession + origin, if available)

setFullName(self, full_name)

Sets the full name of the modification; must NOT contain the origin (or .

setId(self, id_)

Sets the identifier of the modification

setMonoMass(self, mass)

Sets the monoisotopic mass (this must include the weight of the residue itself!)

setName(self, name)

Sets the name of modification

setNeutralLossAverageMasses(self, average_masses)

Sets the neutral loss average weight

setNeutralLossDiffFormulas(self, diff_formulas)

Sets the neutral loss formula

setNeutralLossMonoMasses(self, mono_masses)

Sets the neutral loss mono weight

setOrigin(self, origin)

Sets the origin (i.e.

setPSIMODAccession(self, id_)

Sets the MOD-XXXXX accession of PSI-MOD

setSourceClassification

Overload:

setSynonyms(self, synonyms)

Sets the synonyms of that modification

setTermSpecificity

Overload:

setUniModRecordId(self, id_)

Sets the unimod record id

SourceClassification#

alias of __SourceClassification

TermSpecificity#

alias of __TermSpecificity

addSynonym(self, synonym: bytes | str | String) None#

Adds a synonym to the unique list

getAverageMass(self) float#

Returns the average mass if set

getDiffAverageMass(self) float#

Returns the difference average mass, or 0.0 if not set

getDiffFormula(self) EmpiricalFormula#

Returns the diff formula if one was set

getDiffMonoMass(self) float#

Returns the diff monoisotopic mass, or 0.0 if not set

getFormula(self) bytes | str | String#

Returns the chemical formula if set

getFullId(self) bytes | str | String#
getFullName(self) bytes | str | String#

Returns the full name of the modification

getId(self) bytes | str | String#

Returns the identifier of the modification

getMonoMass(self) float#

Return the monoisotopic mass, or 0.0 if not set

getName(self) bytes | str | String#

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

getNeutralLossAverageMasses(self) List[float]#

Returns the neutral loss average weight

getNeutralLossDiffFormulas(self) List[EmpiricalFormula]#

Returns the neutral loss diff formula (if available)

getNeutralLossMonoMasses(self) List[float]#

Returns the neutral loss mono weight

getOrigin(self) bytes#

Returns the origin (i.e. modified amino acid)

getPSIMODAccession(self) bytes | str | String#

Returns the PSI-MOD accession if available

getSourceClassification(self) int#

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

getSourceClassificationName(self, classification: int) bytes | str | String#

Returns the classification

getSynonyms(self) Set[bytes]#

Returns the set of synonyms

getTermSpecificity(self) int#

Returns terminal specificity

getTermSpecificityName(self, in_0: int) bytes | str | String#

Returns the name of the terminal specificity

getUniModAccession(self) bytes | str | String#

Returns the unimod accession if available

getUniModRecordId(self) int#

Gets the unimod record id

hasNeutralLoss(self) bool#

Returns true if a neutral loss formula is set

isUserDefined(self) bool#

Returns true if it is a user-defined modification (empty id)

setAverageMass(self, mass: float) None#

Sets the average mass

setDiffAverageMass(self, mass: float) None#

Sets the difference average mass

setDiffFormula(self, diff_formula: EmpiricalFormula) None#

Sets diff formula (no masses will be changed)

setDiffMonoMass(self, mass: float) None#

Sets the difference monoisotopic mass

setFormula(self, composition: bytes | str | String) None#

Sets the formula (no masses will be changed)

setFullId(self, full_id: bytes | str | String) None#

Sets the full identifier (Unimod Accession + origin, if available)

setFullName(self, full_name: bytes | str | String) None#

Sets the full name of the modification; must NOT contain the origin (or . for terminals!)

setId(self, id_: bytes | str | String) None#

Sets the identifier of the modification

setMonoMass(self, mass: float) None#

Sets the monoisotopic mass (this must include the weight of the residue itself!)

setName(self, name: bytes | str | String) None#

Sets the name of modification

setNeutralLossAverageMasses(self, average_masses: List[float]) None#

Sets the neutral loss average weight

setNeutralLossDiffFormulas(self, diff_formulas: List[EmpiricalFormula]) None#

Sets the neutral loss formula

setNeutralLossMonoMasses(self, mono_masses: List[float]) None#

Sets the neutral loss mono weight

setOrigin(self, origin: bytes) None#

Sets the origin (i.e. modified amino acid)

setPSIMODAccession(self, id_: bytes | str | String) None#

Sets the MOD-XXXXX accession of PSI-MOD

setSourceClassification()#

Overload:

setSourceClassification(self, classification: bytes | str | String) None

Classification as defined by the PSI-MOD

Overload:

setSourceClassification(self, classification: int) None

Sets the source classification

setSynonyms(self, synonyms: Set[bytes]) None#

Sets the synonyms of that modification

setTermSpecificity()#

Overload:

setTermSpecificity(self, term_spec: int) None

Sets the term specificity

Overload:

setTermSpecificity(self, name: bytes | str | String) None

Sets the terminal specificity using a name

setUniModRecordId(self, id_: int) None#

Sets the unimod record id