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 pyopenms._pyopenms_7.__SourceClassification

TermSpecificity: alias of pyopenms._pyopenms_7.__TermSpecificity

addSynonym(self, synonym: Union[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) → Union[bytes, str, String]: Returns the chemical formula if set

getFullId(self) → Union[bytes, str, String]

getFullName(self) → Union[bytes, str, String]: Returns the full name of the modification

getId(self) → Union[bytes, str, String]: Returns the identifier of the modification

getMonoMass(self) → float: Return the monoisotopic mass, or 0.0 if not set

getName(self) → Union[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) → Union[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) → Union[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) → Union[bytes, str, String]: Returns the name of the terminal specificity

getUniModAccession(self) → Union[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: Union[bytes, str, String]) → None: Sets the formula (no masses will be changed)

setFullId(self, full_id: Union[bytes, str, String]) → None: Sets the full identifier (Unimod Accession + origin, if available)

setFullName(self, full_name: Union[bytes, str, String]) → None: Sets the full name of the modification; must NOT contain the origin (or . for terminals!)

setId(self, id_: Union[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: Union[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_: Union[bytes, str, String]) → None: Sets the MOD-XXXXX accession of PSI-MOD

setSourceClassification()

Overload:

setSourceClassification(self, classification: Union[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: Union[bytes, str, String]) → None

Sets the terminal specificity using a name

setUniModRecordId(self, id_: int) → None: Sets the unimod record id