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
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.
Returns the neutral loss average weight
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
Overload:
setSynonyms
(self, synonyms)Sets the synonyms of that modification
Overload:
setUniModRecordId
(self, id_)Sets the unimod record id
- SourceClassification#
alias of
__SourceClassification
- TermSpecificity#
alias of
__TermSpecificity
- 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
- 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)
- 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
- 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!)
- setMonoMass(self, mass: float) None #
Sets the monoisotopic mass (this must include the weight of the residue itself!)
- 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)
- 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