ResidueModification#

class pyopenms.ResidueModification#

Bases: object

Cython implementation of _ResidueModification

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ResidueModification.html

__init__()#

Cython signature: void ResidueModification()
Cython signature: void ResidueModification(ResidueModification &)

Methods

`__init__`	Cython signature: void ResidueModification()
`addSynonym`	Cython signature: void addSynonym(const String & synonym) Adds a synonym to the unique list
`getAverageMass`	Cython signature: double getAverageMass() Returns the average mass if set
`getDiffAverageMass`	Cython signature: double getDiffAverageMass() Returns the difference average mass, or 0.0 if not set
`getDiffFormula`	Cython signature: EmpiricalFormula getDiffFormula() Returns the diff formula if one was set
`getDiffMonoMass`	Cython signature: double getDiffMonoMass() Returns the diff monoisotopic mass, or 0.0 if not set
`getFormula`	Cython signature: String getFormula() Returns the chemical formula if set
`getFullId`	Cython signature: String getFullId()
`getFullName`	Cython signature: String getFullName() Returns the full name of the modification
`getId`	Cython signature: String getId() Returns the identifier of the modification
`getMonoMass`	Cython signature: double getMonoMass() Return the monoisotopic mass, or 0.0 if not set
`getName`	Cython signature: String getName() Returns the PSI-MS-label if available; e.g.
`getNeutralLossAverageMasses`	Cython signature: libcpp_vector[double] getNeutralLossAverageMasses() Returns the neutral loss average weight
`getNeutralLossDiffFormulas`	Cython signature: libcpp_vector[EmpiricalFormula] getNeutralLossDiffFormulas() Returns the neutral loss diff formula (if available)
`getNeutralLossMonoMasses`	Cython signature: libcpp_vector[double] getNeutralLossMonoMasses() Returns the neutral loss mono weight
`getOrigin`	Cython signature: char getOrigin() Returns the origin (i.e.
`getPSIMODAccession`	Cython signature: String getPSIMODAccession() Returns the PSI-MOD accession if available
`getSourceClassification`	Cython signature: SourceClassification getSourceClassification() Returns the source classification, if none was set, it is unspecific
`getSourceClassificationName`	Cython signature: String getSourceClassificationName(SourceClassification classification) Returns the classification
`getSynonyms`	Cython signature: libcpp_set[String] getSynonyms() Returns the set of synonyms
`getTermSpecificity`	Cython signature: TermSpecificity getTermSpecificity() Returns terminal specificity
`getTermSpecificityName`	Cython signature: String getTermSpecificityName(TermSpecificity) Returns the name of the terminal specificity
`getUniModAccession`	Cython signature: String getUniModAccession() Returns the unimod accession if available
`getUniModRecordId`	Cython signature: int getUniModRecordId() Gets the unimod record id
`hasNeutralLoss`	Cython signature: bool hasNeutralLoss() Returns true if a neutral loss formula is set
`isUserDefined`	Cython signature: bool isUserDefined() Returns true if it is a user-defined modification (empty id)
`setAverageMass`	Cython signature: void setAverageMass(double mass) Sets the average mass
`setDiffAverageMass`	Cython signature: void setDiffAverageMass(double mass) Sets the difference average mass
`setDiffFormula`	Cython signature: void setDiffFormula(EmpiricalFormula & diff_formula) Sets diff formula (no masses will be changed)
`setDiffMonoMass`	Cython signature: void setDiffMonoMass(double mass) Sets the difference monoisotopic mass
`setFormula`	Cython signature: void setFormula(const String & composition) Sets the formula (no masses will be changed)
`setFullId`	Cython signature: void setFullId(const String & full_id) Sets the full identifier (Unimod Accession + origin, if available)
`setFullName`	Cython signature: void setFullName(const String & full_name) Sets the full name of the modification; must NOT contain the origin (or .
`setId`	Cython signature: void setId(const String & id_) Sets the identifier of the modification
`setMonoMass`	Cython signature: void setMonoMass(double mass) Sets the monoisotopic mass (this must include the weight of the residue itself!)
`setName`	Cython signature: void setName(const String & name) Sets the name of modification
`setNeutralLossAverageMasses`	Cython signature: void setNeutralLossAverageMasses(libcpp_vector[double] average_masses) Sets the neutral loss average weight
`setNeutralLossDiffFormulas`	Cython signature: void setNeutralLossDiffFormulas(libcpp_vector[EmpiricalFormula] & diff_formulas) Sets the neutral loss formula
`setNeutralLossMonoMasses`	Cython signature: void setNeutralLossMonoMasses(libcpp_vector[double] mono_masses) Sets the neutral loss mono weight
`setOrigin`	Cython signature: void setOrigin(char origin) Sets the origin (i.e.
`setPSIMODAccession`	Cython signature: void setPSIMODAccession(const String & id_) Sets the MOD-XXXXX accession of PSI-MOD
`setSourceClassification`	Cython signature: void setSourceClassification(const String & classification)
`setSynonyms`	Cython signature: void setSynonyms(libcpp_set[String] & synonyms) Sets the synonyms of that modification
`setTermSpecificity`	Cython signature: void setTermSpecificity(TermSpecificity term_spec)
`setUniModRecordId`	Cython signature: void setUniModRecordId(int id_) Sets the unimod record id

SourceClassification#: alias of pyopenms.pyopenms_8.__SourceClassification

TermSpecificity#: alias of pyopenms.pyopenms_8.__TermSpecificity

addSynonym()#: Cython signature: void addSynonym(const String & synonym) Adds a synonym to the unique list

getAverageMass()#: Cython signature: double getAverageMass() Returns the average mass if set

getDiffAverageMass()#: Cython signature: double getDiffAverageMass() Returns the difference average mass, or 0.0 if not set

getDiffFormula()#: Cython signature: EmpiricalFormula getDiffFormula() Returns the diff formula if one was set

getDiffMonoMass()#: Cython signature: double getDiffMonoMass() Returns the diff monoisotopic mass, or 0.0 if not set

getFormula()#: Cython signature: String getFormula() Returns the chemical formula if set

getFullId()#: Cython signature: String getFullId()

getFullName()#: Cython signature: String getFullName() Returns the full name of the modification

getId()#: Cython signature: String getId() Returns the identifier of the modification

getMonoMass()#: Cython signature: double getMonoMass() Return the monoisotopic mass, or 0.0 if not set

getName()#: Cython signature: String getName() Returns the PSI-MS-label if available; e.g. Mascot uses this name

getNeutralLossAverageMasses()#: Cython signature: libcpp_vector[double] getNeutralLossAverageMasses() Returns the neutral loss average weight

getNeutralLossDiffFormulas()#: Cython signature: libcpp_vector[EmpiricalFormula] getNeutralLossDiffFormulas() Returns the neutral loss diff formula (if available)

getNeutralLossMonoMasses()#: Cython signature: libcpp_vector[double] getNeutralLossMonoMasses() Returns the neutral loss mono weight

getOrigin()#: Cython signature: char getOrigin() Returns the origin (i.e. modified amino acid)

getPSIMODAccession()#: Cython signature: String getPSIMODAccession() Returns the PSI-MOD accession if available

getSourceClassification()#: Cython signature: SourceClassification getSourceClassification() Returns the source classification, if none was set, it is unspecific

getSourceClassificationName()#: Cython signature: String getSourceClassificationName(SourceClassification classification) Returns the classification

getSynonyms()#: Cython signature: libcpp_set[String] getSynonyms() Returns the set of synonyms

getTermSpecificity()#: Cython signature: TermSpecificity getTermSpecificity() Returns terminal specificity

getTermSpecificityName()#: Cython signature: String getTermSpecificityName(TermSpecificity) Returns the name of the terminal specificity

getUniModAccession()#: Cython signature: String getUniModAccession() Returns the unimod accession if available

getUniModRecordId()#: Cython signature: int getUniModRecordId() Gets the unimod record id

hasNeutralLoss()#: Cython signature: bool hasNeutralLoss() Returns true if a neutral loss formula is set

isUserDefined()#: Cython signature: bool isUserDefined() Returns true if it is a user-defined modification (empty id)

setAverageMass()#: Cython signature: void setAverageMass(double mass) Sets the average mass

setDiffAverageMass()#: Cython signature: void setDiffAverageMass(double mass) Sets the difference average mass

setDiffFormula()#: Cython signature: void setDiffFormula(EmpiricalFormula & diff_formula) Sets diff formula (no masses will be changed)

setDiffMonoMass()#: Cython signature: void setDiffMonoMass(double mass) Sets the difference monoisotopic mass

setFormula()#: Cython signature: void setFormula(const String & composition) Sets the formula (no masses will be changed)

setFullId()#: Cython signature: void setFullId(const String & full_id) Sets the full identifier (Unimod Accession + origin, if available)

setFullName()#: Cython signature: void setFullName(const String & full_name) Sets the full name of the modification; must NOT contain the origin (or . for terminals!)

setId()#: Cython signature: void setId(const String & id_) Sets the identifier of the modification

setMonoMass()#: Cython signature: void setMonoMass(double mass) Sets the monoisotopic mass (this must include the weight of the residue itself!)

setName()#: Cython signature: void setName(const String & name) Sets the name of modification

setNeutralLossAverageMasses()#: Cython signature: void setNeutralLossAverageMasses(libcpp_vector[double] average_masses) Sets the neutral loss average weight

setNeutralLossDiffFormulas()#: Cython signature: void setNeutralLossDiffFormulas(libcpp_vector[EmpiricalFormula] & diff_formulas) Sets the neutral loss formula

setNeutralLossMonoMasses()#: Cython signature: void setNeutralLossMonoMasses(libcpp_vector[double] mono_masses) Sets the neutral loss mono weight

setOrigin()#: Cython signature: void setOrigin(char origin) Sets the origin (i.e. modified amino acid)

setPSIMODAccession()#: Cython signature: void setPSIMODAccession(const String & id_) Sets the MOD-XXXXX accession of PSI-MOD

setSourceClassification()#

Cython signature: void setSourceClassification(const String & classification) Classification as defined by the PSI-MOD
Cython signature: void setSourceClassification(SourceClassification classification) Sets the source classification

setSynonyms()#: Cython signature: void setSynonyms(libcpp_set[String] & synonyms) Sets the synonyms of that modification

setTermSpecificity()#

Cython signature: void setTermSpecificity(TermSpecificity term_spec) Sets the term specificity
Cython signature: void setTermSpecificity(const String & name) Sets the terminal specificity using a name

setUniModRecordId()#: Cython signature: void setUniModRecordId(int id_) Sets the unimod record id