ResidueModification
- class pyopenms.ResidueModification
Bases:
objectCython 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
Cython signature: void ResidueModification()
Cython signature: void addSynonym(const String & synonym) Adds a synonym to the unique list
Cython signature: double getAverageMass() Returns the average mass if set
Cython signature: double getDiffAverageMass() Returns the difference average mass, or 0.0 if not set
Cython signature: EmpiricalFormula getDiffFormula() Returns the diff formula if one was set
Cython signature: double getDiffMonoMass() Returns the diff monoisotopic mass, or 0.0 if not set
Cython signature: String getFormula() Returns the chemical formula if set
Cython signature: String getFullId()
Cython signature: String getFullName() Returns the full name of the modification
Cython signature: String getId() Returns the identifier of the modification
Cython signature: double getMonoMass() Return the monoisotopic mass, or 0.0 if not set
Cython signature: String getName() Returns the PSI-MS-label if available; e.g.
Cython signature: libcpp_vector[double] getNeutralLossAverageMasses() Returns the neutral loss average weight
Cython signature: libcpp_vector[EmpiricalFormula] getNeutralLossDiffFormulas() Returns the neutral loss diff formula (if available)
Cython signature: libcpp_vector[double] getNeutralLossMonoMasses() Returns the neutral loss mono weight
Cython signature: char getOrigin() Returns the origin (i.e.
Cython signature: String getPSIMODAccession() Returns the PSI-MOD accession if available
Cython signature: SourceClassification getSourceClassification() Returns the source classification, if none was set, it is unspecific
Cython signature: String getSourceClassificationName(SourceClassification classification) Returns the classification
Cython signature: libcpp_set[String] getSynonyms() Returns the set of synonyms
Cython signature: TermSpecificity getTermSpecificity() Returns terminal specificity
Cython signature: String getTermSpecificityName(TermSpecificity) Returns the name of the terminal specificity
Cython signature: String getUniModAccession() Returns the unimod accession if available
Cython signature: int getUniModRecordId() Gets the unimod record id
Cython signature: bool hasNeutralLoss() Returns true if a neutral loss formula is set
Cython signature: bool isUserDefined() Returns true if it is a user-defined modification (empty id)
Cython signature: void setAverageMass(double mass) Sets the average mass
Cython signature: void setDiffAverageMass(double mass) Sets the difference average mass
Cython signature: void setDiffFormula(EmpiricalFormula & diff_formula) Sets diff formula (no masses will be changed)
Cython signature: void setDiffMonoMass(double mass) Sets the difference monoisotopic mass
Cython signature: void setFormula(const String & composition) Sets the formula (no masses will be changed)
Cython signature: void setFullId(const String & full_id) Sets the full identifier (Unimod Accession + origin, if available)
Cython signature: void setFullName(const String & full_name) Sets the full name of the modification; must NOT contain the origin (or .
Cython signature: void setId(const String & id_) Sets the identifier of the modification
Cython signature: void setMonoMass(double mass) Sets the monoisotopic mass (this must include the weight of the residue itself!)
Cython signature: void setName(const String & name) Sets the name of modification
Cython signature: void setNeutralLossAverageMasses(libcpp_vector[double] average_masses) Sets the neutral loss average weight
Cython signature: void setNeutralLossDiffFormulas(libcpp_vector[EmpiricalFormula] & diff_formulas) Sets the neutral loss formula
Cython signature: void setNeutralLossMonoMasses(libcpp_vector[double] mono_masses) Sets the neutral loss mono weight
Cython signature: void setOrigin(char origin) Sets the origin (i.e.
Cython signature: void setPSIMODAccession(const String & id_) Sets the MOD-XXXXX accession of PSI-MOD
Cython signature: void setSourceClassification(const String & classification)
Cython signature: void setSynonyms(libcpp_set[String] & synonyms) Sets the synonyms of that modification
Cython signature: void setTermSpecificity(TermSpecificity term_spec)
Cython signature: void setUniModRecordId(int id_) Sets the unimod record id
- SourceClassification
alias of
pyopenms.pyopenms_1.__SourceClassification
- TermSpecificity
alias of
pyopenms.pyopenms_1.__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!)
- 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