ModificationDefinitionsSet

class pyopenms.ModificationDefinitionsSet

Bases: object

Cython implementation of _ModificationDefinitionsSet

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ModificationDefinitionsSet.html

__init__()

Cython signature: void ModificationDefinitionsSet()
Cython signature: void ModificationDefinitionsSet(ModificationDefinitionsSet &)
Cython signature: void ModificationDefinitionsSet(StringList fixed_modifications, StringList variable_modifications)

Methods

`__init__`	Cython signature: void ModificationDefinitionsSet()
`addModification`	Cython signature: void addModification(ModificationDefinition & mod_def) Adds a modification definition to the set
`getFixedModificationNames`	Cython signature: libcpp_set[String] getFixedModificationNames() Returns only the names of the fixed modifications
`getFixedModifications`	Cython signature: libcpp_set[ModificationDefinition] getFixedModifications() Returns the stored fixed modification definitions
`getMaxModifications`	Cython signature: size_t getMaxModifications() Return the maximal number of modifications allowed per peptide
`getModificationNames`	Cython signature: void getModificationNames(StringList & fixed_modifications, StringList & variable_modifications)
`getModifications`	Cython signature: libcpp_set[ModificationDefinition] getModifications() Returns the stored modification definitions
`getNumberOfFixedModifications`	Cython signature: size_t getNumberOfFixedModifications() Returns the number of fixed modifications stored in this set
`getNumberOfModifications`	Cython signature: size_t getNumberOfModifications() Returns the number of modifications stored in this set
`getNumberOfVariableModifications`	Cython signature: size_t getNumberOfVariableModifications() Returns the number of variable modifications stored in this set
`getVariableModificationNames`	Cython signature: libcpp_set[String] getVariableModificationNames() Returns only the names of the variable modifications
`getVariableModifications`	Cython signature: libcpp_set[ModificationDefinition] getVariableModifications() Returns the stored variable modification definitions
`inferFromPeptides`	Cython signature: void inferFromPeptides(libcpp_vector[PeptideIdentification] & peptides) Infers the sets of defined modifications from the modifications present on peptide identifications
`isCompatible`	Cython signature: bool isCompatible(AASequence & peptide) Returns true if the peptide is compatible with the definitions, e.g.
`setMaxModifications`	Cython signature: void setMaxModifications(size_t max_mod) Sets the maximal number of modifications allowed per peptide
`setModifications`	Cython signature: void setModifications(libcpp_set[ModificationDefinition] & mod_defs)

addModification(): Cython signature: void addModification(ModificationDefinition & mod_def) Adds a modification definition to the set

getFixedModificationNames(): Cython signature: libcpp_set[String] getFixedModificationNames() Returns only the names of the fixed modifications

getFixedModifications(): Cython signature: libcpp_set[ModificationDefinition] getFixedModifications() Returns the stored fixed modification definitions

getMaxModifications(): Cython signature: size_t getMaxModifications() Return the maximal number of modifications allowed per peptide

getModificationNames()

Cython signature: void getModificationNames(StringList & fixed_modifications, StringList & variable_modifications) Populates the output lists with the modification names (use e.g. for
Cython signature: libcpp_set[String] getModificationNames() Returns only the names of the modifications stored in the set

getModifications(): Cython signature: libcpp_set[ModificationDefinition] getModifications() Returns the stored modification definitions

getNumberOfFixedModifications(): Cython signature: size_t getNumberOfFixedModifications() Returns the number of fixed modifications stored in this set

getNumberOfModifications(): Cython signature: size_t getNumberOfModifications() Returns the number of modifications stored in this set

getNumberOfVariableModifications(): Cython signature: size_t getNumberOfVariableModifications() Returns the number of variable modifications stored in this set

getVariableModificationNames(): Cython signature: libcpp_set[String] getVariableModificationNames() Returns only the names of the variable modifications

getVariableModifications(): Cython signature: libcpp_set[ModificationDefinition] getVariableModifications() Returns the stored variable modification definitions

inferFromPeptides(): Cython signature: void inferFromPeptides(libcpp_vector[PeptideIdentification] & peptides) Infers the sets of defined modifications from the modifications present on peptide identifications

isCompatible(): Cython signature: bool isCompatible(AASequence & peptide) Returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications

setMaxModifications(): Cython signature: void setMaxModifications(size_t max_mod) Sets the maximal number of modifications allowed per peptide

setModifications()

Cython signature: void setModifications(libcpp_set[ModificationDefinition] & mod_defs) Sets the modification definitions

Cython signature: void setModifications(const String & fixed_modifications, String & variable_modifications)

The strings should contain a comma separated list of modifications. The names can be PSI-MOD identifier or any other unique name supported by PSI-MOD. TermSpec definitions and other specific definitions are given by the modifications themselves.

Cython signature: void setModifications(StringList & fixed_modifications, StringList & variable_modifications) Same as above, but using StringList instead of comma separated strings