ModificationDefinitionsSet#

class pyopenms.ModificationDefinitionsSet#

Bases: object

Cython implementation of _ModificationDefinitionsSet

Original C++ documentation is available here

Representation of a set of modification definitions

This class enhances the modification definitions as defined in the class ModificationDefinition into a set of definitions. This is also e.g. used as input parameters in search engines.

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: ModificationDefinitionsSet) → None

Overload:

__init__(self, fixed_modifications: List[bytes], variable_modifications: List[bytes]) → None

Methods

`__init__`	Overload:
`addModification`(self, mod_def)	Adds a modification definition to the set
`getFixedModificationNames`(self)	Returns only the names of the fixed modifications
`getFixedModifications`(self)	Returns the stored fixed modification definitions
`getMaxModifications`(self)	Return the maximal number of modifications allowed per peptide
`getModificationNames`	Overload:
`getModifications`(self)	Returns the stored modification definitions
`getNumberOfFixedModifications`(self)	Returns the number of fixed modifications stored in this set
`getNumberOfModifications`(self)	Returns the number of modifications stored in this set
`getNumberOfVariableModifications`(self)	Returns the number of variable modifications stored in this set
`getVariableModificationNames`(self)	Returns only the names of the variable modifications
`getVariableModifications`(self)	Returns the stored variable modification definitions
`inferFromPeptides`(self, peptides)	Infers the sets of defined modifications from the modifications present on peptide identifications
`isCompatible`(self, peptide)	Returns true if the peptide is compatible with the definitions, e.g.
`setMaxModifications`(self, max_mod)	Sets the maximal number of modifications allowed per peptide
`setModifications`	Overload:

addModification(self, mod_def: ModificationDefinition) → None#: Adds a modification definition to the set

getFixedModificationNames(self) → Set[bytes]#: Returns only the names of the fixed modifications

getFixedModifications(self) → Set[ModificationDefinition]#: Returns the stored fixed modification definitions

getMaxModifications(self) → int#: Return the maximal number of modifications allowed per peptide

getModificationNames()#

Overload:

getModificationNames(self, fixed_modifications: List[bytes], variable_modifications: List[bytes]) → None

Populates the output lists with the modification names (use e.g. for

Overload:

getModificationNames(self) → Set[bytes]

Returns only the names of the modifications stored in the set

getModifications(self) → Set[ModificationDefinition]#: Returns the stored modification definitions

getNumberOfFixedModifications(self) → int#: Returns the number of fixed modifications stored in this set

getNumberOfModifications(self) → int#: Returns the number of modifications stored in this set

getNumberOfVariableModifications(self) → int#: Returns the number of variable modifications stored in this set

getVariableModificationNames(self) → Set[bytes]#: Returns only the names of the variable modifications

getVariableModifications(self) → Set[ModificationDefinition]#: Returns the stored variable modification definitions

inferFromPeptides(self, peptides: List[PeptideIdentification]) → None#: Infers the sets of defined modifications from the modifications present on peptide identifications

isCompatible(self, peptide: AASequence) → bool#: Returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications

setMaxModifications(self, max_mod: int) → None#: Sets the maximal number of modifications allowed per peptide

setModifications()#

Overload:

setModifications(self, mod_defs: Set[ModificationDefinition]) → None

Sets the modification definitions

Overload:

setModifications(self, fixed_modifications: bytes | str | String, variable_modifications: String) → None

Set the modification definitions from a string

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.

Overload:

setModifications(self, fixed_modifications: List[bytes], variable_modifications: List[bytes]) → None

Same as above, but using StringList instead of comma separated strings