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