ModificationsDB#

class pyopenms.ModificationsDB#

Bases: object

Cython implementation of _ModificationsDB

Original C++ documentation is available here

__init__(*args, **kwargs)#

Methods

`__init__`(args, *kwargs)
`addModification`(self, new_mod)	Add a new modification to ModificationsDB.
`findModificationIndex`(self, mod_name)	Returns the index of the modification in the mods_ vector; a unique name must be given
`getAllSearchModifications`(self, modifications)	Collects all modifications that can be used for identification searches
`getBestModificationByDiffMonoMass`(self, ...)	Returns the best matching modification for the given delta mass and residue
`getModification`	Overload:
`getNumberOfModifications`(self)	Returns the number of modifications read from the unimod.xml file
`has`(self, modification)	Returns true if the modification exists
`isInstantiated`(self)	Check whether ModificationsDB was instantiated before
`searchModifications`(self, mods, mod_name, ...)	Collects all modifications which have the given name as synonym
`searchModificationsByDiffMonoMass`(self, ...)	Collects all modifications with delta mass inside a tolerance window

addModification(self, new_mod: ResidueModification) → ResidueModification#: Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. Returns the modification in the ModificationDB (which can differ from input if mod was already present).

findModificationIndex(self, mod_name: bytes | str | String) → int#: Returns the index of the modification in the mods_ vector; a unique name must be given

getAllSearchModifications(self, modifications: List[bytes]) → None#: Collects all modifications that can be used for identification searches

getBestModificationByDiffMonoMass(self, mass: float, max_error: float, residue: bytes | str | String, term_spec: int) → ResidueModification#

Returns the best matching modification for the given delta mass and residue

Query the modifications DB to get the best matching modification with the given delta mass at the given residue (NULL pointer means no result, maybe the maximal error tolerance needs to be increased). Possible input for CAM modification would be a delta mass of 57 and a residue of “C”.

Note: If there are multiple possible matches with equal masses, it will choose the _first_ match which defaults to the first matching UniMod entry.

Parameters:

residue – The residue at which the modifications occurs
mass – The monoisotopic mass of the residue including the mass of the modification
max_error – The maximal mass error in the modification search

Returns:

A pointer to the best matching modification (or NULL if none was found)

getModification()#

Overload:

getModification(self, index: int) → ResidueModification

Returns the modification with the given index

Overload:

getModification(self, mod_name: bytes | str | String) → ResidueModification

Returns the modification with the given name

Overload:

getModification(self, mod_name: bytes | str | String, residue: bytes | str | String, term_spec: int) → ResidueModification

Returns the modification with the given arguments

getNumberOfModifications(self) → int#: Returns the number of modifications read from the unimod.xml file

has(self, modification: bytes | str | String) → bool#: Returns true if the modification exists

isInstantiated(self) → bool#: Check whether ModificationsDB was instantiated before

searchModifications(self, mods: Set[ResidueModification], mod_name: bytes | str | String, residue: bytes | str | String, term_spec: int) → None#

Collects all modifications which have the given name as synonym

If residue is set, only modifications with matching residue of origin are considered If term_spec is set, only modifications with matching term specificity are considered The resulting set of modifications will be empty if no modification exists that fulfills the criteria

searchModificationsByDiffMonoMass(self, mods: List[bytes], mass: float, max_error: float, residue: bytes | str | String, term_spec: int) → None#: Collects all modifications with delta mass inside a tolerance window