Unimod mapper¶

class pyqms.UnimodMapper¶

UnimodMapper class that creates lookup to the unimod.xml located in kb/ext/unimod.xml and offers several helper methods.

Mapping from e.g. name to composition or unimod ID to mass is possible.

Please refer to unimod for further informations on modifications including naming, formulas, masses etc.

appMass2element_list(mass, decimal_places=2)¶

Creates a list of element composition dicts for a given approximate mass

Keyword Arguments:
Parameters:	mass (float) – approximate mass of modification
	decimal_places (int) – Precision with which the masses in the Unimod is compared to the input, i.e. round( mass, decimal_places )
Returns:	Dicts of elements
Return type:	list

Examples:

>>> import pyqms
>>> U = pyqms.UnimodMapper()
>>> U.appMass2element_list(18, decimal_places=0)
    [{'F': 1, 'H': -1}, {'13C': 1, 'H': -1, '2H': 3},
    {'H': -2, 'C': -1, 'S': 1}, {'H': 2, 'C': 4, 'O': -2},
    {'H': -2, 'C': -1, 'O': 2}]

appMass2id_list(mass, decimal_places=2)¶

Creates a list of unimod IDs for a given approximate mass

Keyword Arguments:
Parameters:	mass (float) – approximate mass of modification
	decimal_places (int) – Precision with which the masses in the Unimod is compared to the input, i.e. round( mass, decimal_places )
Returns:	Unimod IDs
Return type:	list

Examples:

>>> import pyqms
>>> U = pyqms.UnimodMapper()
>>> U.appMass2id_list(18, decimal_places=0)
    ['127', '329', '608', '1079', '1167']

appMass2name_list(mass, decimal_places=2)¶

Creates a list of unimod names for a given approximate mass

Keyword Arguments:
Parameters:	mass (float) – approximate mass of modification
	decimal_places (int) – Precision with which the masses in the Unimod is compared to the input, i.e. round( mass, decimal_places )
Returns:	Unimod names
Return type:	list

Examples:

>>> import pyqms
>>> U = pyqms.UnimodMapper()
>>> U.appMass2name_list(18, decimal_places=0)
    ['Fluoro', 'Methyl:2H(3)13C(1)', 'Xle->Met', 'Glu->Phe', 'Pro->Asp']

composition2id_list(composition)¶

Converts unimod composition to unimod name list, since a given composition can map to mutiple entries in the XML.

Parameters:	composition (dict) – element composition (element, count pairs)
Returns:	Unimod IDs
Return type:	list

composition2mass(composition)¶

Converts unimod composition to unimod monoisotopic mass.

Parameters:	composition (dict) – element composition (element, count pairs)
Returns:	monoisotopic mass
Return type:	float

composition2name_list(composition)¶

Converts unimod composition to unimod name list, since a given composition can map to mutiple entries in the XML.

Parameters:	composition (dict) – element composition (element, count pairs)
Returns:	Unimod names
Return type:	list

id2composition(unimod_id)¶

Converts unimod ID to unimod composition

Parameters:	unimod_id (int) – identifier of modification
Returns:	Unimod elemental composition
Return type:	dict

id2mass(unimod_id)¶

Converts unimod ID to unimod mass

Parameters:	unimod_id (int) – identifier of modification
Returns:	Unimod mono isotopic mass
Return type:	float

id2name(unimod_id)¶

Converts unimod ID to unimod name

Parameters:	unimod_id (int) – identifier of modification
Returns:	Unimod name
Return type:	str

mass2composition_list(mass)¶

Converts unimod mass to unimod element composition list, since a given mass can map to mutiple entries in the XML.

Parameters:	mass (float) – mass of modification
Returns:	Unimod elemental compositions
Return type:	list

mass2id_list(mass)¶

Converts unimod mass to unimod name list, since a given mass can map to mutiple entries in the XML.

Parameters:	mass (float) – mass of modification
Returns:	Unimod IDs
Return type:	list

mass2name_list(mass)¶

Converts unimod mass to unimod name list, since a given mass can map to mutiple entries in the XML.

Parameters:	mass (float) – mass of modification
Returns:	Unimod names
Return type:	list

name2composition(unimod_name)¶

Converts unimod name to unimod composition

Parameters:	unimod_name (str) – name of modification (as named in unimod)
Returns:	Unimod elemental composition
Return type:	dict

name2id(unimod_name)¶

Converts unimod name to unimod ID

Parameters:	unimod_name (str) – name of modification (as named in unimod)
Returns:	Unimod ID
Return type:	int

name2mass(unimod_name)¶

Converts unimod name to unimod mono isotopic mass

Parameters:	unimod_name (str) – name of modification (as named in unimod)
Returns:	Unimod mono isotopic mass
Return type:	float

name2specificity_site_list(unimod_name)¶

Converts unimod name to list of specified amino acids or sites

Parameters:	unimod_name (str) – name of modification (as named in unimod)
Returns:	list of specificity sites
Return type:	list