Unimod Mapper¶

class ursgal.UnimodMapper¶

UnimodMapper class that creates lookup to the unimod.xml and userdefined_unimod.xml found located in ursgal/kb/ext and offers several helper methods described below :

appMass2element_list(mass, decimal_places=2)¶

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

Keyword Arguments:
Parameters:	mass (float) –
	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 ursgal
>>> U = ursgal.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) –
	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 ursgal
>>> U = ursgal.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) –
	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 ursgal
>>> U = ursgal.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) –
Returns:	Unimod IDs
Return type:	list

composition2mass(composition)¶

Converts unimod composition to unimod monoisotopic mass,

Parameters:	composition (float) –
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) –
Returns:	Unimod names
Return type:	list

id2composition(unimod_id)¶

Converts unimod id to unimod composition

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

id2mass(unimod_id)¶

Converts unimodID to unimod mass

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

id2name(unimod_id)¶

Converts unimodID to unimod name

Parameters:	unimod_id (int) –
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) –
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) –
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) –
Returns:	Unimod names
Return type:	list

name2composition(unimod_name)¶

Converts unimod name to unimod composition

Parameters:	unimod_name (str) –
Returns:	Unimod elemental composition
Return type:	dict

name2id(unimod_name)¶

Converts unimod name to unimodID

Parameters:	unimod_name (str) –
Returns:	Unimod id
Return type:	int

name2mass(unimod_name)¶

Converts unimod name to unimod mono isotopic mass

Parameters:	unimod_name (str) –
Returns:	Unimod mono isotopic mass
Return type:	float

writeXML(modification_dict, xmlFile=None)¶

Writes a unimod-style userdefined_unimod.xml file in ursal/resources/platform_independent/arc_independent/ext

Parameters:	modification_dict (dict) – dictionary containing at least 'mass' (mass of the modification) – 'name' (name of the modificaton) – 'composition' (chmical composition of the modification as a Hill notation) –