Unimod Mapper¶
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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 :
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appMass2element_list
(mass, decimal_places=2)¶ Creates a list of element composition dicts for a given approximate mass
Parameters: mass (float) – Keyword Arguments: 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}]
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appMass2id_list
(mass, decimal_places=2)¶ Creates a list of unimod ids for a given approximate mass
Parameters: mass (float) – Keyword Arguments: 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']
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appMass2name_list
(mass, decimal_places=2)¶ Creates a list of unimod names for a given approximate mass
Parameters: mass (float) – Keyword Arguments: 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']
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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
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composition2mass
(composition)¶ Converts unimod composition to unimod monoisotopic mass,
Parameters: composition (float) – Returns: monoisotopic mass Return type: float
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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
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id2composition
(unimod_id)¶ Converts unimod id to unimod composition
Parameters: unimod_id (int) – Returns: Unimod elemental composition Return type: dict
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id2mass
(unimod_id)¶ Converts unimodID to unimod mass
Parameters: unimod_id (int) – Returns: Unimod mono isotopic mass Return type: float
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id2name
(unimod_id)¶ Converts unimodID to unimod name
Parameters: unimod_id (int) – Returns: Unimod name Return type: str
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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
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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
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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
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name2composition
(unimod_name)¶ Converts unimod name to unimod composition
Parameters: unimod_name (str) – Returns: Unimod elemental composition Return type: dict
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name2id
(unimod_name)¶ Converts unimod name to unimodID
Parameters: unimod_name (str) – Returns: Unimod id Return type: int
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name2mass
(unimod_name)¶ Converts unimod name to unimod mono isotopic mass
Parameters: unimod_name (str) – Returns: Unimod mono isotopic mass Return type: float
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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) –
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