Identity Testing For Monosaccharides

exception glypy.io.nomenclature.identity.IdentifyException[source]
glypy.io.nomenclature.identity.get_preferred_name(name, selector=<built-in function min>, key=<built-in function len>)[source]

Given a name, of its synonyms, find the name that satisfies the selector criterion function (min()) based on some key function of the name (len())

Parameters:

  • name (str) – Given name to compare to synonyms

  • selector (function) – Function to use to select the preferred name by some statistic

  • key (function) – Function to use to convert names into statistics

Return type:

str

glypy.io.nomenclature.identity.identify(node, blacklist=None, tolerance=0, include_modifications=True, include_substituents=True, ignore_ring=True, **kwargs)[source]

Attempt to find a common usage name for the given Monosaccharide, node. The name is determined by performing an incremental comparison of the traits of node with each named residue in the database accessed at glypy.monosaccharides.

Forwards all unmatched arguments to monosaccharide_similarity()

Parameters:

  • node (Monosaccharide) – Object to be identified

  • blacklist (list) – The set of all monosaccharides to not attempt matching against, because they are too general.

  • tolerance (int) – The error tolerance for the search

  • include_modifications (bool) – Whether or not to include modifications in comparison. Defaults to True

  • include_substituents (bool) – Whether or not to include substituents in comparison. Defaults to True

Return type:

str

Raises:

IdentifyException: – When a suitable name cannot be found.

See also

is_a, preferred_name, monosaccharide_similarity

glypy.io.nomenclature.identity.is_a(node, target, tolerance=0, include_modifications=True, include_substituents=True, exact=True, short_circuit=False, ignore_ring=True, **kwargs)[source]

Perform a semi-fuzzy match between node and target where node is the unqualified residue queried and target is the known residue to be matched against.

Forwards all unmatched arguments to monosaccharide_similarity()

Parameters:

  • node (Monosaccharide or Substituent) – Object to be identified

  • target (Monosaccharide, Substituent or str) – The reference type. May be a str object which is used to look up a Monosaccharide by name in glypy.monosaccharides

  • tolerance (int) – The error tolerance for the search

  • include_modifications (bool) – Whether or not to include modifications in comparison. Defaults to True

  • include_substituents (bool) – Whether or not to include substituents in comparison. Defaults to True

  • exact (bool) – Whether or not to penalize for unmatched attachments. Defaults to True

Return type:

bool

glypy.io.nomenclature.identity.naive_name_monosaccharide(monosaccharide)[source]

Generate a generic name for monosaccharide, based loosely on IUPAC naming schema without including information about linkage.

The tendency for monosaccharides of superclass > 7 to have special names, which will be used preferentially if possible.

Parameters:

monosaccharide (Monosaccharide)

Returns:

A simple name based on SuperClass, modifications, and substituents.

Return type:

str

See also

glypy.io.nomenclature.identity.identify()