Identity Testing For Monosaccharides¶
- 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 somekey
function of the name (len()
)
- 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 ofnode
with each named residue in the database accessed atglypy.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
- 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
andtarget
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 aMonosaccharide
by name inglypy.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
- 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