Monosaccharides

The monosaccharides module provides lookups for glycan monosaccharide units.

Monosaccharide lookups (MONOSACCHARIDE_LOOKUP): query by ProForma name.

class tacular.monosaccharides.Monosaccharide(*values)

Bases: StrEnum

Enumeration of monosaccharide names.

Dec = 'Dec'

Fuc = 'Fuc'

Hep = 'Hep'

Hex = 'Hex'

HexN = 'HexN'

HexNAc = 'HexNAc'

HexNAcS = 'HexNAcS'

HexNS = 'HexNS'

HexP = 'HexP'

HexS = 'HexS'

Neu = 'Neu'

NeuAc = 'NeuAc'

NeuGc = 'NeuGc'

Non = 'Non'

Oct = 'Oct'

Pen = 'Pen'

Phosphate = 'Phosphate'

Sug = 'Sug'

Sulfate = 'Sulfate'

Tet = 'Tet'

Tri = 'Tri'

aHex = 'aHex'

dHex = 'dHex'

en_aHex = 'en,aHex'

classmethod from_str(name)

Get Monosaccharide enum from string

Return type:

Monosaccharide

Parameters:

name (str)

class tacular.monosaccharides.MonosaccharideInfo(id, name, formula, monoisotopic_mass, average_mass, dict_composition)

Bases: OboEntity

Class to store information about a monosaccharide

Parameters:

• id (str)

• name (str)

• formula (str | None)

• monoisotopic_mass (float | None)

• average_mass (float | None)

• dict_composition (Mapping[str, int] | None)

average_mass: float | None

Average (isotope-abundance-weighted) mass delta in Da, or None if not available.

dict_composition: Mapping[str, int] | None

Elemental composition as {symbol: count} (isotope keys like "13C" are supported), or None if not available. Use composition for a version keyed by ElementInfo instead of plain strings.

formula: str | None

Chemical formula string (e.g. "C2H2O"), or None if not available.

id: str

The entry’s id, in whatever format its source ontology uses (e.g. "536" for UNIMOD, "AA0001" for RESID). Use id_tag for a normalized form.

monoisotopic_mass: float | None

Monoisotopic mass delta in Da, or None if not available.

name: str

The entry’s human-readable name, as given by the source ontology.

class tacular.monosaccharides.MonosaccharideLookup(monosaccharide_data)

Bases: object

Parameters:

monosaccharide_data (dict[str, MonosaccharideInfo])

get(key)

Like lookup[key], but return None instead of raising KeyError.

Return type:

MonosaccharideInfo | None

Parameters:

key (str | Monosaccharide)

proforma(name)

Look up by ProForma name (case-insensitive).

Raises:

KeyError – if name matches no monosaccharide.

Return type:

MonosaccharideInfo

Parameters:

name (str)