IUPAClite Monosaccharide and Glycan Notation¶

GlycReSoft uses glypy’s IUPAClite notation for monosaccharides and glycan compositions.

A monosaccharide is denoted using IUPAC notation, omitting ring shape, anomeric state, chirality, and modification positions (optionally). For example, a-D-Manp would be written Man, or b-D-Glcp2NAc would be written GlcNAc.

You can also use generic base types like Hex or Pen for example, to denote a six or five carbon monosaccharide. The notation is composable, so you can specify an arbitrarily modified monosaccharide, like HexNAc(S) to specify a sulfated HexNAc, using the parenthesized convention that separates substituent groups, or dHexN for a deoxy-Hexosamine.

You can also define “floating” substituent groups by prefixing their full lowercase names with an @-sign, like @sulfate for sulfate or @acetyl for an acetyl group.

A glycan composition is written as one or more <monosaccharide>:<count> occurrences separated by a “; “ (semi-colon + space), enclosed in “{ }”. A few examples are shown below:

{Hex:5; HexNAc:4; Neu5Ac:1}
{Hex:5; HexNAc:4; Neu5Ac:2}
{Fuc:1; Hex:5; HexNAc:4; Neu5Ac:2}
{Fuc:2; Hex:6; HexNAc:5; Neu5Ac:1}
{Fuc:1; Hex:6; HexNAc:5; Neu5Ac:2}