Changelog • glyrepr

glyrepr 0.6.1

n_glycan_core() now has a “b1” reducing end anomer, not “?1”.
Add validation to glycan_structure() to ensure no duplicated linkage positions. For example, “Gal(b1-3)[Fuc(a1-3)]GalNAc(b1-” is invalid now becuase both “Gal” and “Fuc” are linked to “GalNAc” at position 3.
Add descriptions about ambiguous linkages and anomers in glycan_structure() documentation.
remove_linkages() now also removes reducing end anomers.
n_glycan_core(), o_glycan_core_1(), and o_glycan_core_2() now have “??” anomers when linkage = FALSE.
Fix a bug in smap_structure(), smap2_structure(), spmap_structure(), and simap_structure() where modifying the structures can create identical structures, but the unique structures are not updated correctly. This automatically fixes a similar bug in remove_linkages().

Remove the “alditol” attribute from glycan_structure() objects. This information is rarely used in glycomics and glycoproteomics data analysis. It is removed according to the razor principle.
as_glycan_structure() now doesn’t allow the input IUPAC-condensed strings to omit the anomer information. Previously, something like “Glc(a1-3)GlcNAc” is valid. as_glycan_structure() assumed that the core “GlcNAc” has a “?1-” anomer and added it automatically. The problem is that this behavior was not easily awared by users and might cause confusion. Again, less is more, so we remove it.

Fix some error message format errors.
Update the abbreviated type name of glyrepr_structure from structure to struct.

Glycan structures now support multiple substituents on a single monosaccharide. Substituents are stored as comma-separated strings internally and concatenated in IUPAC format for display.
Glycan compositions now support substituents. The glycan_composition class can now represent and count substituents alongside monosaccharides.