Test whether each glycan structure contains one or more substituents whose parent residue is unresolved.
Arguments
- x
A
glycan_structure()vector or a glycanigraph.
Value
A logical vector with the same length and names as vector input, or
a logical scalar for graph input. Missing structures produce NA.
Details
In the glyrepr IUPAC extension, floating substituents appear in braces
before the main glycan. {6S}<main> allows every feasible residue in the
complete structure to carry the substituent, {6S|1,2}<main> restricts it
to complete-sequence nodes 1 and 2, and {?S}<main> also leaves the carbon
position unknown. Residue nodes in floating blocks are counted before the
main glycan; substituent blocks contribute no node indices.
Internally, unresolved substituents are stored in the
floating_substituents graph attribute. It is a list with one entry per
substituent. Each entry contains a canonical substituent token and an
integer parents vector of candidate graph vertex indices. An empty vector
means every feasible residue vertex is a candidate.
A singleton candidate set is normalized into that vertex's ordinary sub
attribute. This also happens whenever chemistry leaves only one feasible
residue in the complete structure.
structure_floating_substituents() exposes the metadata as a normalized
table.
Examples
glycans <- as_glycan_structure(c(
floating = "{6S}Gal(a1-3)Gal(a1-",
restricted = "{6S|1,2}Gal(a1-3)Glc(a1-3)Man(a1-",
ordinary = "Gal6S(a1-"
))
has_floating_substituents(glycans)
#> floating restricted ordinary
#> TRUE TRUE FALSE