List Candidate Parents for Floating Metadata

structure_floating_candidates() expands floating-part and floating-substituent metadata to one row per candidate parent. This provides a uniform representation for explicitly restricted and unrestricted floating metadata.

For an unrestricted floating part, every feasible node outside its own component is returned; for an unrestricted floating substituent, every feasible residue node in the complete structure is returned. These rows use scope = "all". For metadata written with an explicit |<parents> suffix, only the declared parent nodes are returned and scope is "explicit".

Floating-part rows have a non-missing part_id, root_node, and linkage. Floating-substituent rows instead have a non-missing substituent_id and substituent. Exactly one of part_id and substituent_id is non-missing in each row.

Node indices refer to structure_nodes()$node_id for the same glycan. Missing structures and structures without floating metadata contribute no rows. Duplicate structures are expanded to their original vector positions. For graph input, node indices are current numeric vertex positions and glycan_id is 1L. If vector input is named, the result also contains a glycan_name column.

Usage

structure_floating_candidates(x)

Arguments

x

A glycan structure vector or one glycan igraph.

Value

A tibble with columns glycan_id, part_id, root_node, parent_node, linkage, scope, substituent_id, and substituent, plus glycan_name when x is named.

Examples

glycans <- as_glycan_structure(c(
  unrestricted = "{Neu5Ac(a2-3)}Gal(b1-3)GalNAc(a1-",
  restricted = "{Neu5Ac(a2-6)|2,3}Gal(b1-3)GalNAc(a1-",
  substituent = "{6S}Gal(a1-3)Gal(a1-"
))
structure_floating_candidates(glycans)
#> # A tibble: 6 × 9
#>   glycan_id glycan_name  part_id root_node parent_node linkage scope   
#>       <int> <chr>          <int>     <int>       <int> <chr>   <chr>   
#> 1         1 unrestricted       1         1           2 a2-3    all     
#> 2         1 unrestricted       1         1           3 a2-3    all     
#> 3         2 restricted         1         1           2 a2-6    explicit
#> 4         2 restricted         1         1           3 a2-6    explicit
#> 5         3 substituent       NA        NA           1 NA      all     
#> 6         3 substituent       NA        NA           2 NA      all     
#> # ℹ 2 more variables: substituent_id <int>, substituent <chr>