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Enumerate Floating Localizations

Source: R/floating-localization.R
enumerate_floating_localizations.Rd

enumerate_floating_localizations() generates every conflict-free, fully localized structure permitted by the candidate-parent domains in x. Each variant records the complete assignment that produced it.

Candidate combinations for floating parts and substituents are validated simultaneously, including linkages or substituents with multiple possible carbon positions. Floating-component dependencies must be acyclic and ultimately connect to the main tree. Variants are canonicalized and, by default, deduplicated by structure. When multiple assignments produce the same canonical structure, the first assignment in deterministic candidate order is retained. Set deduplicate = FALSE to retain every valid assignment and its original-node provenance, including assignments that produce identical canonical structures.

max_variants is a conservative per-input safeguard. It limits the raw Cartesian product before conflict filtering or canonical deduplication, so the function may ask for a higher bound even when fewer variants would ultimately remain.

Missing inputs and structures without floating metadata each produce one row with variant_id = 1L, the original structure, and an empty assignment table. Empty structure vectors produce a zero-row result.

Usage

enumerate_floating_localizations(x, max_variants = 256, deduplicate = TRUE)

Arguments

x

A glycan structure vector.

max_variants

A positive integer giving the maximum raw candidate combinations allowed for each input structure.

deduplicate

A logical value. If TRUE (default), retain only the first assignment for each canonical structure. If FALSE, retain every conflict-free assignment.

Value

A tibble with columns:

  • input_id: the integer position in x.

  • variant_id: the sequential identifier after optional canonical deduplication.

  • structure: a glyrepr_structure vector column containing fully localized variants.

  • assignments: a list-column of tibbles with glycan_id, part_id, parent_node, and substituent_id. Exactly one of part_id and substituent_id is non-missing in each row. Here glycan_id equals input_id.

Examples

glycan <- as_glycan_structure(
  "{Neu5Ac(a2-6)|2,3}Gal(b1-3)GalNAc(a1-"
)
enumerate_floating_localizations(glycan)
#> # A tibble: 2 × 4
#>   input_id variant_id structure                         assignments     
#>      <int>      <int> <struct>                          <list>          
#> 1        1          1 Neu5Ac(a2-6)Gal(b1-3)GalNAc(a1-   <tibble [1 × 4]>
#> 2        1          2 Gal(b1-3)[Neu5Ac(a2-6)]GalNAc(a1- <tibble [1 × 4]>