Extract All Structural Matches

Extract all matching fragments from each glycan.

Usage

rex_extract_all(glycans, pattern)

Arguments

glycans

A character vector of glycan expressions in any format supported by glyparse::auto_parse(), a glyrepr_structure vector, or one glyrepr-compatible igraph. Character inputs may mix formats; malformed structures throw an error.

pattern

A character vector of patterns or one rex_compile() object. Inputs recycle only from length one. Missing glycans or patterns propagate.

Value

A list of character vectors of canonical glyrepr IUPAC strings for character input, or glyrepr structure vectors for structure or graph input. No match returns an empty vector; missing input returns a length-one missing vector. A cut fragment retains the anomer and donor position of its former attachment linkage.

Details

The matching unit is a connected structural trace. As in glycowork, the first successful trace per starting node is retained, then strict subsets of other traces are removed. Distinct branches with equal sequences remain distinct matches. Matches are ordered by decreasing residue count and then starting node ID. Repeats are greedy unless marked lazy; successful traces may overlap. Counts therefore need not equal text-regex counts. Only connected rooted trees are supported; floating topology or floating substituents are rejected explicitly. See rex_compile() for syntax.

See also

Other glycan queries: rex_count(), rex_detect(), rex_extract(), rex_locate(), rex_locate_all(), rex_match(), rex_match_all(), rex_subset(), rex_which()

Examples

x <- c("Gal(b1-4)GlcNAc", "Fuc(a1-3)GlcNAc", NA)
rex_extract_all(x, "HexNAc")
#> [[1]]
#> [1] "GlcNAc(?1-"
#> 
#> [[2]]
#> [1] "GlcNAc(?1-"
#> 
#> [[3]]
#> [1] NA
#>