These functions are low-level variants of have_motif(), count_motif(),
and match_motif() for package code that already has compatible igraph
objects from glyrepr::get_structure_graphs().
Usage
.g_have_motif(
glycan_graph,
motif_graph,
alignment = "substructure",
ignore_linkages = FALSE,
strict_sub = TRUE,
match_degree = NULL
)
.g_count_motif(
glycan_graph,
motif_graph,
alignment = "substructure",
ignore_linkages = FALSE,
strict_sub = TRUE,
match_degree = NULL
)
.g_match_motif(
glycan_graph,
motif_graph,
alignment = "substructure",
ignore_linkages = FALSE,
strict_sub = TRUE,
match_degree = NULL
)Arguments
- glycan_graph
An igraph glycan graph.
- motif_graph
An igraph motif graph.
- alignment
A character scalar:
"substructure","core","terminal", or"whole".- ignore_linkages
A logical scalar. If
TRUE, linkages are ignored.- strict_sub
A logical scalar. If
TRUE, substituents are matched strictly.- match_degree
A logical vector indicating which motif nodes must match the glycan's in- and out-degree exactly. A scalar is recycled to the number of motif nodes.
Value
.g_have_motif()returns a logical scalar..g_count_motif()returns an integer scalar..g_match_motif()returns a list of integer vectors.
Details
These functions do no validation, parsing, naming, or monosaccharide-type
conversion. Callers must provide valid, already-compatible graph objects.
In particular, when matching a generic motif graph, callers must pass a
glycan graph whose mono vertex attributes have already been converted to
the compatible generic representation.
These functions never call glyrepr::as_glycan_structure().