glyrepr
Representation for Glycan Compositions and Structures

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glyrepr: Representation for Glycan Compositions and Structures
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API

API for glyrepr
Representation for Glycan Compositions and Structures

Global functions
.abort_structure_failure Source code
.aggregate_composition_components Source code
.cast_named_vector Source code
.check_array_indices Source code
.check_count_mono_args Source code
.compact_arrays_native Source code
.compact_bliss_labels Source code
.compact_build_graph Source code
.compact_iupac_arrays Source code
.compact_iupac_outcomes Source code
.compact_parse_native Source code
.compact_structure_from_arrays Source code
.composition_component_order Source code
.count_composition_components Source code
.extract_anomer Source code
.extract_base_mono Man page Source code
.extract_combo_args Source code
.extract_from_list_column Source code
.extract_substituent Source code
.extract_substituent_without_configuration Source code
.fill_anomer_pos_single Source code
.fill_anomer_pos_value Source code
.generate_object_hash Source code
.generate_value_key Source code
.get_comp_mono_types Source code
.handle_general_monosaccharide Source code
.handle_neu5ac_variant Source code
.handle_neu5gc_variant Source code
.handle_neu_monosaccharide Source code
.handle_neu_with_marker Source code
.has_linkages_single Source code
.has_neu_marker Source code
.infer_reducing_end_anomer Source code
.is_na_composition_elem Source code
.map_structure_combinations Source code
.match_unusual_configuration_monosaccharide Source code
.natural_configuration_monosaccharide Source code
.neu_marker_pattern Source code
.parse_byonic_comp Source code
.parse_iupac_condensed_single Man page Source code
.parse_iupac_tree_single Source code
.parse_simple_comp Source code
.parse_token Source code
.permute_edges Source code
.rebuild_structure_with_dedup Source code
.remove_linkages_single Source code
.remove_substituents_single Source code
.reorder_by_sequence_order Source code
.reorder_composition_components Source code
.reorder_one_graph Source code
.restore_list_with_na Source code
.restore_structure_with_na Source code
.ringless_monosaccharide Source code
.smap_base Source code
.smap_structure_impl Source code
.structure_array_outcomes Source code
.structure_combo_table Source code
.structure_map_input Source code
.tokenize_iupac Source code
.unique_no_na Source code
.unique_structure_combos Source code
.valid_composition_element Source code
.valid_glycan_composition_input Source code
.validate_brackets Source code
.validate_structure_arrays Source code
.warn_lossy_neuac_linkage Source code
`[.glyrepr_structure` Source code
`[[.glyrepr_structure` Source code
`[[<-.glyrepr_structure` Source code
add_colors Man page Source code
add_gray_linkages Man page Source code
any_dup_linkage_pos Source code
append_vertex_substituent Source code
as.list.glyrepr_composition Source code
as.list.glyrepr_structure Source code
as_glycan_composition Man page Source code
as_glycan_structure Man page Source code
as_glycan_structure_with_na Source code
as_iupac_character Source code
assemble_recovered_structure_outcomes Source code
attach_floating_parts Source code
available_monosaccharides Man page Source code
available_substituents Man page Source code
build_example_graph Source code
build_seq_cache Source code
build_structure_graph_from_table_rows Source code
calculate_depths Source code
calculate_linkage_rank Source code
canonicalize_and_validate_iupac_graphs Source code
canonicalize_floating_graph Source code
canonicalize_glycan_graph Man page Source code
canonicalize_glycan_graphs Man page Source code
canonicalize_graph_with_iupac Source code
canonicalize_parsed_iupac_component Source code
collapse_substituent_tokens Source code
colorize_iupac_string Man page Source code
combine_floating_iupac_graphs Source code
component_sequence_order Source code
convert_glycan_mono_type_impl Source code
convert_mono_type_impl Source code
convert_structure_graph_to_generic Source code
convert_to_generic Man page Source code
convert_to_generic.character Man page Source code
convert_to_generic.glyrepr_composition Man page Source code
convert_to_generic.glyrepr_structure Man page Source code
convert_to_generic.igraph Man page Source code
copy_structure_graph Source code
count_mono Man page Source code
count_mono.glyrepr_composition Man page Source code
count_mono.glyrepr_structure Man page Source code
count_mono.igraph Man page Source code
definitely_occupied_main_slots Source code
delete_floating_parts_attr Source code
delete_floating_substituents_attr Source code
empty_floating_assignments Source code
empty_structure_component_membership Source code
empty_structure_edges Source code
empty_structure_floating_candidates Source code
empty_structure_floating_parts Source code
empty_structure_floating_substituents Source code
empty_structure_nodes Source code
ensure_name_vertex_attr Source code
enumerate_floating_graph_localizations Man page Source code
enumerate_floating_graph_localizations_one Source code
enumerate_floating_localizations Man page Source code
enumerate_floating_localizations_one Source code
extract_substituent_types Source code
fill_anomer_pos Man page Source code
filter_used_structure_graphs Source code
floating_attachment_domain Source code
floating_augmented_main_labels Source code
floating_augmented_structure_labels Source code
floating_components_reach_main Source code
floating_graph_info Source code
floating_linkage_acceptor_positions Source code
floating_main_vertices Source code
floating_metadata_main_vertices Source code
floating_parent_component_domains Source code
floating_part_assignment_closes_cycle Source code
floating_part_assignment_is_acyclic Source code
floating_part_candidate_parents Source code
floating_part_iupac Source code
floating_part_membership Source code
floating_parts_attr Source code
floating_substituent_candidate_parents Source code
floating_substituent_domain Source code
floating_substituent_iupac Source code
floating_substituents_attr Source code
floating_symmetry_main_order Source code
format.glyrepr_composition Source code
format.glyrepr_structure Source code
format_glycan_composition_subset Source code
format_glycan_structure_subset Man page Source code
format_reducing_end_iupac Source code
get_alditol Man page Source code
get_anomer Man page Source code
get_anomer_pos Man page Source code
get_graph_mono_type Source code
get_graph_structure_level Source code
get_mono_color Man page Source code
get_mono_type Man page Source code
get_mono_type.character Man page Source code
get_mono_type.glyrepr_composition Man page Source code
get_mono_type.glyrepr_structure Man page Source code
get_mono_type.igraph Man page Source code
get_mono_type_impl Source code
get_structure_graphs Man page Source code
get_structure_level Man page Source code
glycan_composition Man page Source code
glycan_structure Man page Source code
glycan_structure_from_graph_list_with_na Source code
glycan_structure_from_iupac_character Source code
glycan_structure_from_iupac_character_with_na Source code
glycan_structure_iupac_data Source code
glyrepr Man page
glyrepr-package Man page
glyrepr-vctrs Man page
graph_to_composition Source code
graph_to_iupac Man page Source code
has_conflict_free_assignment Source code
has_conflict_free_attachment_assignment Source code
has_edge_attrs Source code
has_floating_metadata Source code
has_floating_parts Man page Source code
has_floating_parts_graph Source code
has_floating_substituents Man page Source code
has_floating_substituents_graph Source code
has_linkages Man page Source code
has_valid_floating_assignment Source code
has_vertex_attrs Source code
infer_anomer_pos Man page Source code
is.na.glyrepr_composition Source code
is.na.glyrepr_structure Source code
is_canonical_sequence_order Source code
is_directed_graph Source code
is_glycan_composition Man page Source code
is_glycan_structure Man page Source code
is_known_composition_component Source code
is_known_mono Source code
is_known_monosaccharide Man page Source code
is_missing_structure_input Source code
is_out_tree Source code
localize_floating_graph Source code
localize_floating_graph_preserve_ids Source code
localize_floating_parts Man page Source code
main_attachment_domains Source code
main_substituent_domains Source code
materialize_unrestricted_floating_substituents Source code
n_glycan_core Man page Source code
n_glycan_core_base Source code
new_glycan_composition Source code
new_glycan_structure Man page Source code
new_na_glycan_structure Source code
normalize_alditol_attr Source code
normalize_floating_part Source code
normalize_floating_parts Source code
normalize_floating_substituent Source code
normalize_floating_substituents Source code
normalize_structure_failure_reason Source code
normalize_substituent_token Source code
normalize_substituents Source code
o_glycan_core_1 Man page Source code
o_glycan_core_1_base Source code
o_glycan_core_2 Man page Source code
o_glycan_core_2_base Source code
obj_print_data.glyrepr_composition Source code
obj_print_data.glyrepr_structure Source code
obj_print_footer.glyrepr_structure Source code
order_branches Source code
order_branches_with_floating_symmetry Source code
parse_alditol_iupac Source code
parse_floating_iupac_part Source code
parse_single_composition Source code
pillar_shaft.glyrepr_composition Source code
pillar_shaft.glyrepr_structure Source code
possible_linkages Man page Source code
print.glyrepr_composition Source code
print.glyrepr_structure Source code
process_glycan_structure_element Source code
prune_localized_floating_domains Source code
raise_error_for_na Source code
recover_glycan_structure_elements Source code
remove_linkages Man page Source code
remove_substituents Man page Source code
reorder_graphs Source code
reorder_graphs_with_indices Source code
replace_monos_with_colored Man page Source code
resolve_single_parent_floating_parts Source code
resolve_single_parent_floating_substituents Source code
selected_floating_attachment_domain Source code
selected_floating_substituent_domain Source code
seq_glycan_iupac Source code
seq_glycan_order Source code
seq_glycan_order_iupac Source code
seq_glycan_order_with_floating_symmetry Source code
set_floating_parts_attr Source code
set_floating_substituents_attr Source code
severy Man page Source code
simap Man page Source code
simap_chr Man page Source code
simap_dbl Man page Source code
simap_int Man page Source code
simap_lgl Man page Source code
simap_structure Man page Source code
simap_vec Man page Source code
single_identity_localization Source code
smap Man page Source code
smap2 Man page Source code
smap2_chr Man page Source code
smap2_dbl Man page Source code
smap2_int Man page Source code
smap2_lgl Man page Source code
smap2_structure Man page Source code
smap2_vec Man page Source code
smap_chr Man page Source code
smap_dbl Man page Source code
smap_int Man page Source code
smap_lgl Man page Source code
smap_predicates Man page
smap_structure Man page Source code
smap_unique Man page Source code
smap_vec Man page Source code
snone Man page Source code
sort_substituent_tokens Source code
split_floating_iupac Source code
split_floating_iupac_part Source code
spmap Man page Source code
spmap_chr Man page Source code
spmap_dbl Man page Source code
spmap_int Man page Source code
spmap_lgl Man page Source code
spmap_structure Man page Source code
spmap_vec Man page Source code
ssome Man page Source code
structure_candidate_edges Man page Source code
structure_component_membership Man page Source code
structure_component_membership_one Source code
structure_edges Man page Source code
structure_edges_one Source code
structure_floating_candidates Man page Source code
structure_floating_candidates_one Source code
structure_floating_parts Man page Source code
structure_floating_parts_one Source code
structure_floating_substituents Man page Source code
structure_floating_substituents_one Source code
structure_from_arrays Man page Source code
structure_from_tibbles Man page Source code
structure_na_mask Source code
structure_nodes Man page Source code
structure_nodes_one Source code
structure_table_glycan_names Source code
structure_table_glycan_names_from_rows Source code
structure_table_input Source code
structure_table_name_rows Source code
structure_tables Man page
structure_to_iupac Man page Source code
substituent_name_pattern Source code
substituent_position_domains Source code
substituent_position_pattern Source code
substituent_position_tokens Source code
substituent_position_values Source code
valid_anomer Source code
valid_linkages Man page Source code
valid_substituent Source code
validate_character_structure_column Source code
validate_complete_floating_assignment_compatibility Source code
validate_consecutive_structure_ids Source code
validate_example_args Source code
validate_floating_assignment_compatibility Source code
validate_floating_assignments Source code
validate_floating_attachment_slots Source code
validate_floating_graph_shape Source code
validate_floating_max_variants Source code
validate_floating_metadata_assignments Source code
validate_floating_source_parents Source code
validate_floating_substituent_parents Source code
validate_floating_substituent_slots Source code
validate_glycan_graph Man page Source code
validate_glycan_graph_vector Man page Source code
validate_integerish_structure_column Source code
validate_single_glycan_structure Source code
validate_structure_alditols Source code
validate_structure_anomers Source code
validate_structure_edge_nodes Source code
validate_structure_edges_table Source code
validate_structure_floating_parts_table Source code
validate_structure_floating_substituents_table Source code
validate_structure_nodes_table Source code
validate_structure_table Source code
validate_structure_table_glycan_ids Source code
vec_cast.character.glyrepr_composition Source code
vec_cast.character.glyrepr_structure Source code
vec_cast.glyrepr_composition.character Source code
vec_cast.glyrepr_composition.double Source code
vec_cast.glyrepr_composition.glyrepr_composition Source code
vec_cast.glyrepr_composition.glyrepr_structure Source code
vec_cast.glyrepr_composition.integer Source code
vec_cast.glyrepr_composition.list Source code
vec_cast.glyrepr_composition.logical Source code
vec_cast.glyrepr_structure.character Source code
vec_cast.glyrepr_structure.glyrepr_structure Source code
vec_cast.glyrepr_structure.igraph Source code
vec_cast.glyrepr_structure.list Source code
vec_cast.logical.glyrepr_composition Source code
vec_proxy.glyrepr_structure Source code
vec_ptype2.glyrepr_composition.glyrepr_composition Source code
vec_ptype2.glyrepr_composition.logical Source code
vec_ptype2.glyrepr_structure.glyrepr_structure Source code
vec_ptype2.logical.glyrepr_composition Source code
vec_ptype_abbr.glyrepr_composition Source code
vec_ptype_abbr.glyrepr_structure Source code
vec_ptype_full.glyrepr_composition Source code
vec_ptype_full.glyrepr_structure Source code
vec_restore.glyrepr_composition Source code
vec_restore.glyrepr_structure Source code
warn_structure_failures Source code
glyrepr documentation built on Sept. 22, 2026, 5:09 p.m.

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