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validate argument to skip
graph validation for trusted inputs. (#36)parse_glycoct() now supports floating glycan
substructures represented by UND sections, uses implicit
floating parts when every main-tree node is a candidate parent, and
excludes explicit candidates whose acceptor positions are already
occupied. (#40)parse_gwb() parses GlycoWorkbench (GWB/GWS)
sequences, including branches, substituents, furanose and configured
residues, reducing-end alditols, and uncertain antennae.
auto_parse() now detects these sequences. (#48)parse_wurcs() now supports floating monosaccharides and
subtrees, including implicit all-main attachment domains and filtered
explicit candidate parents. It also recognizes generic nonulosonic acids
and sialic acids with unknown ring closure. (#40)glyrepr
monosaccharide names such as Galf, GlcfNAc,
and Neuf5Ac across IUPAC, GlyCAM IUPAC, GlycoCT, WURCS,
LINUCS, Linear Code, and KCF inputs. (#41)glyrepr names such as D-Fuc,
L-Gul, and D-Fucf, while unprefixed names
retain their natural configurations. (#43, #44)auto_parse() and all format-specific parsers now
preserve generic and concrete residues mixed within a glycan and across
parsed vectors. (#50)parse_glycoct() and parse_wurcs() now
preserve declared floating candidate-parent domains in global
floating-parent structures: GlycoCT UND parents remain
restricted to the main graph, while WURCS parents may target other
floating components.parse_glycoct() and parse_wurcs() now
preserve floating substituents with unresolved parent residues,
including their chemistry, carbon positions, and candidate parents.
(#45)parse_glycoct() and parse_wurcs() now
recognize the xylHex encoding of fucose.parse_glycoct(), parse_wurcs(),
parse_iupac_compact(),
parse_iupac_condensed(), parse_linucs(), and
auto_parse() now preserve alditol reducing ends in parsed
structures. (#46)parse_glycoct() now normalizes symmetric
Man-ol acceptor positions so equivalent GlycoCT linkages
parse consistently.parse_glycoct() now preserves repeated and
alternative-position substituents, distinguishes N-acetyl and N-glycolyl
from acetyl, maps generic HexA and HexN
residues, and rejects unrepresentable non-alditol open-chain residues
explicitly. (#47)parse_iupac_extended() now accepts abbreviated generic
reducing ends such as ?-Hex, ?-HexNAc, and
?-HexN, as well as slash-ambiguous acceptor positions such
as 4/?.parse_wurcs() now accepts direct phosphate and
alternative-position substituent encodings, preserves generic-root
anomer positions, and orients ambiguous linkages using alditol-aware
donor semantics. (#47)parse_glycam_iupac() now parses large input vectors
about five times faster. (#49)parse_glycoct() and parse_wurcs() now
reuse indexed residue matching and cached classification to improve
parsing performance. (#37)glyrepr’s public structure
constructor, preventing tidyverse joins on parsed structures from
failing with glyrepr 0.13.0. (#33)auto_parse() now detects GlyCAM IUPAC, IUPAC-compact,
KCF, and LINUCS structures and routes them to the corresponding parser
(#26, #28, #30, #31).progress argument for opt-in
progress bars when parsing large inputs (#29).parse_glycam_iupac() parses GlyCAM IUPAC structures
(#25, #27).parse_iupac_compact() parses IUPAC-compact
structures (#28).parse_kcf() parses KCF structures (#30).parse_linucs() parses LINUCS structures (#31).parse_glycoct() now accepts space-separated GlycoCT
records, such as records stored in CSV exports (#24).parse_glycoct() now parses GlycoCT alditol residues as
regular reducing-end glycans with unknown anomer configurations
(#22).parse_glycoct() now supports generic GlycoCT
HEX, N-acetylated HEX, deoxy-HEX,
and sialic acid descriptors, including direct n-sulfate
substituents on amino sugars (#24).parse_wurcs() now parses WURCS alditol residues as
regular reducing-end glycans with unknown anomer configurations
(#21).parse_wurcs() now supports additional generic residue
descriptors, ambiguous sialic acid descriptors, and uppercase residue
IDs for large structures (#23).parse_wurcs() now supports ambiguous u
residues and unknown ring closure residues (? ring
position).parse_wurcs() now correctly handles WURCS N-sulfate
substituent codes (*NSO/3=O/3=O).parse_glycoct() now preserves unknown reducing-end ring
positions and matches amino sugars with unknown ring bounds.on_failure parameter to all parser functions.
When on_failure = "error", the parser will throw an error
when it encounters an unparsable string. When
on_failure = "na", the parser will return NA for unparsable
strings. The default is “error”, for backwards compatibility.parse_iupac_extended() now accepts input with plain
text equivalents (“alpha”, “beta”, “->”). (#10)dplyr::case_match() with
dplyr::recode_values() in parsers to prevent warnings.parse_iupac_extended() and
parse_iupac_short() now support generic monosaccharides,
e.g. “Hex”, “HexNAc”, “HexN”.parse_linear_code() to parse Linear Code
strings.auto_parse() now supports Linear Code strings.parse_iupac_extended().parse_wurcs().parse_iupac_short().parse_glycoct().glyrepr
v0.7.0.parse_iupac_condensed() and
parse_iupac_short() now require the reducing-end
monosaccharide to have anomer information. For example, “Neu5Ac(a2-” and
“Neu5Aca-” are valid, but “Neu5Ac” is not.parse_pglyco_struc() now support “aH” and “pH”
monosaccharides.auto_parse() to automatically detect and parse
different glycan structure string formats.Better error messages. Before:
> parse_iupac_condensed("bad_glycan")Error in `purrr::map()` at glyparse/R/struc-parser-wrapper.R:13:3:
ℹ In index: 1.
Caused by error in `value[[3L]]()`:
! Could not parse IUPAC-condensed string: {.val {x}}
ℹ Invalid characters or format in IUPAC-condensed string
Run `rlang::last_trace()` to see where the error occurred.Now:
> parse_iupac_condensed("bad_glycan")Error in `parse_iupac_condensed()`:
! Can't parse: "bad_glycan"
Run `rlang::last_trace()` to see where the error occurred.parse_glycoct() to parse glycans in GlycoCT
format.parse_iupac_short(),
parse_iupac_extended(),
parse_iupac_condensed(), parse_wurcs() now
support multiple substituents on the same monosaccharide, to align with
the updates in glyrepr v0.5.0.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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