NEWS

---

glyenzy 0.5.3

Minor improvements and fixes

• Update rules for FUT3, FUT4, FUT5, FUT6, FUT7, and FUT9. (2c6b28b)
• Remove rules for B4GALT5, B4GALT6, and ST3GAL5 because these enzymes are exclusive for glycolipids. (798ea6f, 8dd30c8)
• Update ST3GAL rules to reject Lewis antigen acceptors. (c969912)

glyenzy 0.5.2

Minor improvements and fixes

• Fix rules for FUT3, FUT4, FUT5, FUT6, and FUT9. (5e7d657)

glyenzy 0.5.1

Minor improvements and fixes

• Fix rules for FUT1, FUT2, and B3GALT5. (50f3d5d)

glyenzy 0.5.0

Breaking changes

• Rename APIs to use shorter, consistent names (#2):
  • all_enzymes() to db_enzymes()
  • create_enzyme() to make_enzyme()
  • get_involved_enzymes() to find_enzyme()
  • is_synthesized_by() to have_enzyme()
  • count_enzyme_steps() to count_enzyme()
  • find_synthesis_path() to path_biosynthesis()
  • rebuild_biosynthesis() to trace_biosynthesis()
  • spawn_glycans() to grow_glycans()
  • spawn_glycans_step() to grow_glycans_step()

New features

• Add support for initiating enzymes including DPAGT1, FUT10, FUT11, POFUT1, POFUT2, POGLUT1, POGLUT2, POGLUT3, POMT1, POMT2, TMTC1, TMTC2, TMTC3, TMTC4, and GALNT1 through GALNT19. (#5)
• Add support for N-glycan precursor synthesis enzymes (ALGs). (#6)
• Add match_enzyme() to identify the residues added by a glycosyltransferase. (#3)
• Add view_enzyme() to visualize residues added by an enzyme on a glycan cartoon. (#4)

Minor improvements and fixes

• Fix the bug that find_enzyme didn't support paucimannose glycans. (1c79a04)

glyenzy 0.4.3

Minor improvements and fixes

• Update dependency strategy to use the r-universe repo.

glyenzy 0.4.2

Minor improvements and fixes

• Update internal data to adapt to glyrepr 0.10.0.

glyenzy 0.4.1

Minor improvements and fixes

• glyenzy now depends on the CRAN version of glyparse.

glyenzy 0.4.0

Breaking changes

• Strengthen validation of the rejects field in enzyme rules: each reject must contain the acceptor motif.
• Rework rejects handling in apply_enzyme() (and callers) to evaluate rejects per match rather than per glycan, improving accuracy for glycans with multiple acceptor matches.
• Update built-in rules for MAN2A1, MAN2A2, MGAT3, MGAT4A, and MGAT4B to align with the new reject semantics.
• Remove the now-redundant rejects_alignment field from enzyme_rule objects; acceptor_alignment is reused for reject checks.

New features

• Add make_enzyme(), enabling programmatic construction of custom enzymes.

Minor improvements and fixes

• grow_glycans() now shows live glycan counts in the progress bar.

glyenzy 0.3.2

Minor improvements and fixes

• Fix errors in the rules of some enzymes, including B3GALT1, B3GALT2, and FUT8.
• Fix a bug in progress bar of grow_glycans().

glyenzy 0.3.1

Minor improvements and fixes

• glyenzy now depends on the CRAN version of glyrepr.

glyenzy 0.3.0

Breaking changes

• Remove FUT10, as it belongs to the starting point of some O-Fuc glycans.

New features

• Add many new enzymes, including FUT5, FUT6, ST3GAL5, ST6GALNAC5, ST6GALNAC6, ST8SIA1, ST8SIA5, ST8SIA6, B3GAT3, CHPF, CHPF2, CHSY1, CHSY3, EXT1, EXT2, HAS1, HAS2, HAS3, LARGE1, LARGE2, B3GLCT, A4GALT, ABO, B3GALT6, B4GALT6, GXYLT1, GXYLT2, LARGE1, LARGE2, XXYLT1, B3GALNT1, B4GALNT1, B4GALNT3, B4GALNT4, CSGALNACT1, CSGALNACT2, B3GNT5, B3GNT7, POMGNT1, POMGNT2, LFNG, MFNG, RFNG, EXLT1, EXLT2, EXLT3
• Update the rules of some existing enzymes, including FUT1, FUT2, FUT3, FUT4, FUT7, FUT8, FUT9, ST3GAL2, ST3GAL3, ST3GAL4, ST6GALNAC1, ST6GALNAC3, ST8SIA2, ST8SIA3, ST8SIA4, B3GALT4, B3GALT5, B4GALT1, B4GALT4, B4GALT5, B4GALNT2, MGAT5B, B3GNT8, GCNT2, GCNT3, A4GNT, ST3GAL1
• trace_biosynthesis() now supports many new glycan types, including O-Man, O-GlcNAc, O-Fuc, and O-Glc.

Minor improvements and fixes

• path_biosynthesis() and trace_biosynthesis() has been optimized for large glycans.
• All functions explicitly check if the input glycans are concrete (e.g. "Glc", "GalNAc") and raise errors with helpful messages if not.

glyenzy 0.2.3

Minor improvements and bug fixes

• Updated dependency on glymotif (>= 0.10.0) to ensure compatibility with recent changes in package igraph v2.2.0.

glyenzy 0.2.2

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glymotif v0.7.0 and glyrepr v0.7.0.

glyenzy 0.2.1

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glyenzy 0.2.0

Breaking changes

• Remove return parameter from path_biosynthesis() and trace_biosynthesis(). Now they always return all possible paths.

New features

• trace_biosynthesis() now supports multiple target glycans. The resulting graph contains all given target glycans and intermediate glycans.

Minor improvements and fixes

• Update documentations of path_biosynthesis() and trace_biosynthesis() to include some important notes.
• Fix bugs in path_biosynthesis() and trace_biosynthesis() that glycan structure strings other than IUPAC-condensed format cannot be parsed.
• Add checks in all functions to ensure that the input glycans have intact linkages and no substituents, and raise errors with helpful messages if not.
• Refactor apply_enzyme() to stop using internal glymotif functions to avoid fragile dependency.

glyenzy 0.1.1

Minor improvements and fixes

• Fix bugs introduced by the breaking changes in glyrepr v0.7.0.

glyenzy 0.1.0

First release of glyenzy!