Changelog • glyenzy

glyenzy 0.4.1

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.

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
rebuild_biosynthesis() now supports many new glycan types, including O-Man, O-GlcNAc, O-Fuc, and O-Glc.

find_synthesis_path() and rebuild_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.

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

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

Remove return parameter from find_synthesis_path() and rebuild_biosynthesis(). Now they always return all possible paths.

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

Update documentations of find_synthesis_path() and rebuild_biosynthesis() to include some important notes.
Fix bugs in find_synthesis_path() and rebuild_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.

First release of glyenzy!