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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.0.12 - 2023-08-18

Added

  • Added an efficient rooted traversal strategy for generating Y fragments, DepthFirstLinkTraversal

1.0.11 - 2023-07-28

Fixed

  • More compatibility with Cython 3
  • The WURCS parsing and writing code underwent substantial reworking to fix how substituent linkages are handled. Additional work was done to try to account for multiple substituents attached to the same position or substituents with multiple attachment positions. Several monosaccharides still do not convert correctly, particularly those with non-terminal modifications or those without a known stereocode template.

Changed

  • The wurcs.loads function no longer returns glycan compositions when given a string encoding a single monosaccharide or serialize single Monosaccharide instances differently than a single unit Glycan instance.

1.0.10 - 2023-07-21

Fixed

  • Compatibility with Cython 3

1.0.9 - 2023-05-26

Added

  • glypy.io.gnome - An interface to the GNOme subsumption hierarchy.

Changed

Deprecated

Removed

Fixed

  • Fix type conversion error in Py3.10 in GlycanComposition.serialize

Security

1.0.8 - 2023-03-18

Added

Changed

Deprecated

Removed

Fixed

  • GlycanComposition.mass no longer ignores options which do not match the first invocation of that method on the same object (GH #25)

Security

1.0.7 - 2022-07-22

Added

  • Added two new parameters to plot and draw_tree, pad and pad_factor to control the padding around a drawn glycan in stand-alone mode. Contributed by @michaelmarty (GH #24)

Changed

Deprecated

Removed

Fixed

Security

1.0.6 - 2022-01-15

Added

  • Add specialized path for comparing two fully initialized HashableGlycanComposition instances
  • Updated GlycoRDF to use OWL instead of cached turtle

Changed

Deprecated

Removed

Fixed

Security

1.0.5

Changed

  1. If a user passes Pent to an IUPACLite parser, it will be interpreted as Pen.

1.0.4 - 2021-10-29

Added

  1. Added support for writing UND sections using glypy.io.glycoct. The previous implementation is still available explicitly in glypy.io.glycoct.OrderRespectingGlycoCTWriter, the new behavior is implemented in UNDOrderRespectingGlycoCTWriter, which is now the value of glypy.io.glycoct.GlycoCTWriter.

Changed

  1. Added a C accelerator for GlycanComposition.serialize

Deprecated

Removed

Fixed

  1. Tolerate empty glycan composition strings in the first pass of the tokenizer again

Security

1.0.3 - 2021-09-02

Added

  1. Added simple validation logic when handling malformed glycan composition string

Changed

Deprecated

Removed

Fixed

Security

1.0.2 - 2021-06-21

Added

  1. Added C-extensions for core components of the GlycanComposition class

Changed

Deprecated

Removed

Fixed

Security

1.0.1 - 2021-05-04

Added

  1. Added support for more monomer names to glypy.io.byonic.

Changed

  1. FrozenMonosaccharideResidue.from_iupac_lite now accounts for when the parsed string is different from the canonical name (e.g. "NeuAc" vs "Neu5Ac"). The returned objects are now guaranteed to be identical and both cached properly.
  2. Improved documentation of extra line formats and IUPAClite.
  3. Added support for "O"-prefixed substituents when parsing IUPAC. Does not alter the chemical interpretation, but resolves the name without the "O".

Deprecated

Removed

Fixed

  1. Fixed several pre-canned queries in glypy.io.glyspace which relied on glycan objects having an is-a relationship with glycan:saccharide. This appears to no longer be the case.

Security

0.12.7 - 2021-02-02

Added

  • Added glypy.io.byonic to parse and write Byonic glycan compositions.

Changed

  • Oct is no longer automatically considered a Mannose
  • glypy.io.iupac now accepts unknown positions for substituents for Neu bases.

Deprecated

Removed

Fixed

  • glyspace reading commands do not fail if a structure fails to parse due to a missing structure definition or reference

Security

Released

0.12.6 - 2020-06-21

Added

  • Added a CHANGELOG file
  • EnumValue instances now support the XOR ^ operator
  • WURCS encoded compositions which have edges that connect everything to everything are now treated as un-localized modifications
  • FrozenGlycanComposition and its descendants now explicitly have cache field management as part of their API, see _validate and _invalidate
  • Added a draft CFG text parser to glypy.io.cfg based heavily on the IUPAC parser.

Changed

  • GlycanComposition instances can be compared to any Mapping, not just other GlycanComposition instances.

Fixed

  • Ketoses have their masses properly calculated [GH18][#18]
  • Added a shim for deprecated matplotlib.path.get_path_extents when it is no longer available in recent versions of matplotlib
  • The composition for phospho-ethanolamine has been corrected
  • Fucose and other monosaccharides which are positioned to the side in balanced CFG/SNFG plots are now positioned properly using the topological layout plots