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BojarLab / glycowork

Package for processing and analyzing glycans and their role in biology.
https://Bojarlab.github.io/glycowork
MIT License
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Wrong orientation of core-fucoses in `GlycoDraw`. #45

Closed fubin1999 closed 3 months ago

fubin1999 commented 3 months ago

Hi! Thanks for developing this wonderful package. The GlycoDraw function produces really modern, publish-ready SNFG cartoons.

I've found some bugs though:

  1. GlycoDraw may output empty SVG files when vertical setting to True.
  2. The orientation of the core-fucose is unorthodox. For example, GlycoDraw draws a cartoon for "H4N3F1" as follows:
截屏2024-06-03 14 57 41

However, the core-fucose is more often drawn in another orientation by the N-glycomics community:

截屏2024-06-03 15 01 07
lundstrm commented 3 months ago

Hi & thanks for the interest!

1) This has been fixed with commit 5bee4d9 (already available on the dev branch and will be merged into main with the upcoming 1.3 update) 2) While we acknowledge that various tools may depict the core fucose in different orientations, we have decided to maintain the current behavior of GlycoDraw, as this approach is consistent with the examples provided on the SNFG website (https://www.ncbi.nlm.nih.gov/glycans/snfg.html, version 2.0.4).

fubin1999 commented 3 months ago

I see. I'll go along with the NCBI example then. Thanks a lot!