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glycoinfo / GlycanBuilder2

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The shape of dHex #18

Open Hendricks27 opened 3 years ago

Hendricks27 commented 3 years ago

The shape of dHex is a circle with "6m" on the top, shouldn't this be "6d"? Also, when modification d shows at a position other than 6, it refuses to generate an image. See example: https://gnome.glyomics.org/CompositionBrowser.html?dHex=1&

ReneRanzinger commented 3 years ago

Actually, according to SNFG (https://www.ncbi.nlm.nih.gov/glycans/snfg.html) 6dHex is a white triangle. Circle with a "d" decorator would only apply if the number != 6.

If you look at G00771KP (https://glytoucan.org/Structures/Glycans/G00771KP). That is also not right. The third symbol is 6dHex which as an additional modification which is a 6d.

Hendricks27 commented 3 years ago

Actually, according to SNFG (https://www.ncbi.nlm.nih.gov/glycans/snfg.html) 6dHex is a white triangle. Circle with a "d" decorator would only apply if the number != 6.

If you look at G00771KP (https://glytoucan.org/Structures/Glycans/G00771KP). That is also not right. The third symbol is 6dHex which as an additional modification which is a 6d.

Ok, thanks for the additional material. Something related, it seems that the fucose/dHex is pointing upwards in that SNFG web page. Maybe I should also make Fuc/dHex in the GNOme applet point upwards for consistency reasons?

ReneRanzinger commented 3 years ago

I don't like it. But according to the latest SNFG that would be the correct way. In all examples on their page the triangle always points up (even for vertical/horizontal drawings).

edwardsnj commented 3 years ago

Just to clarify here, this appears to be a regression. GlyTouCan has empty triangle with "6d":

https://glytoucan.org/Structures/Glycans/G82364UA

which is more correct than the image generated from this code-base (empty circle with 6m)

https://glymage.glyomics.org/image/snfg/extended/G82364UA.png

ReneRanzinger commented 3 years ago

https://glytoucan.org/Structures/Glycans/G82364UA

which is more correct than the image generated from this code-base (empty circle with 6m)

Well ... the white triangle itself is correct. The "6d" on top is wrong. Its the same problem as with G00771KP above. "6d6dHex" does not make sense.

e15d5605 commented 3 years ago

I am currently working on resolving the problem of dHex (6-deoxy hexose) be shown with white circular symbol, and the problem an unnecessary notation of modification (ex. 6d) on the symbol of dHex be displayed. Also, I am planning to replace the notation of 6m to 6d in the latest GlycanBuilder2.