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GLYCAM-Web / website

A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.
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DFrupb2-1DFrupa2-OH does not build on carb builder #189

Closed holmess2013 closed 3 weeks ago

holmess2013 commented 3 weeks ago

Using the carbohydrate builder on actual, I've tried building some fructose sugars. A simple one that I haven't been able to build successfully is a fructose disaccharide: DFrupb2-1DFrupa2-OH. It just stays buffering.

To reproduce, you simply: 1) Get on the carb builder on actual 2) Click fructose --> fructose again --> select a B 2-->1 linkage 3) Click Done.

gitoliver commented 3 weeks ago

When I build it in GMML I get a useful error so something is up that it's not getting up to the website. Normally Dan displays these. Dan keep this ticket for figuring out why you didn't get the error. I'll make another in GMML to fix it.

Building DFrupa2-1DFrupa2-OH

Error thrown by the carbohydrateBuilder in gmml during construction was: Problem with the metadata found in gmml for this linkage. The number of identified rotatable dihedrals: 3 is greater than the number of metadata items: 2 found for this linkage: ResidueLinkage Index: 0, Name: DFrupa2-1DFrupa, NumberOfShapes: 1, ids: 0CA3?_?@C2 -- 1CA2?_?@O1 C1, C2, O1, C1: 41.6272. C2, O1, C1, C2: 6.06625. O1, C1, C2, O6: 61.9047.

holmess2013 commented 3 weeks ago

Very good!

gitoliver commented 3 weeks ago

Check in dev env and report back

holmess2013 commented 3 weeks ago

Just started up the Dev Env and it still won't build in the carb builder. However, in hindsight this bug isn't that important if we're going to change the default ring type for fructose anyway. Who the hell would want to build a polymer of fructoses in the pyranose form??? The good news is the exact same sequence converted to the "f" ring type builds fine: DFrufb2-1DFrufa2-OH. Forgive me for bringing up this barely significant bug.

gitoliver commented 3 weeks ago

Closing issue as it bifurcated and became confusing. Follow https://github.com/GLYCAM-Web/gmml/issues/171 for DFrupa2-1DFrupa2-OH not building and https://github.com/GLYCAM-Web/website/issues/190 for the website isn't showing errors from GMML.