GLYCAM-Web / GLYCAM-Web/gmml

Allowing for random placement of derivatives in each iteration of the repeat unit of a glycomaterial

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#176 0 comments 0 reactions 2 assignees Claimed by @gitoliver View on GitHub
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Description

In the spirit of getting closer to an accurate structural model of glycomaterials, I think it would be very valuable to introduce a new feature in GMML that would translate to the polysaccharide modeler and PS lib, allowing for randomization of derivative positions on the repeat unit. For example, if I build a cellulose acetate decasaccharide, I would like to see the linkage position of the acetyl at C2 on the first Glc, then C3 on the next, then back to C2, etc. Just make it unpredictable. Since most glycomaterials, natural or engineered, have a large degree of randomness in their derivitization patterns, this just makes sense.

However, I don't want to open a can of worms. If it's going to be really challenging to do or require a full rewrite of source code then we can table it.

I envision that the user can have a "randomize derivative position" button next to where they specify the chain length, either on the point and click polysaccharide modeler or on the PS lib.

This would just be V1. If that can be done without too much effort, then we can expand to include randomization with weighting, because more realistically, derivative placement is random to a degree, but there are preferences for certain positions when looking over the whole collection of polymers in the sample.

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