cmelab / cmelab/cmeutils

FresnelGSD viewer default colors

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Python
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Description

Would be nice to have colors for the Fresnel GSD viewer. I put together a little video renderer pulled from code used in the HOOMD docs with another student in our lab (Kieran Nehils-Puleo), and think it would be useful to include default colors for particles if you knew their elements from something like a gmso topology. Here's a link to the dict in the file that sets those colors (and radii) https://github.com/mosdef-hub/CECAM-MoSDeF-Workshop/blob/73e87b53b6d01ae7784f8b18c396739e65776d8f/solvated_surface_workflow/hoomd_runners.py#L147C1-L147C1.

There's also a messy version of the render video code at the end of that file. Might be a nice feature to have.

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Research direction

Start with the color and radius dictionary around line 147 of solvated_surface_workflow/hoomd_runners.py, then inspect the render-video code at the end of that file and how the Fresnel GSD viewer is used in cmeutils. Confirm how element information from a GMSO topology can reach the viewer. Done means the viewer has documented default particle colors and radii and renders them correctly from topology data.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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