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[WIP] build package; add pymol Contour Plots#2

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JenkeScheen wants to merge 15 commits intoclhaga:mainfrom
asapdiscovery:first_steps
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[WIP] build package; add pymol Contour Plots#2
JenkeScheen wants to merge 15 commits intoclhaga:mainfrom
asapdiscovery:first_steps

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@JenkeScheen
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@JenkeScheen JenkeScheen commented Mar 5, 2026

Hi @clhaga, thanks for this work! We're building out an API-ified version of this package so that we can test it out internally. In addition to extending the CLI, making some components in the workflow more object-oriented and adding a test suite, we'll make the Contour plots' output be PyMOL session files so users can interactively interrogate the contours given any incoming structural data.

If this PR is of interest I'm happy to merge it in once it's reached MVP. If not I'll close it and continue on our fork.

@JenkeScheen JenkeScheen changed the title build package; add pymol Contour Plots [WIP] build package; add pymol Contour Plots Mar 5, 2026
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clhaga commented Mar 8, 2026

As long as it maintains the original functionality as well (due to it being in the publication), it can be merged. Interested to see if you can get it working correctly in Pymol. I always had issues with the plotting when I tried to do it given the coordinates are different. Converting back from a linear vector to Pymol 3D space never worked properly for me.

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