AndrewRadev / protein-runway

Integrated Bioinformatics Project
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Surround group of atoms with a surface #25

Closed AndrewRadev closed 1 day ago

AndrewRadev commented 3 weeks ago

For now, we're drawing atoms and bonds, but ultimately, we want to have a mesh surrounding groups of them. The term is "convex hull": https://docs.blender.org/manual/en/latest/modeling/meshes/editing/mesh/convex_hull.html

Update: A convex hull might not be right. If we just take the points and take the volume that contains them, we'll miss holes. We still need to try, but we might have to do something different, like pick the "surface" points and draw triangular faces with normal vectors pointing "out".

We may have to create "nodes" and operate through those:

These need to be researched and understood.

AndrewRadev commented 1 day ago

Closed by #58. A convex hull seems to be the best we can hope for, since a "surface" that wraps the atoms is a poorly-defined concept (how do you decide which points are on the "inside" and which are on the "surface"?). With a good enough clustering, convex hulls seem reasonable, at least for the one protein I tested with.