Sphere tree generator script

[meganrm]

Use Case

We want to be able to create simplified representations of PDBs without using Cellpack as a plugin. The sphere tree maker file was written to be used within 3D software. The sphere tree files are used for more detailed collision detection than just one encapsulating sphere.

here is an example of a current sphere tree file: https://github.com/mesoscope/cellPACK_data/blob/master/cellPACK_database_1.1.0/collisionTrees/1ASY_4mer1.sph

Solution

Given a recipe file, walk through the objects, for any that have pdbs but no no sphere tree file, generate a new one. We can default to 3 levels, with a rules that the simplest level sphere has to encompass all other spheres.

Could start as a stand alone script, but should be integrated into the recipe loading script.

Alternatives

Please describe any alternatives you've considered, even if you've dismissed them

[aditnath]

Level 1 of the sphere tree is a sphere that encompasses the entire protein
Layers below allow more abstraction.
Think about keeping sizes of all spheres at each level the same, may not be possible though.
Recursively go through and see if you can encompass all atoms with more spheres
Algorithm idea: find geometry farthest from sphere, create a sphere, and then mask out all atoms that are encompassed by new sphere
Look into k-means algorithm, choose number of clusters for each level where variance in radii are minimized
https://github.com/mesoscope/autoPACK/blob/develop/autopack/scripts/sblSphereTree.py