I’m interested in working with 3D molecular poses as point clouds.
This has been done in at least one paper (https://arxiv.org/abs/1908.11267) but the authors don’t provide code to replicate the point cloud creation process.
The ideal data format would be a list of tuples
(x, y, z, c1, ... cn) where
x, y, z are the coordinates of a given point and
c1 .. cn and properties calculated at that point (electron density, etc). A simple example might be calculating electrostatic potential along the solvent accessible surface of a molecule.
Does anyone know a set of Python tools to do this? Currently the best I’ve got is using proprietary software to generate ESP surfaces which are saved to a CCP4 file (which is basically a voxelized density grid), loading that CCP4 file into Python and extracting an isosurface from the density grid. Pretty round about.