Coordinates and weights computations are spread out

[shervinea]

Context. The pdb.py file encodes extraction-related operations. We need to ensure all extraction operations produce objects that are comparable with each other, as it is the hidden assumption behind the volume computation code volume.py.

Current behavior. Coordinates and weights are separately extracted following almost duplicate logic. There is no safeguard in place that prevents coordinates and weight output from not being comparable anymore.

Desired behavior. Coordinates and weights share a maximum amount of logic with each other.