I'm wondering how well Blender is suited for producing images from existing 2D (CDX, SMILES etc.) or 3D (PDB, XYZ, CIF etc.) chemical structures. Basically, the task is to convert a set of coordinates to a finite (e.g. a molecule) or a subset of infinite (e.g. a unit cell) graphical representation. Ideally it would be nice if a certain level of "chemistry awareness" would be present, such as typical interatomic distances, coordination numbers, atomic and ionic radii.
Is there an addon that can help chemists to use blender for their routine work?
There is a related question about crystal structure generation with Blender. I'm assuming that structure is already established.