Multiple atoms should not coincide (fall into each other) given the same positions

[blokhin]

Here's one example, so we need some position coordinates tolerance, controlling if the atom should be rendered in the proximity of another. On the other hand, this should not break the partial occupancy concept (different types of atoms at the same place), so the above applies strictly to the same atom types. That is, even if some attribute (like charge) is different, then we allow coinciding (and re-calculate the label).