Do you think they 'mapped' the organism. In other words, a very general map?
It’s hard to say what they actually did without reading the paper itself, but I can assure you that they did not simulate every molecule in that organism.
The knowledge for doing that is insufficient by at least a thousand orders of magnitude not to mention that the necessary computing power is a million orders of magnitude lacking. For instance, look at something as relatively simple as protein folding; given any specific gene sequence for a functional protein, science is still unable to predict what it’s folded 3-D structure will be.
And besides, one is getting close to quantum-level behavior in dealing with massively complex molecular machines, in which case total predictability is impossible anyway. The best that could be done might be a statistical simulation in that case. But that’s a long ways off too.