I want to solve a problem: There are some atoms in 3-dimensional space, those atoms belong to some molecules, we know the kind and coordinate of the atoms, but we don' t know which atom belong to which kind of molecule, we need to classify the atoms. How to deal with it in Mathematica? For example, I have a alcohol-water blend, but I only know the kind and coordinate of the atoms, as shown in the figure：
I want to classify the atoms into molecules by calculating the coordinate, the goal is like this: 
How to achieve it in Mathematica?
