getting the center of mass of each part of a molecule
Yes, I wrote: "The atoms of the first part/half according to the main COM of the ligand are C2, C7, C8 and C9. As for the second part they are C3, C4, C5 and C6 atoms." It was just an example. In fact, I don't know which atoms belong to each half. The code should do it of course.
That is, I gave it as an example. I thought someone can understand what the two parts of molecule are and what I am trying to do if I give such an example.