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getting the center of mass of each part of a molecule


@Gary:
No, I don't have any algorithm. Well, I can define what I want:
1) The script will read the atom coordinates of the ligand from the input file sent in previous message.

2) It will calculate the center of mass (COM) for all the ligand atoms and find the ligand heavy atom closest to its COM.
I already do these two steps but 3. and 4.steps

3) The script should be able to seperate ligand atoms into two equal parts according to the main COM (COM for all atoms). Consider that the the main COM is reference point.

4) It should find the COM each of both equal parts.