code: public static List<Point3d> atomsToPoints(Collection<Atom> atoms) {
  		ArrayList<Point3d> points = new ArrayList<>(atoms.size());
  		for (Atom atom : atoms) {
  			points.add(atom.getCoordsAsPoint3d());
  		}
  		return points;
  	}
docs: Convert an array of atoms into an array of vecmath points
  
  @param atoms
  list of atoms
  @return list of Point3ds storing the x,y,z coordinates of each atom