code: public static Point3d[] atomsToPoints(Atom[] atoms) {
  		Point3d[] points = new Point3d[atoms.length];
  		for(int i = 0; i< atoms.length;i++) {
  			points[i] = atoms[i].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