code: private void backupCoords(Point2d[] dest, IntStack stack) {
          for (int i = 0; i < stack.len; i++) {
              int v = stack.xs[i];
              dest[v].x = atoms[v].getPoint2d().x;
              dest[v].y = atoms[v].getPoint2d().y;
          }
      }
docs: Backup the coordinates of atoms (idxs) in the stack to the provided
  destination.
  
  @param dest  destination
  @param stack atom indexes to backup