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