code: private boolean haveCrossingBonds(int u, int v) {
          int[] us = adjList[u];
          int[] vs = adjList[v];
          for (int u1 : us) {
              for (int v1 : vs) {
                  if (u1 == v || v1 == u || u1 == v1)
                      continue;
                  if (isCrossed(atoms[u].getPoint2d(), atoms[u1].getPoint2d(), atoms[v].getPoint2d(), atoms[v1].getPoint2d()))
                      return true;
              }
          }
          return false;
      }
docs: Check if any of the bonds adjacent to u, v (not bonded) are crossing.
  
  @param u an atom (idx)
  @param v another atom (idx)
  @return there are crossing bonds