code: private boolean isBonded(double covalentRadiusA, double covalentRadiusB, double distance2) {
          double maxAcceptable = covalentRadiusA + covalentRadiusB + bondTolerance;
          double maxAcceptable2 = maxAcceptable * maxAcceptable;
          double minBondDistance2 = this.minBondDistance * this.minBondDistance;
          if (distance2 < minBondDistance2) return false;
          return distance2 <= maxAcceptable2;
      }
docs: Returns the bond order for the bond. At this moment, it only returns
  0 or 1, but not 2 or 3, or aromatic bond order.