code: @Override
      public void removeAtom(IAtom atom) {
          int position = getAtomNumber(atom);
          if (position != -1) {
              for (int i = 0; i < bondCount; i++) {
                  if (bonds[i].contains(atom)) {
                      removeBond(i);
                      --i;
                  }
              }
              for (int i = 0; i < lonePairCount; i++) {
                  if (lonePairs[i].contains(atom)) {
                      removeLonePair(i);
                      --i;
                  }
              }
              for (int i = 0; i < singleElectronCount; i++) {
                  if (singleElectrons[i].contains(atom)) {
                      removeSingleElectron(i);
                      --i;
                  }
              }
              removeAtomOnly(position);
          }
          notifyChanged();
      }
docs: Removes the given atom and all connected electronContainers from the
  AtomContainer.
  
  @param  atom  The atom to be removed