for(Atom a: thisGroup.getAtoms()){
String spaceX = getSpace(10, df.format(a.getX()));
String spaceY = getSpace(10, df.format(a.getY()));
String spaceZ = getSpace(10, df.format(a.getZ()));
String spaceEle = getSpace(4, a.getElement().toString());
atomList.append(spaceX+df.format(a.getX())+spaceY+df.format(a.getY())+spaceZ+df.format(a.getZ())+" "+a.getElement().toString()+spaceEle+"0 0 0 0 0 0 0 0 0 0 0 0\n");
for(Bond b: a.getBonds()){
String index = Integer.toString(atoms.indexOf(a)+1);
String order = Integer.toString(b.getBondOrder());
String spaceIndOne = getSpace(3, index);
String spaceIndTwo = getSpace(3, indexOther);
String spaceOrder = getSpace(3, order);
bondOrders.append(spaceIndOne).append(index).append(spaceIndTwo).append(indexOther).append(spaceOrder).append(order).append(" 0\n");
String spaceNumAtoms = getSpace(3, Integer.toString(thisGroup.getAtoms().size()));
String spaceNumBonds = getSpace(3, Integer.toString(numBonds));
header.append("\n");
header.append(spaceNumAtoms).append(thisGroup.getAtoms().size()).append(spaceNumBonds).append(numBonds).append(" 0 0 0 0 0 0 0 0999 V2000\n");
outString.append(atomList.toString());
outString.append(bondOrders.toString());
outString.append(getCharges(thisGroup));