MdlAromFix.java

static int aromStatus(IAtomContainer mol) {
    int res = 0;
    for (IAtom atom : mol.atoms()) {
        if (atom.getImplicitHydrogenCount() == null && atom.getFlag(CDKConstants.ISAROMATIC)) {
            // N and P are ambiguous
            if (atom.getAtomicNumber() == 7 || atom.getAtomicNumber() == 15)
                res = 2;
            else if (res < 2)
                res = 1;
        }
    }
    return res;
}

public static void main(String[] args) throws CDKException, FileNotFoundException {
    final MDLV2000Reader mdlr = new MDLV2000Reader(new FileInputStream("/Users/john/Desktop/bad.mol"));

    IAtomContainer mol = mdlr.read(new AtomContainer(0, 0, 0, 0));

    // if res=2 it's ambiguous, res=1 should be fine.
    // here we try to fix both
    if (aromStatus(mol) > 0) {
        for (IBond bond : mol.bonds()) {
            if (bond.getOrder() == IBond.Order.UNSET) {
                bond.setFlag(CDKConstants.ISAROMATIC, true); // needed?
                bond.setOrder(IBond.Order.SINGLE);
            }
        }

        // need hydrogen counts, can add via other method
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
        CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol);

        // percieveAtomTypesAndConfigureAtoms wipes arom flags on atoms (bug)
        for (IBond bond : mol.bonds()) {
            if (bond.getFlag(CDKConstants.ISAROMATIC)) {
                bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
                bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
            }
        }

        Kekulization.kekulize(mol);
    }

    System.out.println(SmilesGenerator.generic().create(mol));
}