gistfile1.java

BufferedReader     brdr   = ...;

// create once and reuse
IChemObjectBuilder bldr   = SilentChemObjectBuilder.getInstance();
Aromaticity        arom   = new Aromaticity(ElectronDonation.daylight(),
                                            Cycles.or(Cycles.all(), Cycles.all(6)));

// SMILES, implicit h already present
SmilesParser smipar = new SmilesParser(bldr);
String line;
while ((line = brdr.readLine()) != null) {
    try {
        IAtomContainer mol = smipar.parseSmiles(line);
        arom.apply(mol);
        AtomContainerManipulator.suppressHydrogens(mol);
    } catch (InvalidSmilesException ex) {
        // log.. normally bad Kekulé input
    } catch (CDKException e) {
        // log.. complex ring system couldn't calc arom - avoid SSSR
    }
}

// SDfile V2000, implicit h already present
MDLV2000Reader mdlr = new MDLV2000Reader(brdr);
IAtomContainer mol;
while ((mol = mdlr.read(bldr.newInstance(IAtomContainer.class, 0,0,0,0))) != null) {
    try {
        arom.apply(mol);
        AtomContainerManipulator.suppressHydrogens(mol);
    } catch (CDKException e) {
        // log.. complex ring system couldn't calc arom - avoid SSSR
    }
}

// InChI, implicit h already present
// CML, implicit h maybe present -> atom type + guess hydrogen counts