IntraHBond.java

IChemObjectBuilder bldr   = SilentChemObjectBuilder.getInstance();
SmilesParser       smipar = new SmilesParser(bldr);

final String fname = "/data/nci_aug00.smi";

SMARTSQueryTool sqt = new SMARTSQueryTool("O=[C,N]aa[N,O;!H0]");

int num_hits = 0;
try (BufferedReader brdr = new BufferedReader(new FileReader(fname))) {
    String line;
    while ((line = brdr.readLine()) != null) {
        IMolecule mol = smipar.parseSmiles(line);
        if (sqt.matches(mol))
            num_hits++;
    }
}