protected synchronized void prepareKeySequences(List<String> keys, int nKeys) {
smartsKeys = keys;
IQueryAtomContainer query;
sequences.clear();
smartsQueries.clear();
SmartsParser parser = new SmartsParser();
for (int i = 0; i < nKeys; i++) {
query = parser.parse(smartsKeys.get(i));
// parser.setNeededDataFlags(); --> This should not be needed for the key smarts queries
isoTester.setQuery(query);
List<QuerySequenceElement> sequence = isoTester.transferSequenceToOwner();
sequences.add(sequence);
smartsQueries.add(query);
}
}
public void match(String smarts, String smiles) throws Exception {
// Testing the algorithm via SmartsManager
IMolecule mol = SmartsHelper.getMoleculeFromSmiles(smiles);
man.setUseCDKIsomorphismTester(false);
man.setQuery(smarts);
boolResult = man.searchIn(mol);
// Direct test of class IsomorphismTester
IQueryAtomContainer query = sp.parse(smarts);
sp.setNeededDataFlags();
String errorMsg = sp.getErrorMessages();
if (!errorMsg.equals("")) {
System.out.println("Smarts Parser errors:\n" + errorMsg);
return;
}
isoTester.setQuery(query);
sp.setSMARTSData(mol);
List<Integer> pos = isoTester.getIsomorphismPositions(mol);
mappingPosCount = pos.size();
}
protected synchronized BitSet getStructureKeyBits(IAtomContainer ac) {
// quick workaround for aromatic compounds, to avoid matching non-aromatic keys
// TODO remove this when isoTester/keys processing is fixed
// isoTester is fixed, but CDK isomorphism tester still needs the workaround, should be fixed in
// CDK nightly Mar 2010
for (IBond bond : ac.bonds())
if (bond.getFlag(CDKConstants.ISAROMATIC)) {
for (IAtom a : bond.atoms()) a.setFlag(CDKConstants.ISAROMATIC, true);
// in e.g. triazole the atoms are not set as aromatics, but bonds are!
if (cleanKekuleBonds) bond.setOrder(Order.SINGLE);
}
// end of the workaround
BitSet keys = new BitSet(nKeys);
boolean res;
for (int i = 0; i < nKeys; i++) {
isoTester.setSequence(smartsQueries.get(i), sequences.get(i));
res = isoTester.hasIsomorphism(ac);
keys.set(i, res);
}
return (keys);
}