static Graph convert(
IAtomContainer ac,
boolean perceiveAromaticity,
boolean isomeric,
boolean aromatic,
boolean atomClasses)
throws Exception {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance()).addImplicitHydrogens(ac);
if (perceiveAromaticity) Aromaticity.cdkLegacy().apply(ac);
return new CDKToBeam(isomeric, aromatic, atomClasses).toBeamGraph(ac);
}
@Test
public void testGenerateFingerprintNaphthalene() throws InvalidSmilesException, Exception {
String smiles = "C1=CC2=CC=CC=C2C=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.cdkLegacy().apply(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprint1;
fingerprint1 = fingerprint.getBitFingerprint(molecule).asBitSet();
org.junit.Assert.assertEquals(8, fingerprint1.cardinality());
}
/**
* Generates a shortest path based BitSet fingerprint for the given AtomContainer.
*
* @param ac The AtomContainer for which a fingerprint is generated
* @exception CDKException if there error in aromaticity perception or other CDK functions
* @return A {@link BitSet} representing the fingerprint
*/
@Override
public IBitFingerprint getBitFingerprint(IAtomContainer ac) throws CDKException {
IAtomContainer atomContainer = null;
try {
atomContainer = (IAtomContainer) ac.clone();
} catch (CloneNotSupportedException ex) {
logger.error("Failed to clone the molecule:", ex);
}
Aromaticity.cdkLegacy().apply(atomContainer);
BitSet bitSet = new BitSet(fingerprintLength);
if (!ConnectivityChecker.isConnected(atomContainer)) {
IAtomContainerSet partitionedMolecules =
ConnectivityChecker.partitionIntoMolecules(atomContainer);
for (IAtomContainer container : partitionedMolecules.atomContainers()) {
addUniquePath(container, bitSet);
}
} else {
addUniquePath(atomContainer, bitSet);
}
return new BitSetFingerprint(bitSet);
}
private void prepareInput(IAtomContainer input) throws CDKException {
SmartsMatchers.prepare(input, true);
arom.apply(input);
}