@Test
public void testMakeAtomContainer() {
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
IAtom atom = builder.newInstance(IAtom.class, "C");
IAtom exclude = builder.newInstance(IAtom.class, "C");
IAtom a1 = builder.newInstance(IAtom.class, "C");
IAtom a2 = builder.newInstance(IAtom.class, "C");
IBond[] bonds =
new IBond[] {
builder.newInstance(IBond.class, atom, exclude),
builder.newInstance(IBond.class, a1, a2),
builder.newInstance(IBond.class, a1, atom),
builder.newInstance(IBond.class, a2, exclude)
};
IAtomContainer part = FragmentUtils.makeAtomContainer(atom, Arrays.asList(bonds), exclude);
assertThat(part.getAtomCount(), is(3));
assertThat(part.getBondCount(), is(2));
Assert.assertTrue(part.contains(atom));
Assert.assertTrue(part.contains(a1));
Assert.assertTrue(part.contains(a2));
Assert.assertFalse(part.contains(exclude));
Assert.assertTrue(part.contains(bonds[1]));
Assert.assertTrue(part.contains(bonds[2]));
}
public ChemWizard() {
smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
smrkMan.setFlagProcessResultStructures(true);
smrkMan.setFlagAddImplicitHAtomsOnResultProcess(true);
LOGGER.setLevel(Level.FINEST);
}
/** @author John May */
public class ChemSpiderAdapter extends AbstractSoapService<ChemSpiderIdentifier>
implements StructureService<ChemSpiderIdentifier> {
private static final Logger LOGGER = Logger.getLogger(ChemSpiderAdapter.class);
private static final IChemObjectBuilder BUILDER = SilentChemObjectBuilder.getInstance();
private SearchSoap service;
private SearchLocator locator = new SearchLocator();
@Override
public ChemSpiderIdentifier getIdentifier() {
return new ChemSpiderIdentifier();
}
@Override
public IAtomContainer getStructure(ChemSpiderIdentifier identifier) {
try {
StringPreference key = ServicePreferences.getInstance().getPreference("CHEM_SPIDER_KEY");
if (key.get().isEmpty()) {
System.err.println("No ChemSpider key available: please input the key via preferences!");
return BUILDER.newInstance(IAtomContainer.class);
}
CompoundInfo info =
service.getCompoundInfo(Integer.parseInt(identifier.getAccession()), key.get());
InChIGeneratorFactory inchiFactory = InChIGeneratorFactory.getInstance();
InChIToStructure inchi2structure = inchiFactory.getInChIToStructure(info.getInChI(), BUILDER);
return inchi2structure.getAtomContainer();
} catch (CDKException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
} catch (RemoteException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
return BUILDER.newInstance(IAtomContainer.class);
}
@Override
public boolean startup() {
if (service != null) return true;
try {
service = locator.getSearchSoap();
} catch (ServiceException ex) {
LOGGER.error("Startup failed on SOAP Web Service: " + ex.getMessage());
}
return service != null;
}
}
/**
* Just to ensure it doesn't throw exceptions
*
* @throws Exception
*/
@Test(timeout = 1000)
public void testAcyclic() throws Exception {
String smiles = "CCCCCCC";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
}
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);
}
private IAtomContainer parseSMILES() {
if (SMILES_PARSER == null) {
SMILES_PARSER = new SmilesParser(SilentChemObjectBuilder.getInstance());
}
try {
atomContainer = new AtomContainer(SMILES_PARSER.parseSmiles(getValue()));
} catch (CDKException ex) {
LOGGER.error("Could not parse SMILES ", ex);
atomContainer = new AtomContainer();
}
return atomContainer;
}
@Test
public void testTraversal_Chain() {
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
IAtom[] atoms =
new IAtom[] {
builder.newInstance(IAtom.class, "C"),
builder.newInstance(IAtom.class, "C"),
builder.newInstance(IAtom.class, "C"),
builder.newInstance(IAtom.class, "C"),
builder.newInstance(IAtom.class, "C"),
builder.newInstance(IAtom.class, "C")
};
IBond[] bonds =
new IBond[] {
builder.newInstance(IBond.class, atoms[0], atoms[1]),
builder.newInstance(IBond.class, atoms[1], atoms[2]),
builder.newInstance(IBond.class, atoms[2], atoms[3]),
builder.newInstance(IBond.class, atoms[3], atoms[4]),
builder.newInstance(IBond.class, atoms[4], atoms[5])
};
IAtomContainer m = builder.newInstance(IAtomContainer.class, 0, 0, 0, 0);
m.setAtoms(atoms);
m.setBonds(bonds);
List<IBond> accumulator = new ArrayList<IBond>();
// traverse from one end
FragmentUtils.traverse(m, atoms[0], accumulator);
assertThat(accumulator.size(), is(5));
assertThat(accumulator.get(0), is(bonds[0]));
assertThat(accumulator.get(1), is(bonds[1]));
assertThat(accumulator.get(2), is(bonds[2]));
assertThat(accumulator.get(3), is(bonds[3]));
assertThat(accumulator.get(4), is(bonds[4]));
// traverse from the middle
accumulator.clear();
FragmentUtils.traverse(m, atoms[3], accumulator);
assertThat(accumulator.size(), is(5));
assertThat(accumulator.get(0), is(bonds[2]));
assertThat(accumulator.get(1), is(bonds[1]));
assertThat(accumulator.get(2), is(bonds[0]));
assertThat(accumulator.get(3), is(bonds[3]));
assertThat(accumulator.get(4), is(bonds[4]));
}
private void updatePageComplete(Text field) {
setPageComplete(false);
String smiles = field.getText();
if (smiles.length() != 0) {
SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
try {
parser.parseSmiles(smiles);
wizard.setSMILES(smiles);
} catch (InvalidSmilesException exception) {
setMessage(exception.getMessage());
setErrorMessage("The given SMILES is invalid.");
return;
}
}
setPageComplete(true);
setMessage(null);
setErrorMessage(null);
}
@Test(timeout = 1000)
public void testPyrrole_Silent() throws Exception {
String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(6, doubleBondCount);
}
/**
* TestSuite that runs all QSAR tests.
*
* @cdk.module test-qsaratomic
*/
public class StabilizationPlusChargeDescriptorTest extends AtomicDescriptorTest {
private static final IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
public StabilizationPlusChargeDescriptorTest() {
descriptor = new StabilizationPlusChargeDescriptor();
}
@Before
public void setUp() throws Exception {
setDescriptor(StabilizationPlusChargeDescriptor.class);
}
/**
* A unit test for JUnit
*
* @throws Exception
*/
@Test
public void testStabilizationPlusChargeDescriptor() throws Exception {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(0).setFormalCharge(-1);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(1).setFormalCharge(1);
mol.addBond(0, 1, Order.SINGLE);
mol.addAtom(builder.newInstance(IAtom.class, "F"));
mol.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol);
lpcheck.saturate(mol);
DoubleResult result = ((DoubleResult) descriptor.calculate(mol.getAtom(1), mol).getValue());
Assert.assertNotSame(0.0, result.doubleValue());
}
/** */
@Test
public void testNotCharged() throws Exception {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(0).setFormalCharge(-1);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.addBond(0, 1, Order.DOUBLE);
mol.addAtom(builder.newInstance(IAtom.class, "F"));
mol.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol);
lpcheck.saturate(mol);
DoubleResult result = ((DoubleResult) descriptor.calculate(mol.getAtom(0), mol).getValue());
Assert.assertEquals(0.0, result.doubleValue(), 0.00001);
}
/**
* A unit test for JUnit
*
* @throws Exception
*/
@Test
public void testStabilizationPlusChargeDescriptor2() throws Exception {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(0).setFormalCharge(-1);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(1).setFormalCharge(1);
mol.addBond(0, 1, Order.SINGLE);
mol.addAtom(builder.newInstance(IAtom.class, "F"));
mol.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol);
lpcheck.saturate(mol);
DoubleResult result = ((DoubleResult) descriptor.calculate(mol.getAtom(1), mol).getValue());
Assert.assertNotSame(0.0, result.doubleValue());
}
/**
* A unit test for JUnit
*
* @throws Exception
*/
@Test
public void testStabilizationComparative() throws Exception {
IAtomContainer mol1 = builder.newInstance(IAtomContainer.class);
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.getAtom(1).setFormalCharge(1);
mol1.addBond(0, 1, Order.SINGLE);
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.addBond(1, 2, Order.SINGLE);
mol1.addAtom(builder.newInstance(IAtom.class, "O"));
mol1.addBond(1, 3, Order.SINGLE);
addExplicitHydrogens(mol1);
lpcheck.saturate(mol1);
DoubleResult result1 = ((DoubleResult) descriptor.calculate(mol1.getAtom(1), mol1).getValue());
IAtomContainer mol2 = builder.newInstance(IAtomContainer.class);
mol2.addAtom(builder.newInstance(IAtom.class, "C"));
mol2.addAtom(builder.newInstance(IAtom.class, "C"));
mol2.getAtom(1).setFormalCharge(1);
mol2.addBond(0, 1, Order.SINGLE);
mol2.addAtom(builder.newInstance(IAtom.class, "O"));
mol2.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol2);
lpcheck.saturate(mol2);
DoubleResult result2 = ((DoubleResult) descriptor.calculate(mol2.getAtom(1), mol2).getValue());
IAtomContainer mol3 = builder.newInstance(IAtomContainer.class);
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.getAtom(1).setFormalCharge(1);
mol3.addBond(0, 1, Order.SINGLE);
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol3);
lpcheck.saturate(mol3);
DoubleResult result3 = ((DoubleResult) descriptor.calculate(mol3.getAtom(1), mol3).getValue());
Assert.assertTrue(result3.doubleValue() < result2.doubleValue());
Assert.assertTrue(result2.doubleValue() < result1.doubleValue());
}
/**
* A unit test for JUnit with C=CCCl # C=CC[Cl+*]
*
* @cdk.inchi InChI=1/C3H7Cl/c1-2-3-4/h2-3H2,1H3
*/
@Test
public void testCompareIonized() throws Exception {
IAtomContainer molA = builder.newInstance(IAtomContainer.class);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(0, 1, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(1, 2, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
molA.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molA);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
lpcheck.saturate(molA);
double resultA =
((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
IAtomContainer molB = builder.newInstance(IAtomContainer.class);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(0, 1, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(1, 2, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
molB.getAtom(3).setFormalCharge(1);
molB.addSingleElectron(3);
molB.addLonePair(3);
molB.addLonePair(3);
molB.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molB);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
lpcheck.saturate(molB);
Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
double resultB =
((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
Assert.assertNotSame(resultA, resultB);
}
}
/**
* TestSuite that runs a test for the RadicalSiteHrBetaReaction.
*
* @cdk.module test-reaction
*/
public class RadicalSiteHrBetaReactionTest extends ReactionProcessTest {
private IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
/** The JUnit setup method */
public RadicalSiteHrBetaReactionTest() throws Exception {
setReaction(RadicalSiteHrBetaReaction.class);
}
/** The JUnit setup method */
@Test
public void testRadicalSiteHrBetaReaction() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
Assert.assertNotNull(type);
}
/**
* A unit test suite for JUnit. Reaction:
*
* @return The test suite
*/
@Test
@Override
public void testInitiate_IAtomContainerSet_IAtomContainerSet() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
/* initiate */
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
type.setParameterList(paramList);
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
Assert.assertEquals(3, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
IAtomContainer molecule2 = getExpectedProducts().getAtomContainer(0);
IQueryAtomContainer queryAtom =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(new UniversalIsomorphismTester().isIsomorph(molecule2, queryAtom));
}
/**
* create the compound
*
* @return The IAtomContainerSet
*/
private IAtomContainerSet getExampleReactants() {
IAtomContainerSet setOfReactants =
DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.getAtom(3).setFormalCharge(1);
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(3, 4, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(4, 5, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
} catch (Exception e) {
e.printStackTrace();
}
molecule.getAtom(3).setFormalCharge(0);
molecule.addSingleElectron(new SingleElectron(molecule.getAtom(3)));
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
makeSureAtomTypesAreRecognized(molecule);
} catch (CDKException e) {
e.printStackTrace();
}
setOfReactants.addAtomContainer(molecule);
return setOfReactants;
}
/**
* Get the expected set of molecules.
*
* @return The IAtomContainerSet
*/
private IAtomContainerSet getExpectedProducts() {
IAtomContainerSet setOfProducts = builder.newInstance(IAtomContainerSet.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.getAtom(0).setFormalCharge(1);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(3, 4, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(4, 5, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
} catch (Exception e) {
e.printStackTrace();
}
molecule.getAtom(0).setFormalCharge(0);
molecule.addSingleElectron(new SingleElectron(molecule.getAtom(0)));
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
makeSureAtomTypesAreRecognized(molecule);
} catch (CDKException e) {
e.printStackTrace();
}
setOfProducts.addAtomContainer(molecule);
return setOfProducts;
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* manually put the reactive center */
molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER, true);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0);
Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testMapping() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* automatic search of the center active */
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
Assert.assertEquals(19, setOfReactions.getReaction(0).getMappingCount());
IAtom mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(0));
Assert.assertEquals(mappedProductA1, product.getAtom(0));
IAtom mappedProductA2 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(6));
Assert.assertEquals(mappedProductA2, product.getAtom(6));
IAtom mappedProductA3 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(3));
Assert.assertEquals(mappedProductA3, product.getAtom(3));
}
/**
* Test to recognize if a IAtomContainer matcher correctly identifies the CDKAtomTypes.
*
* @param molecule The IAtomContainer to analyze
* @throws CDKException
*/
private void makeSureAtomTypesAreRecognized(IAtomContainer molecule) throws CDKException {
Iterator<IAtom> atoms = molecule.atoms().iterator();
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
while (atoms.hasNext()) {
IAtom nextAtom = atoms.next();
Assert.assertNotNull(
"Missing atom type for: " + nextAtom, matcher.findMatchingAtomType(molecule, nextAtom));
}
}
}
public class TestIsomorphismTester extends TestCase {
public LoggingTool logger;
public SmartsParser sp = new SmartsParser();
public SmartsManager man = new SmartsManager(SilentChemObjectBuilder.getInstance());
public IsomorphismTester isoTester = new IsomorphismTester();
// Helper variable where the results from match function is stored
boolean boolResult;
int mappingPosCount;
public TestIsomorphismTester() {
logger = new LoggingTool(this);
}
public static Test suite() {
return new TestSuite(TestIsomorphismTester.class);
}
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();
}
// ---------------------------------------------------------------------------------
/** Tests from From http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html */
public void testPropertyCharge1() throws Exception {
match("[+1]", "[OH-].[Mg+2]");
assertEquals(false, boolResult);
assertEquals(0, mappingPosCount);
}
public void testPropertyCharge2() throws Exception {
match("[+1]", "COCC(O)Cn1ccnc1[N+](=O)[O-]");
assertEquals(true, boolResult);
assertEquals(1, mappingPosCount);
}
public void testPropertyCharge3() throws Exception {
match("[+1]", "[NH4+]");
assertEquals(true, boolResult);
assertEquals(1, mappingPosCount);
}
public void testPropertyCharge4() throws Exception {
match("[+1]", "CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12");
assertEquals(false, boolResult);
assertEquals(0, mappingPosCount);
}
public void testPropertyCharge5() throws Exception {
match("[+1]", "[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2");
assertEquals(true, boolResult);
assertEquals(2, mappingPosCount);
}
public void testPropertyAromatic1() throws Exception {
match("[a]", "c1cc(C)c(N)cc1");
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyAromatic2() throws Exception {
match("[a]", "c1c(C)c(N)cnc1");
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyAromatic3() throws Exception {
match("[a]", "c1(C)c(N)cco1");
assertEquals(true, boolResult);
assertEquals(5, mappingPosCount);
}
public void testPropertyAromatic4() throws Exception {
match("[a]", "c1c(C)c(N)c[nH]1");
assertEquals(true, boolResult);
assertEquals(5, mappingPosCount);
}
public void testPropertyAromatic5() throws Exception {
match("[a]", "n1cc(O)ccc1"); // On1ccccc1 is not recognized as aromatic
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyAromatic6() throws Exception {
match("[a]", "[O-][n+]1ccccc1");
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyAromatic7() throws Exception {
match("[a]", "c1ncccc1C1CCCN1C");
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyAromatic8() throws Exception {
match("[a]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC");
assertEquals(true, boolResult);
assertEquals(6, mappingPosCount);
}
public void testPropertyRing3() throws Exception {
match("CC=1CC=1", "CC=1CC=1");
assertEquals(true, boolResult);
assertEquals(1, mappingPosCount);
}
public void testDoubleNonAromaticBond1() throws Exception {
match("cc=c", "C1=CC=CC=C1C2=CC=CC=C2");
assertEquals(false, boolResult);
}
public void testDoubleNonAromaticBond2() throws Exception {
match("cc=c", "c1ccccc1c2ccccc2");
assertEquals(false, boolResult);
}
// ---------------- Test recursive SMARTS -------------------
public void testRecursiveSmarts4() throws Exception {
match("[$(*O);$(*CC)]", "c1ncccc1C1CCCN1C");
assertEquals(false, boolResult);
// assertEquals(0, mappingPosCount);
}
public void testRecursiveSmarts5() throws Exception {
match("[$(*O);$(*CC)]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76");
assertEquals(true, boolResult);
// assertEquals(1, mappingPosCount);
}
public void testRecursiveSmarts6() throws Exception {
match("[$([CX3]=[CX1]),$([CX3+]-[CX1-])]", "CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12");
assertEquals(false, boolResult);
// assertEquals(0, mappingPosCount);
}
}
