@Test
public void testBuilder() {
TetrahedralChirality chirality =
new TetrahedralChirality(molecule.getAtom(1), ligands, Stereo.CLOCKWISE);
Assert.assertNull(chirality.getBuilder());
chirality.setBuilder(DefaultChemObjectBuilder.getInstance());
Assert.assertEquals(DefaultChemObjectBuilder.getInstance(), chirality.getBuilder());
}
@Before
public void setUp() {
this.parser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
this.builder = DefaultChemObjectBuilder.getInstance();
mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.addBond(0, 1, IBond.Order.SINGLE);
molSig = new MoleculeSignature(mol);
}
/** @cdk.bug 826942 */
@Test
public void testSFBug826942() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("C1CCC2C(C1)C4CCC3(CCCCC23)(C4)");
IRingSet ringSet = new SSSRFinder(molecule).findSSSR();
Assert.assertEquals(4, ringSet.getAtomContainerCount());
}
/**
* 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;
}
/** @cdk.bug 1535055 */
@Test
public void testBug1535055() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("COC(=O)c1ccc2c(c1)c1ccccc1[nH]2");
CDKHueckelAromaticityDetector.detectAromaticity(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
SmilesGenerator sg = new SmilesGenerator();
sg.setUseAromaticityFlag(true);
String s1 = sg.createSMILES(mol);
String filename = "data/cml/bug1535055.cml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CMLReader reader = new CMLReader(ins);
IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
// test the resulting ChemFile content
Assert.assertNotNull(chemFile);
IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
CDKHueckelAromaticityDetector.detectAromaticity(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
String s2 = sg.createSMILES(mol2);
Assert.assertTrue(s1.contains("[nH]"));
Assert.assertTrue(s2.contains("[nH]"));
}
@Test
public void testGetAtomContainerCount() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("c1ccccc1");
IRingSet ringSet = new SSSRFinder(molecule).findSSSR();
Assert.assertEquals(1, ringSet.getAtomContainerCount());
}
/**
* A unit test suite for JUnit for Ethene. Reaction: O=C-C-H => O(H)-C=C. Automatic looking for
* active center.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testInitiate_IMoleculeSet_IMoleculeSet() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMolecule molecule = getEthene();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
/* 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(2, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
IMolecule molecule2 = getExpected();
IQueryAtomContainer queryAtom =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2, queryAtom));
}
@Override
public MoleculeType convertFromStream(InputStream is) throws MSMLConversionException {
ArrayList<IMolecule> sdfMolecules = new ArrayList<IMolecule>();
boolean skip = true;
IteratingMDLReader reader =
new IteratingMDLReader(is, DefaultChemObjectBuilder.getInstance(), skip);
while (reader.hasNext()) {
IMolecule sdfMolecule = (IMolecule) reader.next();
sdfMolecules.add(sdfMolecule);
}
MoleculeType converted = new MoleculeType();
if (sdfMolecules.size() < 1) {
throw new MSMLConversionException(
"Cannot convert molecule(s) because MDL file (.mol or .sdf) is empty");
} else if (sdfMolecules.size() == 1) {
converted = convert(sdfMolecules.get(0));
} else {
converted = convert(sdfMolecules);
}
converted.setMoleculeClass(MoleculeClassType.MOLECULE_LIST);
// set convention
converted.setConvention("convention:molecular");
// set the origin format
converted.setOrigin(OriginType.SDF);
return converted;
}
public static IAtomContainer getMcsAsNewContainer(IAtomContainer mol1, IAtomContainer mol2)
throws CDKException, CloneNotSupportedException {
Isomorphism mcs = new Isomorphism(org.openscience.cdk.smsd.interfaces.Algorithm.DEFAULT, true);
mcs.init(mol1, mol2, true, true);
mcs.setChemFilters(true, true, true);
mol1 = mcs.getReactantMolecule();
mol2 = mcs.getProductMolecule();
IAtomContainer mcsmolecule =
DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class, mol1);
List<IAtom> atomsToBeRemoved = new ArrayList<IAtom>();
for (IAtom atom : mcsmolecule.atoms()) {
int index = mcsmolecule.getAtomNumber(atom);
if (!mcs.getFirstMapping().containsKey(index)) {
atomsToBeRemoved.add(atom);
}
}
for (IAtom atom : atomsToBeRemoved) {
mcsmolecule.removeAtomAndConnectedElectronContainers(atom);
}
return mcsmolecule;
}
@Test
public void testGetInstance() {
Object builder = DefaultChemObjectBuilder.getInstance();
Assert.assertNotNull(builder);
Assert.assertTrue(builder instanceof IChemObjectBuilder);
Assert.assertTrue(builder instanceof DefaultChemObjectBuilder);
}
@Test
public void testAromaticAtomsCountDescriptor() throws java.lang.Exception {
Object[] params = {true};
descriptor.setParameters(params);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("CCOc1ccccc1"); // ethanol
Assert.assertEquals(6, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue());
}
public static IAtomContainer makeFragment4() {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
return mol;
}
@Test
public void testEmpty() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
MoleculeSignature signature = new MoleculeSignature(mol);
String signatureString = signature.toCanonicalString();
String expected = "";
Assert.assertEquals(expected, signatureString);
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @param reactants reactants of the reaction
* @param agents agents of the reaction (Must be in this case null)
* @exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException {
logger.debug("initiate reaction: HeterolyticCleavagePBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavagePBReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IMolecule reactant = reactants.getMolecule(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() != IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER)
&& atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
/**/
for (int j = 0; j < 2; j++) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0) {
atomList.add(atom1);
atomList.add(atom2);
} else {
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class);
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
return setOfReactions;
}
public static IChemModel emptyModel() {
final IChemModel chemModel = DefaultChemObjectBuilder.getInstance()
.newInstance(IChemModel.class);
chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(
IAtomContainerSet.class));
chemModel.getMoleculeSet().addAtomContainer(
chemModel.getBuilder().newInstance(IAtomContainer.class));
return chemModel;
}
@Test
public void testBug70() throws FileNotFoundException, CDKException {
JPanelFixture jcppanel = applet.panel("appletframe");
JChemPaintPanel panel = (JChemPaintPanel) jcppanel.target;
applet.button("hexagon").click();
applet.click();
Point2d point = getAtomPoint(panel, 0);
applet
.panel("renderpanel")
.robot
.click(
applet.panel("renderpanel").component(),
new Point((int) point.x, (int) point.y),
MouseButton.RIGHT_BUTTON,
1);
applet
.panel("renderpanel")
.robot
.click(
applet.panel("renderpanel").component(),
new Point((int) point.x, (int) point.y),
MouseButton.RIGHT_BUTTON,
1);
applet.menuItem("showACProperties").click();
DialogFixture dialog = applet.dialog();
JTextComponent textfield = dialog.robot.finder().find(JTextComponentMatcher.withName("Title"));
textfield.setText("aaa");
JButtonFixture okbutton =
new JButtonFixture(
dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("OK")));
okbutton.click();
applet.menuItem("save").click();
dialog = applet.dialog();
File file = new File(System.getProperty("java.io.tmpdir") + File.separator + "test.mol");
if (file.exists()) file.delete();
JComboBox combobox =
dialog
.robot
.finder()
.find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
JTextComponentFixture text = dialog.textBox();
text.setText(file.toString());
JButtonFixture savebutton =
new JButtonFixture(
dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
savebutton.click();
MDLReader reader = new MDLReader(new FileInputStream(file));
IAtomContainer mol =
(IAtomContainer)
reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
Assert.assertEquals("aaa", (String) mol.getProperty(CDKConstants.TITLE));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testDefaultValidFalse() throws ClassNotFoundException, CDKException, Exception {
IRule rule = new ChargeRule();
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"), 2);
formula.addIsotope(builder.newIsotope("H"), 200);
formula.setCharge(1);
Assert.assertEquals(0.0, rule.validate(formula), 0.0001);
}
public class EquivalentClassPartitionerTest {
public static final IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
@Test
public void testQuinone() throws Exception {
IAtomContainer mol = MoleculeFactory.makeQuinone();
Assert.assertNotNull("Created molecule was null", mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(mol);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(mol);
Partition autP = ArrayToPartition.convert(eqCl, 1);
Assert.assertEquals("Wrong number of equivalent classes", 3, autP.size());
Partition expected = Partition.fromString("0,7|1,4|2,3,5,6");
Assert.assertEquals("Wrong class assignment", expected, autP);
}
@Test
public void one_four_cyclohexadiene() throws NoSuchAtomException {
String acpString = "C0C1C2C3C4C5 0:1(2),0:5(1),1:2(1),2:3(1),3:4(2),4:5(1)";
IAtomContainer cyclohexadiene = AtomContainerPrinter.fromString(acpString, builder);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(cyclohexadiene);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(cyclohexadiene);
System.out.println(Arrays.toString(eqCl));
System.out.println(ArrayToPartition.convert(eqCl, 1));
}
@Test
public void four_H_pyran() throws NoSuchAtomException {
String acpString = "C0C1C2C3C4O5 0:1(2),0:5(1),1:2(1),2:3(1),3:4(2),4:5(1)";
IAtomContainer fourHpyran = AtomContainerPrinter.fromString(acpString, builder);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(fourHpyran);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(fourHpyran);
System.out.println(Arrays.toString(eqCl));
System.out.println(ArrayToPartition.convert(eqCl, 1));
}
@Test
public void cuneane() throws NoSuchAtomException {
String acpString =
"C0C1C2C3C4C5C6C7 0:1(1),0:5(1),1:2(1),1:7(1),2:3(1),2:7(1),3:4(1),4:5(1),4:6(1),5:6(1),6:7(1)";
IAtomContainer cuneane = AtomContainerPrinter.fromString(acpString, builder);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(cuneane);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(cuneane);
System.out.println(Arrays.toString(eqCl));
System.out.println(ArrayToPartition.convert(eqCl, 1));
}
}
@Test
public void testVdWRadiusDescriptor()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {1.7};
IAtomicDescriptor descriptor = new VdWRadiusDescriptor();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles("NCCN(C)(C)");
double retval =
((DoubleResult) descriptor.calculate(mol.getAtom(1), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[0], retval, 0.01);
}
/**
* @cdk.bug 1965254
* @throws Exception
*/
@Test
public void testjunk() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("COC1=CC2=C(C=C1)NC3=C2CCNC3");
TemplateHandler3D template = TemplateHandler3D.getInstance();
ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template, "mm2");
molecule = mb3d.generate3DCoordinates(molecule, true);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
engine.process(molecule);
}
@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());
}
@Test
public void testModelBuilder3D_CccccC() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "CccccC";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles(smile);
addExplicitHydrogens(mol);
mol = mb3d.generate3DCoordinates(mol, false);
for (int i = 0; i < mol.getAtomCount(); i++) {
Assert.assertNotNull(mol.getAtom(i).getPoint3d());
}
checkAverageBondLength(mol);
// logger.debug("Layout molecule with SMILE: "+smile);
}
@Test
public void testRingFlags1() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("c1ccccc1");
new SSSRFinder(molecule).findSSSR();
int count = 0;
Iterator atoms = molecule.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = (IAtom) atoms.next();
if (atom.getFlag(CDKConstants.ISINRING)) count++;
}
Assert.assertEquals("All atoms in benzene were not marked as being in a ring", 6, count);
}
/**
* Checks if the given structures are isomorph.
*
* @param candidate1 the candidate1
* @param candidate2 the candidate2
* @return true, if is isomorph
* @throws CDKException the CDK exception
*/
public boolean isIsomorph(String candidate1, String candidate2) throws CDKException {
IAtomContainer cand1 = null;
IAtomContainer cand2 = null;
if (hasAtomContainer) {
cand1 = this.candidateToStructure.get(candidate1);
cand2 = this.candidateToStructure.get(candidate2);
} else {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
cand1 = sp.parseSmiles(candidatesToSmiles.get(candidate1));
cand2 = sp.parseSmiles(candidatesToSmiles.get(candidate2));
}
return UniversalIsomorphismTester.isIsomorph(cand1, cand2);
}
@Test
public void testModelBuilder3D_C1CCCCCCC1CC() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "C1CCCCCCC1CC";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles(smile);
addExplicitHydrogens(mol);
mol = mb3d.generate3DCoordinates(mol, false);
for (int i = 0; i < mol.getAtomCount(); i++) {
Assert.assertNotNull(mol.getAtom(i).getPoint3d());
}
checkAverageBondLength(mol);
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testDefaultValidFalse_SetParam()
throws ClassNotFoundException, CDKException, Exception {
IRule rule = new ChargeRule();
Object[] params = new Object[1];
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"), 2);
formula.addIsotope(builder.newIsotope("H"), 200);
formula.setCharge(1);
params[0] = -1.0;
rule.setParameters(params);
Assert.assertEquals(0.0, rule.validate(formula), 0.0001);
}
/**
* A unit test for JUnit
*
* @exception Exception Description of the Exception
*/
@Test
public void testResolveOverlap5() throws Exception {
double overlapScore = 0;
logger.debug("Test case with atom clash");
IAtomContainer atomContainer =
new SmilesParser(DefaultChemObjectBuilder.getInstance())
.parseSmiles("OC4C(N2C1=C(C(=NC(=N1)SC)SC)C3=C2N=CN=C3N)OC(C4O)CO");
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(new AtomContainer(atomContainer));
sdg.generateCoordinates();
atomContainer = sdg.getMolecule();
OverlapResolver or = new OverlapResolver();
overlapScore = or.resolveOverlap(atomContainer, null);
// MoleculeViewer2D.display(new AtomContainer(atomContainer), true);
Assert.assertEquals(0.0, overlapScore, 0.0001);
logger.debug("End of test case with atom clash");
}
/**
* Fixes Aromaticity of the molecule i.e. need to find rings and aromaticity again since added H's
*
* @param mol
*/
@TestMethod("testFixAromaticity")
public static void configure(IAtomContainer mol) {
// need to find rings and aromaticity again since added H's
IRingSet ringSet = null;
try {
AllRingsFinder arf = new AllRingsFinder();
ringSet = arf.findAllRings(mol);
} catch (Exception e) {
e.printStackTrace();
}
try {
// figure out which atoms are in aromatic rings:
CDKHydrogenAdder cdk = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
cdk.addImplicitHydrogens(mol);
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
// figure out which rings are aromatic:
RingSetManipulator.markAromaticRings(ringSet);
// figure out which simple (non cycles) rings are aromatic:
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is a part of
for (int i = 0; i < mol.getAtomCount(); i++) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, false);
jloop:
for (int j = 0; j < ringSet.getAtomContainerCount(); j++) {
// logger.debug(i+"\t"+j);
IRing ring = (IRing) ringSet.getAtomContainer(j);
if (!ring.getFlag(CDKConstants.ISAROMATIC)) {
continue jloop;
}
boolean haveatom = ring.contains(mol.getAtom(i));
// logger.debug("haveatom="+haveatom);
if (haveatom && ring.getAtomCount() == 6) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
@Test(timeout = 1000)
public void testPyrrole() throws Exception {
String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.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);
}
public static IAtomContainer makeFragment3() {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addAtom(new Atom("C")); // 6
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(0, 2, IBond.Order.SINGLE); // 2
mol.addBond(0, 3, IBond.Order.SINGLE); // 3
mol.addBond(0, 4, IBond.Order.SINGLE); // 4
mol.addBond(3, 5, IBond.Order.DOUBLE); // 5
mol.addBond(5, 6, IBond.Order.SINGLE); // 6
return mol;
}