/** A unit test for JUnit */
@Test
public void testAlanin() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("N", new Point2d(1, 0)));
// 1
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 2
mol1.addAtom(new Atom("F", new Point2d(1, 2)));
// 3
mol1.addAtom(new Atom("C", new Point2d(0, 0)));
// 4
mol1.addAtom(new Atom("C", new Point2d(1, 4)));
// 5
mol1.addAtom(new Atom("O", new Point2d(1, 5)));
// 6
mol1.addAtom(new Atom("O", new Point2d(1, 6)));
// 7
mol1.addBond(0, 1, IBond.Order.SINGLE);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE, IBond.Stereo.UP);
// 2
mol1.addBond(1, 3, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 3
mol1.addBond(1, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(4, 5, IBond.Order.SINGLE);
// 5
mol1.addBond(4, 6, IBond.Order.DOUBLE);
// 6
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
String smiles1 = null;
if (standAlone) {
display(mol1);
}
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("[H]OC(=O)[C@](F)(N([H])[H])C([H])([H])[H]", smiles1);
mol1.getBond(1).setStereo(IBond.Stereo.DOWN);
mol1.getBond(2).setStereo(IBond.Stereo.UP);
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("[H]OC(=O)[C@](F)(C([H])([H])[H])N([H])[H]", smiles1);
}
/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers of another
* AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
@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]));
}
private boolean unMappedAtomsEqualsIndexJ(
IAtomContainer target,
int mappingSize,
int atomIndex,
int counter,
List<Integer> mapped_atoms,
Integer indexI,
Integer indexJ,
Integer order) {
boolean normal_bond = true;
for (int c = 0; c < mappingSize; c++) {
if (mapped_atoms.get(c * 2 + 1).equals(indexI)) {
setBondNeighbors(indexI, indexJ, order);
if (cTab2Copy.get(atomIndex * 4 + 2).compareToIgnoreCase("X") == 0) {
step3(atomIndex, counter);
McGregorChecks.changeCharBonds(
indexI, signArray[counter], target.getBondCount(), target, cTab2Copy);
int cor_atom =
McGregorChecks.searchCorrespondingAtom(mappingSize, indexI, 2, mapped_atoms);
McGregorChecks.changeCharBonds(
cor_atom, signArray[counter], newNeighborNumA, newINeighborsA, newCNeighborsA);
// changeCharBonds(cor_atom, signArray[counter],
// query.getBondCount(), query, cTab1Copy);
counter++;
} else {
step4(atomIndex);
}
normal_bond = false;
neighborBondNumB++;
}
}
return normal_bond;
}
/**
* Helper method, used to help construct a configuration.
*
* @param bond
* @param container
* @return the array position of the bond in the container
*/
private int getBondPosition(IBond bond, IAtomContainer container) {
for (int i = 0; i < container.getBondCount(); i++) {
if (bond.equals(container.getBond(i))) {
return i;
}
}
return -1;
}
/**
* Creates a bucky ball molecule.
*
* @return bucky ball molecule
*/
private IAtomContainer createBuckyBall() throws CDKException {
IAtomContainer molecule = null;
String filename = "data/mdl/buckyball.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
molecule = (IAtomContainer) reader.read(new AtomContainer());
Assert.assertTrue("Atom count is 60 ", molecule.getAtomCount() == 60);
Assert.assertTrue("Bond count is 90 ", molecule.getBondCount() == 90);
return molecule;
}
public static void checkAverageBondLength(IAtomContainer ac) {
double avlength = GeometryTools.getBondLengthAverage3D(ac);
for (int i = 0; i < ac.getBondCount(); i++) {
double distance =
ac.getBond(i).getAtom(0).getPoint3d().distance(ac.getBond(i).getAtom(1).getPoint3d());
Assert.assertTrue(
"Unreasonable bond length (" + distance + ") for bond " + i,
distance >= avlength / 2 && distance <= avlength * 2);
}
}
/**
* Removes all atoms and electronContainers of a given atomcontainer from this container.
*
* @param atomContainer The atomcontainer to be removed
*/
public void remove(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
removeAtom(atomContainer.getAtom(f));
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
removeBond(atomContainer.getBond(f));
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
removeLonePair(atomContainer.getLonePair(f));
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
removeSingleElectron(atomContainer.getSingleElectron(f));
}
}
/**
* Prepare a collection of molecules for rendering. If coordinates are not present they are
* generated, if coordinates exists they are scaled to be consistent (length=1.5).
*
* @param mols molecules
* @return coordinates
* @throws CDKException
*/
private List<Double> prepareCoords(Iterable<IAtomContainer> mols) throws CDKException {
List<Double> scaleFactors = new ArrayList<>();
for (IAtomContainer mol : mols) {
if (ensure2dLayout(mol)) {
scaleFactors.add(Double.NaN);
} else if (mol.getBondCount() > 0) {
final double factor = GeometryUtil.getScaleFactor(mol, 1.5);
GeometryUtil.scaleMolecule(mol, factor);
scaleFactors.add(factor);
} else {
scaleFactors.add(1d); // no bonds
}
}
return scaleFactors;
}
private synchronized IQuery build(IAtomContainer queryMolecule) {
VFQueryBuilder result = new VFQueryBuilder();
for (IAtom atom : queryMolecule.atoms()) {
AtomMatcher matcher = createAtomMatcher(queryMolecule, atom);
if (matcher != null) {
result.addNode(matcher, atom);
}
}
for (int i = 0; i < queryMolecule.getBondCount(); i++) {
IBond bond = queryMolecule.getBond(i);
IAtom atomI = bond.getAtom(0);
IAtom atomJ = bond.getAtom(1);
result.connect(
result.getNode(atomI), result.getNode(atomJ), createBondMatcher(queryMolecule, bond));
}
return result;
}
public String getSMILES(IAtomContainer molecule) throws CDKException {
String smiles = "";
if (molecule.getAtomCount() == 0) {
return smiles;
}
SmilesGenerator sg = new SmilesGenerator(true);
AllRingsFinder arf = new AllRingsFinder();
IRingSet findAllRings = arf.findAllRings(molecule);
sg.setRings(findAllRings);
sg.setRingFinder(arf);
smiles = sg.createSMILES(molecule, false, new boolean[molecule.getBondCount()]);
return smiles;
}
@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);
}
protected void process(
IAtomContainer target,
List<Integer> unmapped_atoms_molB,
int mappingSize,
List<Integer> i_bond_setB,
List<String> c_bond_setB,
List<Integer> mapped_atoms,
int counter) {
int unmapped_numB = unmapped_atoms_molB.size();
boolean bond_considered = false;
boolean normal_bond = true;
for (int atomIndex = 0; atomIndex < target.getBondCount(); atomIndex++) {
Integer indexI = target.getAtomNumber(target.getBond(atomIndex).getAtom(0));
Integer indexJ = target.getAtomNumber(target.getBond(atomIndex).getAtom(1));
IBond bond = target.getBond(atomIndex);
Integer order = (bond.getOrder().ordinal() + 1);
for (int b = 0; b < unmapped_numB; b++) {
if (unmapped_atoms_molB.get(b).equals(indexI)) {
normal_bond =
unMappedAtomsEqualsIndexI(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
} else if (unmapped_atoms_molB.get(b) == indexJ) {
normal_bond =
unMappedAtomsEqualsIndexJ(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
}
if (normal_bond && bond_considered) {
markNormalBonds(atomIndex, i_bond_setB, c_bond_setB, indexI, indexJ, order);
normal_bond = true;
break;
}
}
bond_considered = false;
}
}
@Test
public void testLargeRingSystem() throws Exception {
String smiles = "O=C1Oc6ccccc6(C(O)C1C5c2ccccc2CC(c3ccc(cc3)c4ccccc4)C5)";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(34, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(13, doubleBondCount);
}
/** @cdk.bug 3506770 */
@Test
public void testLargeBioclipseUseCase() throws Exception {
String smiles =
"COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(40, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(10, doubleBondCount);
}
@Test
public void testSplit() throws CDKException {
IAtomContainer mol = smilesParser.parseSmiles("C1CC1C2CCC2");
SpanningTree st = new SpanningTree(mol);
IRingSet rings = st.getAllRings();
IBond splitBond = null;
for (int i = 0; i < mol.getBondCount(); i++) {
if (rings.getRings(mol.getBond(i)).getAtomContainerCount() == 0) {
splitBond = mol.getBond(i);
break;
}
}
List<IAtomContainer> frags = FragmentUtils.splitMolecule(mol, splitBond);
SmilesGenerator sg = new SmilesGenerator();
Set<String> uniqueFrags = new HashSet<String>();
for (IAtomContainer frag : frags) {
uniqueFrags.add(sg.createSMILES(frag));
}
Assert.assertEquals(2, uniqueFrags.size());
// You can put the fragments back together with a ring closure and dot
// [CH]12CC1.[CH]12CCC1
Assert.assertThat(uniqueFrags, hasItems("[CH]1CC1", "[CH]1CCC1"));
}
/** A unit test for JUnit */
@Test
public void testCisResorcinol() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("O", new Point2d(3, 1)));
// 1
mol1.addAtom(new Atom("H", new Point2d(2, 0)));
// 2
mol1.addAtom(new Atom("C", new Point2d(2, 1)));
// 3
mol1.addAtom(new Atom("C", new Point2d(1, 1)));
// 4
mol1.addAtom(new Atom("C", new Point2d(1, 4)));
// 5
mol1.addAtom(new Atom("C", new Point2d(1, 5)));
// 6
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 7
mol1.addAtom(new Atom("C", new Point2d(2, 2)));
// 1
mol1.addAtom(new Atom("O", new Point2d(3, 2)));
// 2
mol1.addAtom(new Atom("H", new Point2d(2, 3)));
// 3
mol1.addBond(0, 2, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE, IBond.Stereo.UP);
// 2
mol1.addBond(2, 3, IBond.Order.SINGLE);
// 3
mol1.addBond(3, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(4, 5, IBond.Order.SINGLE);
// 5
mol1.addBond(5, 6, IBond.Order.SINGLE);
// 6
mol1.addBond(6, 7, IBond.Order.SINGLE);
// 3
mol1.addBond(7, 8, IBond.Order.SINGLE, IBond.Stereo.UP);
// 4
mol1.addBond(7, 9, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 5
mol1.addBond(7, 2, IBond.Order.SINGLE);
// 6
try {
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
} catch (IOException ex) {
} catch (ClassNotFoundException ex) {
}
String smiles1 = null;
if (standAlone) {
display(mol1);
}
try {
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals(
"[H]O[C@]1(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1(O[H])([H]))([H])", smiles1);
mol1 = AtomContainerManipulator.removeHydrogens(mol1);
try {
smiles1 = sg.createSMILES(mol1);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("OC1CCCCC1(O)", smiles1);
}
/** A unit test for JUnit */
@Test
public void testCisTransDecalin() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("H", new Point2d(1, 0)));
// 1
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 2
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 3
mol1.addAtom(new Atom("C", new Point2d(0, 0)));
// 4
mol1.addAtom(new Atom("C", new Point2d(1, 4)));
// 5
mol1.addAtom(new Atom("C", new Point2d(1, 5)));
// 6
mol1.addAtom(new Atom("C", new Point2d(1, 6)));
// 7
mol1.addAtom(new Atom("H", new Point2d(1, 0)));
// 1
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 2
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 3
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 2
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 3
mol1.addBond(0, 1, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE);
// 2
mol1.addBond(2, 3, IBond.Order.SINGLE);
// 3
mol1.addBond(3, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(4, 5, IBond.Order.SINGLE);
// 5
mol1.addBond(5, 6, IBond.Order.SINGLE);
// 6
mol1.addBond(6, 7, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 3
mol1.addBond(6, 8, IBond.Order.SINGLE);
// 4
mol1.addBond(8, 9, IBond.Order.SINGLE);
// 5
mol1.addBond(9, 10, IBond.Order.SINGLE);
// 6
mol1.addBond(10, 11, IBond.Order.SINGLE);
// 6
mol1.addBond(11, 1, IBond.Order.SINGLE);
// 6
mol1.addBond(1, 6, IBond.Order.SINGLE);
// 6
try {
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
} catch (IOException ex) {
} catch (ClassNotFoundException ex) {
}
String smiles1 = null;
if (standAlone) {
display(mol1);
}
try {
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals(
"[H]C1([H])(C([H])([H])C([H])([H])C\\2([H])(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C\\2([H])(C1([H])([H]))))",
smiles1);
mol1.getBond(6).setStereo(IBond.Stereo.UP);
String smiles3 = null;
try {
smiles3 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
Assert.assertNotSame(smiles3, smiles1);
}
/** A unit test for JUnit */
@Test
public void testDoubleBondConfiguration() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("S", new Point2d(0, 0)));
// 1
mol1.addAtom(new Atom("C", new Point2d(1, 1)));
// 2
mol1.addAtom(new Atom("F", new Point2d(2, 0)));
// 3
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 4
mol1.addAtom(new Atom("F", new Point2d(2, 3)));
// 5
mol1.addAtom(new Atom("S", new Point2d(0, 3)));
// 1
mol1.addBond(0, 1, IBond.Order.SINGLE);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE);
// 2
mol1.addBond(1, 3, IBond.Order.DOUBLE);
// 3
mol1.addBond(3, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(3, 5, IBond.Order.SINGLE);
// 4
try {
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
} catch (IOException ex) {
}
String smiles1 = null;
if (standAlone) {
display(mol1);
}
boolean[] bool = new boolean[mol1.getBondCount()];
bool[2] = true;
try {
smiles1 = sg.createSMILES(mol1, true, bool);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("F/C(=C/(F)S)S", smiles1);
mol1.getAtom(4).setPoint2d(new Point2d(0, 3));
mol1.getAtom(5).setPoint2d(new Point2d(2, 3));
try {
smiles1 = sg.createSMILES(mol1, true, bool);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("F/C(=C\\(F)S)S", smiles1);
try {
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
} catch (IOException ex) {
} catch (ClassNotFoundException ex) {
}
bool = new boolean[mol1.getBondCount()];
bool[2] = true;
try {
smiles1 = sg.createSMILES(mol1, true, bool);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
Assert.assertEquals("[H]S/C(F)=C/(F)S[H]", smiles1);
mol1.getAtom(5).setPoint2d(new Point2d(0, 3));
mol1.getAtom(4).setPoint2d(new Point2d(2, 3));
try {
smiles1 = sg.createSMILES(mol1, true, bool);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
Assert.assertEquals("[H]S/C(F)=C\\(F)S[H]", smiles1);
}