/** 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);
}
/**
* Place all hydrogens connected to atoms which have already been laid out.
*
* @param container atom container
* @param bondLength bond length to user
*/
@TestMethod("testBug933572,testH2")
public void placeHydrogens2D(final IAtomContainer container, final double bondLength) {
logger.debug("placing hydrogens on all atoms");
for (IAtom atom : container.atoms()) {
// only place hydrogens for atoms which have coordinates
if (atom.getPoint2d() != null) {
placeHydrogens2D(container, atom, bondLength);
}
}
logger.debug("hydrogen placement complete");
}
/**
* Place hydrogens connected to the given atom using the average bond length in the container.
*
* @param container atom container of which <i>atom</i> is a member
* @param atom the atom of which to place connected hydrogens
* @throws IllegalArgumentException if the <i>atom</i> does not have 2d coordinates
* @see #placeHydrogens2D(org.openscience.cdk.interfaces.IAtomContainer, double)
*/
@TestMethod("testPlaceHydrogens2D")
public void placeHydrogens2D(IAtomContainer container, IAtom atom) {
double bondLength = GeometryTools.getBondLengthAverage(container);
placeHydrogens2D(container, atom, bondLength);
}
/** 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);
}
/** 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 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);
}