/** 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);
}
/**
* Loads one or more files into IAtomContainer objects.
*
* <p>This method does not need knowledge of the format since it is autodetected. Note that if
* aromaticity detection or atom typing is specified and fails for a specific molecule, that
* molecule will be set to <i>null</i>
*
* @param filenames An array of String's containing the filenames of the structures we want to
* load
* @param doAromaticity If true, then aromaticity perception is performed
* @param doTyping If true, atom typing and configuration is performed. This will use the internal
* CDK atom typing scheme
* @return An array of AtoContainer's
* @throws CDKException if there is an error when reading a file
*/
public static IAtomContainer[] loadMolecules(
String[] filenames, boolean doAromaticity, boolean doTyping, boolean doIsotopes)
throws CDKException, IOException {
Vector<IAtomContainer> v = new Vector<IAtomContainer>();
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
try {
int i;
int j;
for (i = 0; i < filenames.length; i++) {
File input = new File(filenames[i]);
ReaderFactory readerFactory = new ReaderFactory();
ISimpleChemObjectReader reader = readerFactory.createReader(new FileReader(input));
if (reader == null) { // see if it's a SMI file
if (filenames[i].endsWith(".smi")) {
reader = new SMILESReader(new FileReader(input));
}
}
IChemFile content = (IChemFile) reader.read(builder.newInstance(IChemFile.class));
if (content == null) continue;
List<IAtomContainer> c = ChemFileManipulator.getAllAtomContainers(content);
// we should do this loop in case we have files
// that contain multiple molecules
v.addAll(c);
}
} catch (Exception e) {
e.printStackTrace();
throw new CDKException(e.toString());
}
// convert the vector to a simple array
IAtomContainer[] retValues = new IAtomContainer[v.size()];
for (int i = 0; i < v.size(); i++) {
retValues[i] = v.get(i);
}
// before returning, lets make see if we
// need to perceive aromaticity and atom typing
if (doAromaticity) {
for (int i = 0; i < retValues.length; i++) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doTyping) {
for (int i = 0; i < retValues.length; i++) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doIsotopes) {
IsotopeFactory ifac = IsotopeFactory.getInstance(DefaultChemObjectBuilder.getInstance());
for (IAtomContainer retValue : retValues) {
ifac.configureAtoms(retValue);
}
}
return retValues;
}
/**
* Calculates the 3 MI's, 3 ration and the R_gyr value.
*
* <p>The molecule should have hydrogens
*
* @param container Parameter is the atom container.
* @return An ArrayList containing 7 elements in the order described above
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
if (!GeometryTools.has3DCoordinates(container))
return getDummyDescriptorValue(new CDKException("Molecule must have 3D coordinates"));
IAtomContainer clone;
IsotopeFactory factory;
try {
clone = (IAtomContainer) container.clone();
factory = IsotopeFactory.getInstance(container.getBuilder());
factory.configureAtoms(clone);
} catch (Exception e) {
logger.debug(e);
return getDummyDescriptorValue(e);
}
DoubleArrayResult retval = new DoubleArrayResult(7);
double ccf = 1.000138;
double eps = 1e-5;
double[][] imat = new double[3][3];
Point3d centerOfMass = GeometryTools.get3DCentreOfMass(clone);
double xdif;
double ydif;
double zdif;
double xsq;
double ysq;
double zsq;
for (int i = 0; i < clone.getAtomCount(); i++) {
IAtom currentAtom = clone.getAtom(i);
double mass = factory.getMajorIsotope(currentAtom.getSymbol()).getExactMass();
xdif = currentAtom.getPoint3d().x - centerOfMass.x;
ydif = currentAtom.getPoint3d().y - centerOfMass.y;
zdif = currentAtom.getPoint3d().z - centerOfMass.z;
xsq = xdif * xdif;
ysq = ydif * ydif;
zsq = zdif * zdif;
imat[0][0] += mass * (ysq + zsq);
imat[1][1] += mass * (xsq + zsq);
imat[2][2] += mass * (xsq + ysq);
imat[1][0] += -1 * mass * ydif * xdif;
imat[0][1] = imat[1][0];
imat[2][0] += -1 * mass * xdif * zdif;
imat[0][2] = imat[2][0];
imat[2][1] += -1 * mass * ydif * zdif;
imat[1][2] = imat[2][1];
}
// diagonalize the MI tensor
Matrix tmp = new Matrix(imat);
EigenvalueDecomposition eigenDecomp = tmp.eig();
double[] eval = eigenDecomp.getRealEigenvalues();
retval.add(eval[2]);
retval.add(eval[1]);
retval.add(eval[0]);
double etmp = eval[0];
eval[0] = eval[2];
eval[2] = etmp;
if (Math.abs(eval[1]) > 1e-3) retval.add(eval[0] / eval[1]);
else retval.add(1000);
if (Math.abs(eval[2]) > 1e-3) {
retval.add(eval[0] / eval[2]);
retval.add(eval[1] / eval[2]);
} else {
retval.add(1000);
retval.add(1000);
}
// finally get the radius of gyration
double pri;
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(clone);
if (Math.abs(eval[2]) > eps) pri = Math.pow(eval[0] * eval[1] * eval[2], 1.0 / 3.0);
else pri = Math.sqrt(eval[0] * ccf / MolecularFormulaManipulator.getTotalExactMass(formula));
retval.add(
Math.sqrt(
Math.PI * 2 * pri * ccf / MolecularFormulaManipulator.getTotalExactMass(formula)));
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), retval, getDescriptorNames());
}
/** 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);
}