/**
* A unit test suite for JUnit.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMoleculeSet setOfReactants = builder.newMoleculeSet();
IMolecule molecule = getEthene();
/*manually putting the active center*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
setOfReactants.addMolecule(molecule);
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);
IMolecule reactant = setOfReactions.getReaction(0).getReactants().getMolecule(0);
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
}
@Test
public void testFractional3D() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray atomID='a1 a2' xFract='0.0 0.1' yFract='1.2 1.3' zFract='2.1 2.5'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertNull(mol.getAtom(0).getPoint3d());
Assert.assertNull(mol.getAtom(1).getPoint3d());
Assert.assertNotNull(mol.getAtom(0).getFractionalPoint3d());
Assert.assertNotNull(mol.getAtom(1).getFractionalPoint3d());
}
/**
* A unit test suite for JUnit for Ethene. Reaction: O=C-C-H => O(H)-C=C. Manually putting for
* active center.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testManuallyCentreActive() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMolecule molecule = getEthene();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
/*manually putting the active center*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
/* initiate */
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
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));
}
/** A unit test for JUnit with ethoxyethane */
@Test
public void testPartialTotalChargeDescriptor_Ethoxyethane()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
0.28, -0.56, 0.28,
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
// IMolecule mol = sp.parseSmiles("COC");
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom carbon = builder.newInstance(IAtom.class, Elements.CARBON);
IAtom oxygen = builder.newInstance(IAtom.class, Elements.OXYGEN);
IAtom carbon2 = builder.newInstance(IAtom.class, Elements.CARBON);
// making sure the order matches the test results
mol.addAtom(carbon);
mol.addAtom(oxygen);
mol.addAtom(carbon2);
mol.addBond(builder.newInstance(IBond.class, carbon, oxygen, CDKConstants.BONDORDER_SINGLE));
mol.addBond(builder.newInstance(IBond.class, carbon2, oxygen, CDKConstants.BONDORDER_SINGLE));
addExplicitHydrogens(mol);
for (int i = 0; i < 3; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
/** @cdk.bug 2142400 */
@Test
public void testHydrogenCount2() throws Exception {
String cmlString =
"<molecule><atomArray>"
+ "<atom id='a1' elementType='C' hydrogenCount='4'/>"
+ "<atom id='a2' elementType='H'/>"
+ "<atom id='a3' elementType='H'/>"
+ "<atom id='a4' elementType='H'/>"
+ "<atom id='a5' elementType='H'/>"
+ "</atomArray>"
+ "<bondArray>"
+ "<bond id='b1' atomRefs2='a1 a2' order='S'/>"
+ "<bond id='b2' atomRefs2='a1 a3' order='S'/>"
+ "<bond id='b3' atomRefs2='a1 a4' order='S'/>"
+ "<bond id='b4' atomRefs2='a1 a5' order='S'/>"
+ "</bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(5, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertNotNull(atom);
Assert.assertEquals("C", atom.getSymbol());
Assert.assertNotNull(atom.getImplicitHydrogenCount());
Assert.assertEquals(0, atom.getImplicitHydrogenCount().intValue());
}
@Test
public void testMissing3DCoordinates() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray><atom id='a1' xyz3='0.0 0.1 0.2'/><atom id='a2'/><atom id='a3' xyz3='0.1 0.0 0.2'/></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(3, mol.getAtomCount());
IAtom atom1 = mol.getAtom(0);
IAtom atom2 = mol.getAtom(1);
IAtom atom3 = mol.getAtom(2);
Assert.assertNotNull(atom1.getPoint3d());
Assert.assertNull(atom2.getPoint3d());
Assert.assertNotNull(atom3.getPoint3d());
}
@Test
public void testReading3DCoords() throws Exception {
String filename = "data/asn/pubchem/cid176.xml";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
PCCompoundXMLReader reader = new PCCompoundXMLReader(ins);
IMolecule molecule = (IMolecule) reader.read(new Molecule());
Assert.assertNotNull(molecule);
// check atom stuff
Assert.assertEquals(8, molecule.getAtomCount());
Assert.assertNull(molecule.getAtom(0).getPoint2d());
Point3d point = molecule.getAtom(0).getPoint3d();
Assert.assertNotNull(point);
Assert.assertEquals(-0.9598, point.x, 0.0001);
Assert.assertEquals(1.5616, point.y, 0.0001);
Assert.assertEquals(1.8714, point.z, 0.0001);
}
/**
* Bug #1610997 says the modelbuilder does not work if 2d coordinates exist before - we test this
* here
*
* @cdk.bug 1610997
*/
@Test
public void testModelBuilder3D_CCCCCCCCCC_with2d() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "CCCCCCCCCC";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles(smile);
for (int i = 0; i < mol.getAtomCount(); i++) {
mol.getAtom(i).setPoint2d(new Point2d(1, 1));
}
addExplicitHydrogens(mol);
mol = mb3d.generate3DCoordinates(mol, false);
for (int i = 0; i < mol.getAtomCount(); i++) {
Assert.assertNotNull(mol.getAtom(i).getPoint3d());
}
checkAverageBondLength(mol);
}
@Test
public void testAtomElementType3() throws Exception {
String cmlString = "<molecule id='m1'><atomArray atomID='a1' elementType='C'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertEquals("C", atom.getSymbol());
}
@Test
public void testAtomId3() throws Exception {
String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2 a3'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(3, mol.getAtomCount());
IAtom atom = mol.getAtom(1);
Assert.assertEquals("a2", atom.getID());
}
@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);
}
// A unit test for JUnit with methylenfluoride\
@Test
public void testModelBuilder3D_CF() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
Point3d c_coord = new Point3d(1.392, 0.0, 0.0);
Point3d f_coord = new Point3d(0.0, 0.0, 0.0);
Point3d h1_coord = new Point3d(1.7439615035767404, 1.0558845107302222, 0.0);
Point3d h2_coord = new Point3d(1.7439615035767404, -0.5279422553651107, 0.914422809754875);
Point3d h3_coord = new Point3d(1.7439615035767402, -0.5279422553651113, -0.9144228097548747);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles("CF");
addExplicitHydrogens(mol);
// mb3d.setTemplateHandler();
mol = mb3d.generate3DCoordinates(mol, false);
assertEquals(c_coord, mol.getAtom(0).getPoint3d(), 0.0001);
assertEquals(f_coord, mol.getAtom(1).getPoint3d(), 0.0001);
assertEquals(h1_coord, mol.getAtom(2).getPoint3d(), 0.0001);
assertEquals(h2_coord, mol.getAtom(3).getPoint3d(), 0.0001);
assertEquals(h3_coord, mol.getAtom(4).getPoint3d(), 0.0001);
checkAverageBondLength(mol);
}
@Test
public void testReading() throws Exception {
String filename = "data/asn/pubchem/cid1145.xml";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
PCCompoundXMLReader reader = new PCCompoundXMLReader(ins);
IMolecule molecule = (IMolecule) reader.read(new Molecule());
Assert.assertNotNull(molecule);
// check atom stuff
Assert.assertEquals(14, molecule.getAtomCount());
Assert.assertEquals("O", molecule.getAtom(0).getSymbol());
Assert.assertEquals(Integer.valueOf(-1), molecule.getAtom(0).getFormalCharge());
Assert.assertEquals("N", molecule.getAtom(1).getSymbol());
Assert.assertEquals(Integer.valueOf(1), molecule.getAtom(1).getFormalCharge());
// check bond stuff
Assert.assertEquals(13, molecule.getBondCount());
Assert.assertNotNull(molecule.getBond(3));
// coordinates
Assert.assertNull(molecule.getAtom(0).getPoint3d());
Point2d point = molecule.getAtom(0).getPoint2d();
Assert.assertNotNull(point);
Assert.assertEquals(3.7320508956909, point.x, 0.00000001);
Assert.assertEquals(0.5, point.y, 0.00000001);
}
/**
* A unit test suite for JUnit.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testMapping() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
IMolecule molecule = getEthene();
setOfReactants.addMolecule(molecule);
/*automatic looking for active center*/
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);
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
Assert.assertEquals(3, setOfReactions.getReaction(0).getMappingCount());
IAtom mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(0));
Assert.assertEquals(mappedProductA1, product.getAtom(0));
mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(1));
Assert.assertEquals(mappedProductA1, product.getAtom(1));
IBond mappedProductB1 =
(IBond)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getBond(0));
Assert.assertEquals(mappedProductB1, product.getBond(0));
}
@Test
public void testIsotopicMass() throws Exception {
String cmlString =
"<molecule><atomArray><atom id='a1' elementType=\"C\"><scalar dataType=\"xsd:float\" dictRef=\"cdk:isotopicMass\">12.0</scalar></atom></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertEquals("C", atom.getSymbol());
Assert.assertEquals(12.0, atom.getExactMass().doubleValue(), 0.01);
}
@Test
public void testMassNumber() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray><atom id='a1' elementType='C' isotopeNumber='12'/></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertEquals("C", atom.getSymbol());
Assert.assertEquals(12, atom.getMassNumber().intValue());
}
@Test
public void testAtomicNumber() throws Exception {
String cmlString =
"<molecule><atomArray><atom id='a1' elementType=\"C\"><scalar dataType=\"xsd:integer\" dictRef=\"cdk:atomicNumber\">6</scalar></atom></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertEquals("C", atom.getSymbol());
Assert.assertEquals(6, atom.getAtomicNumber().intValue());
}
@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);
}
/** @cdk.bug 2142400 */
@Test
public void testHydrogenCount1() throws Exception {
String cmlString =
"<molecule><atomArray><atom id='a1' elementType='C' hydrogenCount='4'/></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertNotNull(atom);
Assert.assertNotNull(atom.getImplicitHydrogenCount());
Assert.assertEquals(4, atom.getImplicitHydrogenCount().intValue());
}
@Test
public void testModelBuilder3D_reserpine() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/reserpine.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
ac = mb3d.generate3DCoordinates(ac, false);
for (int i = 0; i < ac.getAtomCount(); i++) {
Assert.assertNotNull(ac.getAtom(i).getPoint3d());
}
checkAverageBondLength(ac);
}
@Test
public void testModelBuilder3D_Konstanz() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile =
"C12(-[H])-C3(-C(-[H])(-[H])-C(-C4(-C5(-C(-Cl)(-Cl)-C(-C-3-4-[H])(-Cl)-C(-Cl)(-[H])-C-5(-Cl)-[H])-Cl)-[H])(-[H])-C-2(-O-1)-[H])-[H]";
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);
}
/** @cdk.bug 1315823 */
@Test
public void testModelBuilder3D_232() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/allmol232.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
addExplicitHydrogens(ac);
ac = mb3d.generate3DCoordinates(ac, false);
Assert.assertNotNull(ac.getAtom(0).getPoint3d());
checkAverageBondLength(ac);
}
/** A unit test for JUnit with Water */
@Test
public void testPartialTotalChargeDescriptor_Water()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
-0.86, 0.43, 0.43
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom oxygen = builder.newInstance(IAtom.class, Elements.OXYGEN);
// making sure the order matches the test results
mol.addAtom(oxygen);
addExplicitHydrogens(mol);
for (int i = 0; i < 3; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
/**
* Get the expected structure.
*
* @return The IMolecule
* @throws CDKException
*/
private IMolecule getExpected() throws Exception {
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.getAtom(0).setFormalCharge(1);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addBond(0, 2, IBond.Order.SINGLE);
molecule.addBond(0, 3, IBond.Order.SINGLE);
molecule.addBond(1, 4, IBond.Order.SINGLE);
molecule.addBond(1, 5, IBond.Order.SINGLE);
molecule.addBond(1, 6, IBond.Order.SINGLE);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(molecule);
return molecule;
}
/**
* Choose any possible quadruple of the set of atoms in ac and establish all of the possible
* bonding schemes according to Faulon's equations.
*/
public static List sample(IMolecule ac) {
logger.debug("RandomGenerator->mutate() Start");
List structures = new ArrayList();
int nrOfAtoms = ac.getAtomCount();
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
double b12 = 0;
double b21 = 0;
double b22 = 0;
double[] cmax = new double[4];
double[] cmin = new double[4];
IAtomContainer newAc = null;
IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
IBond b1 = null, b2 = null, b3 = null, b4 = null;
// int[] choices = new int[3];
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
for (int x1 = 0; x1 < nrOfAtoms; x1++) {
for (int x2 = x1 + 1; x2 < nrOfAtoms; x2++) {
for (int y1 = x2 + 1; y1 < nrOfAtoms; y1++) {
for (int y2 = y1 + 1; y2 < nrOfAtoms; y2++) {
nonZeroBondsCounter = 0;
ax1 = ac.getAtom(x1);
ay1 = ac.getAtom(y1);
ax2 = ac.getAtom(x2);
ay2 = ac.getAtom(y2);
/* Get four bonds for these four atoms */
b1 = ac.getBond(ax1, ay1);
if (b1 != null) {
a11 = BondManipulator.destroyBondOrder(b1.getOrder());
nonZeroBondsCounter++;
} else {
a11 = 0;
}
b2 = ac.getBond(ax1, ay2);
if (b2 != null) {
a12 = BondManipulator.destroyBondOrder(b2.getOrder());
nonZeroBondsCounter++;
} else {
a12 = 0;
}
b3 = ac.getBond(ax2, ay1);
if (b3 != null) {
a21 = BondManipulator.destroyBondOrder(b3.getOrder());
nonZeroBondsCounter++;
} else {
a21 = 0;
}
b4 = ac.getBond(ax2, ay2);
if (b4 != null) {
a22 = BondManipulator.destroyBondOrder(b4.getOrder());
nonZeroBondsCounter++;
} else {
a22 = 0;
}
if (nonZeroBondsCounter > 1) {
/* Compute the range for b11 (see Faulons formulae for details) */
cmax[0] = 0;
cmax[1] = a11 - a22;
cmax[2] = a11 + a12 - 3;
cmax[3] = a11 + a21 - 3;
cmin[0] = 3;
cmin[1] = a11 + a12;
cmin[2] = a11 + a21;
cmin[3] = a11 - a22 + 3;
lowerborder = MathTools.max(cmax);
upperborder = MathTools.min(cmin);
for (b11 = lowerborder; b11 <= upperborder; b11++) {
if (b11 != a11) {
b12 = a11 + a12 - b11;
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
logger.debug("Trying atom combination : " + x1 + ":" + x2 + ":" + y1 + ":" + y2);
try {
newAc = (IAtomContainer) ac.clone();
change(newAc, x1, y1, x2, y2, b11, b12, b21, b22);
if (ConnectivityChecker.isConnected(newAc)) {
structures.add(newAc);
} else {
logger.debug("not connected");
}
} catch (CloneNotSupportedException e) {
logger.error("Cloning exception: " + e.getMessage());
logger.debug(e);
}
}
}
}
}
}
}
}
return structures;
}
/** A unit test for JUnit with Benzene */
@Test
public void testPartialTotalChargeDescriptor_Benzene()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
// IMolecule mol = sp.parseSmiles("c1ccccc1");
IMolecule mol = builder.newInstance(IMolecule.class);
for (int i = 0; i < 6; i++) {
IAtom carbon = builder.newInstance(IAtom.class, Elements.CARBON);
carbon.setFlag(CDKConstants.ISAROMATIC, true);
// making sure the order matches the test results
mol.addAtom(carbon);
}
IBond ringBond =
builder.newInstance(
IBond.class, mol.getAtom(0), mol.getAtom(1), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(1), mol.getAtom(2), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(2), mol.getAtom(3), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(3), mol.getAtom(4), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(4), mol.getAtom(5), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(5), mol.getAtom(0), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
addExplicitHydrogens(mol);
for (int i = 0; i < 12; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
