/**
* 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));
}
/**
* 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));
}
@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);
}
@Test
public void testBond5() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' order='1 1'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(3, mol.getAtomCount());
Assert.assertEquals(2, mol.getBondCount());
org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
Assert.assertEquals(2, bond.getAtomCount());
Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
bond = mol.getBond(1);
Assert.assertEquals(2, bond.getAtomCount());
Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
}
@Test
public void testBond4() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' bondID='b1 b2'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(3, mol.getAtomCount());
Assert.assertEquals(2, mol.getBondCount());
org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
Assert.assertEquals(2, bond.getAtomCount());
IAtom atom1 = bond.getAtom(0);
IAtom atom2 = bond.getAtom(1);
Assert.assertEquals("a1", atom1.getID());
Assert.assertEquals("a2", atom2.getID());
Assert.assertEquals("b2", mol.getBond(1).getID());
}
@Test
public void testBondStereo() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'><bondStereo dictRef='cml:H'/></bond></bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
IBond bond = mol.getBond(0);
Assert.assertEquals(IBond.Stereo.DOWN, bond.getStereo());
}
/**
* 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 testBondAromatic2() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray atomID='a1 a2'/><bondArray><bond atomRefs='a1 a2' order='2'><bondType dictRef='cdk:aromaticBond'/></bond></bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond.getOrder());
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
}
@Test
public void testBondId() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
Assert.assertEquals("b1", bond.getID());
}
/**
* 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;
}
/**
* Get the container which is found resonance from a IMolecule. It is based on looking if the
* order of the bond changes.
*
* @param molecule The IMolecule to analyze
* @return The different containers
*/
@TestMethod("testGetContainers_IMolecule")
public IAtomContainerSet getContainers(IMolecule molecule) {
IAtomContainerSet setOfCont = molecule.getBuilder().newAtomContainerSet();
IMoleculeSet setOfMol = getStructures(molecule);
if (setOfMol.getMoleculeCount() == 0) return setOfCont;
/*extraction of all bonds which has been produced a changes of order*/
List<IBond> bondList = new ArrayList<IBond>();
for (int i = 1; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (int j = 0; j < mol.getBondCount(); j++) {
IBond bond = molecule.getBond(j);
if (!mol.getBond(j).getOrder().equals(bond.getOrder())) {
if (!bondList.contains(bond)) bondList.add(bond);
}
}
}
if (bondList.size() == 0) return null;
int[] flagBelonging = new int[bondList.size()];
for (int i = 0; i < flagBelonging.length; i++) flagBelonging[i] = 0;
int[] position = new int[bondList.size()];
int maxGroup = 1;
/*Analysis if the bond are linked together*/
List<IBond> newBondList = new ArrayList<IBond>();
newBondList.add(bondList.get(0));
int pos = 0;
for (int i = 0; i < newBondList.size(); i++) {
if (i == 0) flagBelonging[i] = maxGroup;
else {
if (flagBelonging[position[i]] == 0) {
maxGroup++;
flagBelonging[position[i]] = maxGroup;
}
}
IBond bondA = newBondList.get(i);
for (int ato = 0; ato < 2; ato++) {
IAtom atomA1 = bondA.getAtom(ato);
List<IBond> bondA1s = molecule.getConnectedBondsList(atomA1);
for (int j = 0; j < bondA1s.size(); j++) {
IBond bondB = bondA1s.get(j);
if (!newBondList.contains(bondB))
for (int k = 0; k < bondList.size(); k++)
if (bondList.get(k).equals(bondB))
if (flagBelonging[k] == 0) {
flagBelonging[k] = maxGroup;
pos++;
newBondList.add(bondB);
position[pos] = k;
}
}
}
// if it is final size and not all are added
if (newBondList.size() - 1 == i)
for (int k = 0; k < bondList.size(); k++)
if (!newBondList.contains(bondList.get(k))) {
newBondList.add(bondList.get(k));
position[i + 1] = k;
break;
}
}
/*creating containers according groups*/
for (int i = 0; i < maxGroup; i++) {
IAtomContainer container = molecule.getBuilder().newAtomContainer();
for (int j = 0; j < bondList.size(); j++) {
if (flagBelonging[j] != i + 1) continue;
IBond bond = bondList.get(j);
IAtom atomA1 = bond.getAtom(0);
IAtom atomA2 = bond.getAtom(1);
if (!container.contains(atomA1)) container.addAtom(atomA1);
if (!container.contains(atomA2)) container.addAtom(atomA2);
container.addBond(bond);
}
setOfCont.addAtomContainer(container);
}
return setOfCont;
}