/**
* Modules for cleaning a molecule
*
* @param molecule
* @return cleaned AtomContainer
*/
@TestMethod("testCheckAndCleanMolecule")
public static IAtomContainer checkAndCleanMolecule(IAtomContainer molecule) {
boolean isMarkush = false;
for (IAtom atom : molecule.atoms()) {
if (atom.getSymbol().equals("R")) {
isMarkush = true;
break;
}
}
if (isMarkush) {
System.err.println("Skipping Markush structure for sanity check");
}
// Check for salts and such
if (!ConnectivityChecker.isConnected(molecule)) {
// lets see if we have just two parts if so, we assume its a salt and just work
// on the larger part. Ideally we should have a check to ensure that the smaller
// part is a metal/halogen etc.
IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(molecule);
if (fragments.getMoleculeCount() > 2) {
System.err.println("More than 2 components. Skipped");
} else {
IMolecule frag1 = fragments.getMolecule(0);
IMolecule frag2 = fragments.getMolecule(1);
if (frag1.getAtomCount() > frag2.getAtomCount()) {
molecule = frag1;
} else {
molecule = frag2;
}
}
}
configure(molecule);
return molecule;
}
/** @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 for SF bug #1309731.
*
* @cdk.bug 1309731
*/
@Test
public void testModelBuilder3D_keepChemObjectIDs() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
IMolecule methanol = new org.openscience.cdk.Molecule();
IChemObjectBuilder builder = methanol.getBuilder();
IAtom carbon1 = builder.newInstance(IAtom.class, "C");
carbon1.setID("carbon1");
methanol.addAtom(carbon1);
for (int i = 0; i < 3; i++) {
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE));
}
IAtom oxygen1 = builder.newInstance(IAtom.class, "O");
oxygen1.setID("oxygen1");
methanol.addAtom(oxygen1);
methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE));
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE));
Assert.assertEquals(6, methanol.getAtomCount());
Assert.assertEquals(5, methanol.getBondCount());
mb3d.generate3DCoordinates(methanol, false);
checkAverageBondLength(methanol);
Assert.assertEquals("carbon1", carbon1.getID());
Assert.assertEquals("oxygen1", oxygen1.getID());
}
@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);
}
/**
* 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 testNNMolecule_int_int_int_int() {
IMolecule m = new NNMolecule(5, 5, 1, 1);
Assert.assertNotNull(m);
Assert.assertEquals(0, m.getAtomCount());
Assert.assertEquals(0, m.getBondCount());
Assert.assertEquals(0, m.getLonePairCount());
Assert.assertEquals(0, m.getSingleElectronCount());
}
/** Sets the format origin and tries to find a good title */
protected void setMetaData(MoleculeType molMolecule, IMolecule molStructure) {
if (molStructure != null) {
if (molStructure.getProperty("cdk:Title") != null) {
molMolecule.setTitle(molStructure.getProperty("cdk:Title").toString());
} else {
molMolecule.setTitle("Unknown molecule");
}
if (molStructure.getID() != null) {
molMolecule.setId(molStructure.getID().toString());
} else {
molMolecule.setId("ID" + Integer.toString(molStructure.hashCode()));
}
if (molStructure.getAtomCount() > 0) {
molMolecule.setCount((double) molStructure.getAtomCount());
}
// ToDo add additional properties from the >property block and/or M
// block
}
}
@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 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());
}
@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 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());
}
@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 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());
}
@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);
}
@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 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);
}
@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());
}
/** A unit test for JUnit with Methanol */
@Test
public void testPartialTotalChargeDescriptor_Methanol()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
0.28, -0.67, 0.0, 0.0, 0.0, 0.4
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom carbon = builder.newInstance(IAtom.class, Elements.CARBON);
IAtom oxygen = builder.newInstance(IAtom.class, Elements.OXYGEN);
// making sure the order matches the test results
mol.addAtom(carbon);
mol.addAtom(oxygen);
mol.addBond(builder.newInstance(IBond.class, carbon, oxygen, CDKConstants.BONDORDER_SINGLE));
addExplicitHydrogens(mol);
for (int i = 0; i < mol.getAtomCount(); i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
@Test
public void testNNMolecule_IAtomContainer() {
IAtomContainer acetone = new org.openscience.cdk.AtomContainer();
IAtom c1 = acetone.getBuilder().newAtom("C");
IAtom c2 = acetone.getBuilder().newAtom("C");
IAtom o = acetone.getBuilder().newAtom("O");
IAtom c3 = acetone.getBuilder().newAtom("C");
acetone.addAtom(c1);
acetone.addAtom(c2);
acetone.addAtom(c3);
acetone.addAtom(o);
IBond b1 = acetone.getBuilder().newBond(c1, c2, IBond.Order.SINGLE);
IBond b2 = acetone.getBuilder().newBond(c1, o, IBond.Order.DOUBLE);
IBond b3 = acetone.getBuilder().newBond(c1, c3, IBond.Order.SINGLE);
acetone.addBond(b1);
acetone.addBond(b2);
acetone.addBond(b3);
IMolecule m = new NNMolecule(acetone);
Assert.assertNotNull(m);
Assert.assertEquals(4, m.getAtomCount());
Assert.assertEquals(3, m.getBondCount());
}
/**
* 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;
}