/** @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());
}
/**
* Get the resonance structures from an IMolecule.
*
* @param molecule The IMolecule to analyze
* @return The different resonance structures
*/
@TestMethod("testGetStructures_IMolecule")
public IMoleculeSet getStructures(IMolecule molecule) {
int countStructure = 0;
IMoleculeSet setOfMol = molecule.getBuilder().newMoleculeSet();
setOfMol.addMolecule(molecule);
for (int i = 0; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (IReactionProcess aReactionsList : reactionsList) {
IReactionProcess reaction = aReactionsList;
IMoleculeSet setOfReactants = molecule.getBuilder().newMoleculeSet();
setOfReactants.addMolecule(mol);
try {
IReactionSet setOfReactions = reaction.initiate(setOfReactants, null);
if (setOfReactions.getReactionCount() != 0)
for (int k = 0; k < setOfReactions.getReactionCount(); k++)
for (int j = 0;
j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount();
j++) {
IMolecule product = setOfReactions.getReaction(k).getProducts().getMolecule(j);
if (!existAC(setOfMol, product)) {
setOfMol.addMolecule(product);
countStructure++;
if (countStructure > maxStructures) return setOfMol;
}
}
} catch (CDKException e) {
e.printStackTrace();
}
}
}
return setOfMol;
}
/**
* 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;
}
public IIteratingChemObjectReader getSearchReader(
Connection connection, Object query, int page, int pagesize) throws AmbitException {
String cas = "50-00-0";
Object c = null;
if (query instanceof IMolecule) {
c = ((IMolecule) query).getProperty(CDKConstants.CASRN);
if (c != null) cas = c.toString();
}
if (c == null) {
IMolecule m = ((AmbitDatabaseToolsData) userData).getMolecule();
if (m != null) {
c = m.getProperty(CDKConstants.CASRN);
if (c != null) cas = c.toString();
}
}
cas =
getSearchCriteria(
"Search database by CAS Registry Number", "Enter CAS Registry Number\n", cas);
// If a string was returned, say so.
if ((cas != null) && (cas.length() > 0)) {
try {
cas = IdentifiersProcessor.hyphenateCAS(cas);
} catch (Exception x) {
logger.error(x);
}
if (CASNumber.isValid(cas.trim())) {
return new DbStructureReader(connection, sql + '"' + cas.trim() + "\" limit 0,1");
} else JOptionPane.showMessageDialog(mainFrame, "Invalid CAS Registry Number!\n" + cas);
}
return null;
}
@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 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 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));
}
/** Converts a Molecule Element from a CDK Molecule object */
public MoleculeType convert(IMolecule molecule) throws MSMLConversionException {
try {
MoleculeType molMoleculeElement = ObjectFactorySingelton.getFactory().createMoleculeType();
setMetaData(molMoleculeElement, molecule);
// molMoleculeElement.setMoleculeClass(MoleculeClassType.HETERO);//?
// Add Atom block:
Iterable<IAtom> atomBlock = molecule.atoms();
AtomArrayType atomArrayElement = convertAtoms(atomBlock, molMoleculeElement.getId());
// Save hashes of atoms to map the atom back to the atom ID
ArrayList<String> hashes = generateHashCodes(atomBlock);
molMoleculeElement.setAtomArray(atomArrayElement);
// Add bond block
Iterable<IBond> bondBlock = molecule.bonds();
BondArrayType bondArrayElement = convertBonds(bondBlock, molMoleculeElement.getId(), hashes);
molMoleculeElement.setBondArray(bondArrayElement);
// Add properties block
for (Entry<Object, Object> prop : molecule.getProperties().entrySet()) {
if (_excludedProperties.contains(prop.getKey())) continue;
CustomProperty cmlProp = ObjectFactorySingelton.getFactory().createCustomProperty();
cmlProp.setKey((String) prop.getKey());
cmlProp.setValue((String) prop.getValue());
molMoleculeElement.getCustomProperty().add(cmlProp);
}
return molMoleculeElement;
} catch (Exception e) {
String msg = "Conversion of MDL molecule structure failed! " + e.getMessage();
LOGGER.error(msg, e);
throw new MSMLConversionException(msg, e);
}
}
@Test
public void testViaFlags() throws Exception {
IMolecule molecule = MoleculeFactory.makeBenzene();
for (Iterator atoms = molecule.atoms().iterator(); atoms.hasNext(); ) {
((IAtom) atoms.next()).setFlag(CDKConstants.ISAROMATIC, true);
}
Assert.assertEquals(6, ((IntegerResult) descriptor.calculate(molecule).getValue()).intValue());
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @param reactants reactants of the reaction
* @param agents agents of the reaction (Must be in this case null)
* @exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException {
logger.debug("initiate reaction: HeterolyticCleavagePBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavagePBReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IMolecule reactant = reactants.getMolecule(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() != IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER)
&& atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
/**/
for (int j = 0; j < 2; j++) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0) {
atomList.add(atom1);
atomList.add(atom2);
} else {
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class);
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
return setOfReactions;
}
@Test
public void testMoleculeId() throws Exception {
String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals("m1", mol.getID());
}
@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());
}
@Test
public void testName() throws Exception {
String cmlString =
"<molecule id='m1'><name>acetic acid</name><atomArray atomID='a1 a2 a3'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals("acetic acid", mol.getProperty(CDKConstants.TITLE));
}
@Test
public void testInChI() throws Exception {
String cmlString =
"<molecule id='m1'><identifier convention='iupac:inchi' value='InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)'/><atomArray atomID='a1 a2 a3'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals("InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)", mol.getProperty(CDKConstants.INCHI));
}
@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);
}
@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 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 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 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));
}
/** @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 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);
}
@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_C1CCCCCCC1CC() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "C1CCCCCCC1CC";
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);
}
@Test
public void testDictRef() throws Exception {
String cmlString =
"<molecule id=\"alanine\" dictRef=\"pdb:aminoAcid\"><name>alanine</name><name dictRef=\"pdb:residueName\">Ala</name><name dictRef=\"pdb:oneLetterCode\">A</name><scalar dictRef=\"pdb:id\">3</scalar><atomArray><atom id=\"a1\" elementType=\"C\" x2=\"265.0\" y2=\"989.0\"/><atom id=\"a2\" elementType=\"N\" x2=\"234.0\" y2=\"972.0\" dictRef=\"pdb:nTerminus\"/><atom id=\"a3\" elementType=\"C\" x2=\"265.0\" y2=\"1025.0\"/><atom id=\"a4\" elementType=\"C\" x2=\"296.0\" y2=\"971.0\" dictRef=\"pdb:cTerminus\"/><atom id=\"a5\" elementType=\"O\" x2=\"296.0\" y2=\"935.0\"/><atom id=\"a6\" elementType=\"O\" x2=\"327.0\" y2=\"988.0\"/></atomArray><bondArray><bond id=\"b1\" atomRefs2=\"a2 a1\" order=\"S\"/><bond id=\"b2\" atomRefs2=\"a1 a3\" order=\"S\"/><bond id=\"b3\" atomRefs2=\"a1 a4\" order=\"S\"/><bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"D\"/><bond id=\"b5\" atomRefs2=\"a4 a6\" order=\"S\"/></bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Iterator<Object> props = mol.getProperties().keySet().iterator();
boolean foundDictRefs = false;
while (props.hasNext()) {
Object next = props.next();
if (next instanceof DictRef) foundDictRefs = true;
}
Assert.assertTrue(foundDictRefs);
}