@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 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 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 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 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 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 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());
}
/**
* 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;
}