@Test public void testKeepingIDs() { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); atom.setID("atom1"); mol.addAtom(atom); IDCreator.createIDs(mol); Assert.assertEquals("atom1", atom.getID()); Assert.assertNotNull(mol.getID()); List<String> ids = AtomContainerManipulator.getAllIDs(mol); Assert.assertEquals(2, ids.size()); }
@Test public void testNoDuplicateCreation() { IAtomContainer mol = new AtomContainer(); Atom atom1 = new Atom("C"); Atom atom2 = new Atom("C"); atom1.setID("a1"); mol.addAtom(atom2); mol.addAtom(atom1); IDCreator.createIDs(mol); Assert.assertEquals("a2", atom2.getID()); List<String> ids = AtomContainerManipulator.getAllIDs(mol); Assert.assertEquals(3, ids.size()); }
@Test public void testCreateIDs_IChemObject() { IAtomContainer mol = new AtomContainer(); Atom atom1 = new Atom("C"); Atom atom2 = new Atom("C"); mol.addAtom(atom1); mol.addAtom(atom2); Bond bond = new Bond(atom1, atom2); mol.addBond(bond); IDCreator.createIDs(mol); Assert.assertEquals("a1", atom1.getID()); Assert.assertEquals("b1", bond.getID()); List<String> ids = AtomContainerManipulator.getAllIDs(mol); Assert.assertEquals(4, ids.size()); }
@Test public void testAtomId() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("N"); atom.setID("N1"); mol.addAtom(atom); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); Assert.assertEquals(atom.getID(), roundTrippedAtom.getID()); }
/** * Test for SF bug #903551 */ @Test public void testPartitionIntoMoleculesKeepsAtomIDs() { AtomContainer atomCon = new org.openscience.cdk.AtomContainer(); Atom atom1 = new Atom("C"); atom1.setID("atom1"); Atom atom2 = new Atom("C"); atom2.setID("atom2"); atomCon.addAtom(atom1); atomCon.addAtom(atom2); IAtomContainerSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(atomCon); Assert.assertNotNull(moleculeSet); Assert.assertEquals(2, moleculeSet.getAtomContainerCount()); org.openscience.cdk.interfaces.IAtom copy1 = moleculeSet.getAtomContainer(0).getAtom(0); org.openscience.cdk.interfaces.IAtom copy2 = moleculeSet.getAtomContainer(1).getAtom(0); Assert.assertEquals(atom1.getID(), copy1.getID()); Assert.assertEquals(atom2.getID(), copy2.getID()); }