/** {@inheritDoc} */ @Override public void setID(String identifier) { logger.debug("Setting ID: ", identifier); super.setID(identifier); }
public static IAtomContainer makePropylAmine() { IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); Atom atom = new Atom("C"); atom.setID("0"); mol.addAtom(atom); // 0 atom = new Atom("C"); atom.setID("1"); mol.addAtom(atom); // 1 atom = new Atom("C"); atom.setID("2"); mol.addAtom(atom); // 2 atom = new Atom("N"); atom.setID("3"); mol.addAtom(atom); // 3 mol.addBond(0, 1, IBond.Order.SINGLE); // 1 mol.addBond(1, 2, IBond.Order.SINGLE); // 2 mol.addBond(2, 3, IBond.Order.SINGLE); // 3 return mol; }
public static IAtomContainer makeButane() { IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); Atom atom = new Atom("C"); atom.setID("0"); mol.addAtom(atom); // 0 atom = new Atom("C"); atom.setID("1"); mol.addAtom(atom); // 1 atom = new Atom("C"); atom.setID("2"); mol.addAtom(atom); // 2 atom = new Atom("C"); atom.setID("3"); mol.addAtom(atom); // 3 mol.addBond(0, 1, IBond.Order.SINGLE); // 1 mol.addBond(1, 2, IBond.Order.SINGLE); // 2 mol.addBond(2, 3, IBond.Order.SINGLE); // 3 return mol; }
@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 testGetAllIDs_IReaction() { Reaction reaction = new Reaction(); reaction.setID("r1"); IAtomContainer water = new AtomContainer(); water.setID("m1"); Atom oxygen = new Atom("O"); oxygen.setID("a1"); water.addAtom(oxygen); reaction.addReactant(water); reaction.addProduct(water); List<String> ids = ReactionManipulator.getAllIDs(reaction); Assert.assertNotNull(ids); Assert.assertEquals(5, ids.size()); }
Atom atom0 = new Atom("C"); Atom atom2 = new Atom("C"); atom0.setID("a1"); mol.addAtom(atom2); mol.addAtom(atom0); Atom atom1 = new Atom("C"); atom2 = new Atom("C"); atom1.setID("a2"); mol.addAtom(atom2); mol.addAtom(atom1); molSet.addAtomContainer(mol); atom0.setID("atomX"); ids = MoleculeSetManipulator.getAllIDs(molSet); Assert.assertFalse(ids.contains("a1"));
@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()); }
@Test public void testGetAllIDs_IReactionSet() { IReactionSet set = builder.newInstance(IReactionSet.class); IReaction reaction1 = builder.newInstance(IReaction.class); set.addReaction(reaction1); reaction1.setID("r1"); IAtomContainer water = new AtomContainer(); water.setID("m1"); Atom oxygen = new Atom("O"); oxygen.setID("a1"); water.addAtom(oxygen); reaction1.addReactant(water); reaction1.addProduct(water); IReaction reaction2 = builder.newInstance(IReaction.class); reaction2.setID("r2"); set.addReaction(reaction2); List<String> ids = ReactionSetManipulator.getAllIDs(set); Assert.assertNotNull(ids); Assert.assertEquals(6, ids.size()); }